Planet NoName e.V.


sECuREs website

A quick introduction to MQTT for IOT

While I had heard the abbreviation MQTT many times, I never had a closer look at what MQTT is.

Here are a few quick notes about using MQTT as Pub/Sub bus in a home IOT network.


Once you have a few IOT devices, an obvious question is how to network them.

If all your devices are from the same vendor, the vendor takes care of it.

In my home, I have many different vendors/devices, such as (incomplete list):

Here is how I combine these devices:

  • When I’m close to my home (geo-fencing), the Nuki Opener enables Ring To Open (RTO): when I ring the door bell, it opens the door for me.
  • When I open the apartment door, the Smart Lights in the hallway turn on.
  • When I’m home, my stereo speakers should be powered on so I can play music.

A conceptually simple way to hook this up is to connect things directly: listen to the Aqara Door Sensor and instruct the Smart Lights to turn on, for example.

But, connecting everything to an MQTT bus has a couple of advantages:

  1. Unification: everything is visible in one place, the same tools work for all devices.
  2. Your custom logic is uncoupled from vendor details: you can receive and send MQTT.
  3. Compatibility with existing software, such as Home Assistant or openHAB

Step 1. Set up an MQTT broker (server)

A broker is what relays messages between publishers and subscribers. As an optimization, the most recent value of a topic can be retained, so that e.g. a subscriber does not need to wait for the next change to obtain the current state.

The most popular choice for broker software seems to be Mosquitto, but since I like to run Go software on, I kept looking and found

One downside of hmq might be that it does not seem to support persisting retained messages to disk. I’ll treat this as a feature for the time being, enforcing a fresh start on every daily reboot.

To restrict hmq to only listen in my local network, I’m using gokrazy’s flag file feature:

mkdir -p flags/
echo --host= > flags/

Note that you’ll need in case your network does not come up quickly.

MQTT broker setup: displaying/sending test messages

To display all messages going through your MQTT broker, subscribe using the Mosquitto tools:

% sudo pacman -S mosquitto
% mosquitto_sub --id "${HOST}_all" --host dr.lan --topic '#' --verbose

The # sign denotes an MQTT wildcard, meaning subscribe to all topics in this case.

Be sure to set a unique id for each mosquitto_sub command you run, so that you can see which subscribers are connected to your MQTT bus. Avoid id clashes, otherwise the subscribers will disconnect each other!

Now, when you send a test message, you should see it:

% mosquitto_pub --host dr.lan --topic 'cmnd/tasmota_68462F/Power' -m 'ON'

Tip: If you have binary data on your MQTT bus, you can display it in hex with timestamps:

% mosquitto_sub \
  --id "${HOST}_bell" \
  --host dr.lan \
  --topic 'doorbell/#' \
  -F '@Y-@m-@dT@H:@M:@S@z : %t : %x'

Step 2. Integrate with MQTT

Now that communication via the bus works, what messages do we publish on which topics?

MQTT only defines that topics are hierarchical; messages are arbitrary byte sequences.

There are a few popular conventions for what to put onto MQTT:

If you design everything yourself, Homie seems like a good option. If you plan to use Home Assistant or similar, stick to the Home Assistant convention.

Best practices for your own structure

In case you want/need to define your own topics, keep these tips in mind:

  • devices publish their state on a single, retained topic
    • the topic name could be e.g. stat/tasmota_68462F/POWER
    • retaining the topic allows consumers to catch up after (re-)connecting to the bus
  • publish commands on a single, possibly-retained topic
    • e.g. publish ON to topic cmnd/tasmota_68462F/Power
    • publish the desired state: publish ON or OFF instead of TOGGLE
    • if you retain the topic and publish TOGGLE commands, your lights will mysteriously go off/on when they unexpectedly re-establish their MQTT connection

Integration: Shelly devices with MQTT built-in

Shelly has a number of smart devices that come with MQTT out of the box! This sounds like the easiest solution if you’re starting from scratch.

I haven’t used these devices personally, but I hear good things about them.

Integration: Zigbee2MQTT for Zigbee devices

Zigbee2MQTT supports well over 1000 Zigbee devices and exposes them on the MQTT bus.

For example, this is what you would use to connect your IKEA TRÅDFRI Smart Lights to MQTT.

Integration: ESPHome for micro controllers + sensors

The ESPHome system is a ready-made solution to connect a wide array of sensors and devices to your home network via MQTT.

If you want to use your own ESP-based micro controllers and sensors, this seems like the easiest way to get them programmed.

Integration: Mongoose OS for micro controllers

Mongoose OS is an IOT firmware development framework, taking care of device management, Over-The-Air updates, and more.

Mongoose comes with MQTT support, and with just a few lines you can build, flash and configure your device. Here’s an example for the NodeMCU (ESP8266-based):

% yay -S mos-bin
% mos clone app1
% cd app1
% mos --platform esp8266 build
% mos --platform esp8266 --port /dev/ttyUSB1 flash
% mos --port /dev/ttyUSB1 config-set mqtt.enable=true mqtt.server=dr.lan:1883

Pressing the button on the NodeMCU publishes a message to MQTT:

% mosquitto_sub --host dr.lan --topic devices/esp8266_F4B37C/events

Integration: Arduino for custom micro controller firmware

Arduino has an MQTT Client library. If your microcontroller is networked, e.g. an ESP32 with WiFi, you can publish MQTT messages from your Arduino sketch:

#include <WiFi.h>
#include <PubSubClient.h>

WiFiClient wificlient;
PubSubClient client(wificlient);

void callback(char* topic, byte* payload, unsigned int length) {
    Serial.print("Message arrived [");
    Serial.print("] ");
    for (int i = 0; i < length; i++) {
    if (strcmp(topic, "doorbell/cmd/unlock") == 0) {
  		// …

void taskmqtt(void *pvParameters) {
	for (;;) {
		if (!client.connected()) {
			client.connect("doorbell" /* clientid */);

		// Poll PubSubClient for new messages and invoke the callback.
		// Should be called as infrequent as one is willing to delay
		// reacting to MQTT messages.
		// Should not be called too frequently to avoid strain on
		// the network hardware:

void setup() {
	connectToWiFi(); // WiFi configuration omitted for brevity

	client.setServer("dr.lan", 1883);

	xTaskCreatePinnedToCore(taskmqtt, "MQTT", 2048, NULL, 1, NULL, PRO_CPU_NUM);

void processEvent(void *buf, int telegramLen) {
	client.publish("doorbell/events/scs", buf, telegramLen);

Integration: Webhook to MQTT

The Nuki Opener doesn’t support MQTT out of the box, but the Nuki Bridge can send Webhook requests. In a few lines of Go, you can forward what the Nuki Bridge sends to MQTT:

package main

import (

	mqtt ""

func nukiBridge() error {
	opts := mqtt.NewClientOptions().AddBroker("tcp://dr.lan:1883")
	mqttClient := mqtt.NewClient(opts)
	if token := mqttClient.Connect(); token.Wait() && token.Error() != nil {
		return fmt.Errorf("MQTT connection failed: %v", token.Error())

	mux := http.NewServeMux()
	mux.HandleFunc("/nuki", func(w http.ResponseWriter, r *http.Request) {
		b, err := ioutil.ReadAll(r.Body)
		if err != nil {
			http.Error(w, err.Error(), http.StatusInternalServerError)

			"zkj-nuki/webhook", // topic
			0, // qos
			true, // retained
			string(b)) // payload

	return http.ListenAndServe(":8319", mux)

func main() {
	if err := nukiBridge(); err != nil {

See Nuki’s Bridge HTTP-API document for details on how to configure your bridge to send webhook callbacks.

Step 3. Express your logic

Home Assistant and Node-RED are both popular options, but also large software packages.

Personally, I find it more fun to express my logic directly in a full programming language (Go).

I call the resulting program regelwerk (“collection of rules”). The program consists of:

  1. various control loops that progress independently from each other
  2. an MQTT message dispatcher feeding these control loops
  3. a debugging web interface to visualize state

This architecture is by no means a new approach: as moquette describes it, this is to MQTT what inetd is to IP. I find moquette’s one-process-per-message model to be too heavyweight and clumsy to deploy to, so regelwerk is entirely in-process and a single, easy-to-deploy binary, both to computers for notifications, or to headless Raspberry Pis.

regelwerk: control loops definition

regelwerk defines a control loop as a stateful function that accepts an event (from MQTT) and returns messages to publish to MQTT, if any:

type controlLoop interface {

	StatusString() string // for human introspection

	ProcessEvent(MQTTEvent) []MQTTPublish

// Like mqtt.Message, but with timestamp
type MQTTEvent struct {
	Timestamp time.Time
	Topic     string
	Payload   interface{}

// Parameters for mqtt.Client.Publish()
type MQTTPublish struct {
	Topic    string
	Qos      byte
	Retained bool
	Payload  interface{}

regelwerk: MQTT dispatcher

Our MQTT message handler dispatches each incoming message to all control loops, in one goroutine per message and loop. With typical message volumes on a personal MQTT bus, this is a simple yet effective design that brings just enough isolation.

type mqttMessageHandler struct {
	dryRun bool
	loops  []controlLoop

func (h *mqttMessageHandler) handle(client mqtt.Client, m mqtt.Message) {
	log.Printf("received message %q on %q", m.Payload(), m.Topic())
	ev := MQTTEvent{
		Timestamp: time.Now(), // consistent for all loops
		Topic:     m.Topic(),
		Payload:   m.Payload(),

	for _, l := range h.loops {
		l := l // copy
		go func() {
			// For reliability, we call each loop in its own goroutine
			// (yes, one per message), so that when one loop gets stuck,
			// the others still make progress.
			results := l.ProcessEvent(ev)
			if len(results) == 0 {
			for _, r := range results {
				log.Printf("publishing: %+v", r)
				if !h.dryRun {
					client.Publish(r.Topic, r.Qos, r.Retained, r.Payload)
			// …input/output logging omitted for brevity…

regelwerk: control loop example

Now that we have the definition and dispatching out of the way, let’s take a look at an actual example control loop.

This control loops looks at whether my PC is unlocked (in use) or whether my phone is home, and then turns off/on my stereo speakers accordingly.

The inputs come from runstatus and dhcp4d, the output goes to a Sonoff S26 Smart Power Plug running Tasmota.

type avrPowerLoop struct {
	statusLoop // for l.statusf() debugging

	midnaUnlocked          bool
	michaelPhoneExpiration time.Time

func (l *avrPowerLoop) ProcessEvent(ev MQTTEvent) []MQTTPublish {
	// Update loop state based on inputs:
	switch ev.Topic {
	case "runstatus/midna/i3lock":
		var status struct {
			Running bool `json:"running"`
		if err := json.Unmarshal(ev.Payload.([]byte), &status); err != nil {
			l.statusf("unmarshaling runstatus: %v", err)
			return nil
		l.midnaUnlocked = !status.Running

	case "router7/dhcp4d/lease/Michaels-iPhone":
		var lease struct {
			Expiration time.Time `json:"expiration"`
		if err := json.Unmarshal(ev.Payload.([]byte), &lease); err != nil {
			l.statusf("unmarshaling router7 lease: %v", err)
			return nil
		l.michaelPhoneExpiration = lease.Expiration

		return nil // event did not influence our state

	// Publish desired state changes:
	now := ev.Timestamp
	phoneHome := l.michaelPhoneExpiration.After(now)
	anyoneHome := l.midnaUnlocked || (now.Hour() > 8 && phoneHome)
	l.statusf("midnaUnlocked=%v || (now.Hour=%v > 8 && phoneHome=%v)",
		l.midnaUnlocked, now.Hour(), phoneHome)

	payload := "OFF"
	if anyoneHome {
		payload = "ON"
	return []MQTTPublish{
			Topic:    "cmnd/tasmota_68462F/Power",
			Payload:  payload,
			Retained: true,


I like the Pub/Sub pattern for home automation, as it nicely uncouples all components.

It’s a shame that standards such as The Homie convention aren’t more widely supported, but it looks like software makes up for that via configuration options.

There are plenty of existing integrations that should cover most needs.

Ideally, more Smart Home and IOT vendors would add MQTT support out of the box, like Shelly.

at 2021-01-10 14:26


High-throughput density-functional theory calculations: An interdisciplinary challenge

Last Thursday I was invited to give a virtual talk at the Scientific Computing Seminar of working group of Prof. Nicolas Gauger at TU Kaiserslautern. Since the research in Prof. Gauger's group mostly concerns topics which are not directly related to electronic structure theory and density-functional theory (DFT), I chose to present my current research from a rather broad and introductory angle. Main focus of my talk was thus to hint at the interdisciplinary challenges arising in high-throughput methods in DFT simulations, followed by a summary of a few of my recent projects in the field.

I was glad for the opportunity to spread the word about the difficulties with high-throughput methods in DFT. Firstly because I think it is an absolutely fascinating topic, but secondly because it is one where input from fields beyond the standard "culprits" of chemistry, physics and materials science is beneficial to solve the upcoming problems. In fact exactly this hope to get other fields and people with non-standard backgrounds involved was one of the driving forces behind our density-functional toolkit DFT code, which I also briefly presented.

I hope that my talk got some of the audience more interested in DFT and I look forward to continue the discussions at a later point, hopefully meeting the Gauger group in person in Kaiserslautern.

Link Licence
High-throughput density-functional theory calculations: An interdisciplinary challenge (Slides) Creative Commons License

by Michael F. Herbst at 2020-12-23 17:00 under talk, electronic structure theory, Julia, DFTK, theoretical chemistry, numerical analysis, Kohn-Sham, high-throughput, invited talk, dft, solid state


sECuREs website

Fixing the Nuki Opener smart intercom IOT device (on the BTicino SCS bus intercom system)

I recently bought a Nuki Opener, which “turns your existing intercom into a smart door opener”.

Unfortunately, I have had a lot of trouble getting it to work.

I finally got the device working by interjecting my own micro controller between the intercom bus and the Nuki Opener, then driving the Nuki Opener in its Analogue mode:

The rest of this article outlines how this setup works at a high level.


For reliable interpretation and transmission of SCS bus data, we’ll need:

  1. SCS receive/transmit circuits. These can be prototyped on a breadboard if you have the required diodes, transistors, resistors and capacitors.

  2. A microcontroller with an Analog Comparator. If your microcontroller has one, you’ll find a corresponding section in the datasheet. This function is sometimes abbreviated to CMP or AC, or might be part of a larger Analog/Digital Converter (ADC).

  3. A UART (serial) decoder. Most microcontrollers have at least one UART, but if you don’t have one available for whichever reason, you could use a software UART implementation, too.

SCS receive circuit

SCS receive circuit

An R-C network, directly connected to the SCS bus, is used for incoming signal conditioning.

The resistor values have been chosen to divide the voltage of the input signal from 28V down to approx. 2V, i.e. well within the 0-3.3V range for modern microcontroller GPIO pins.

A zener diode limits the 28V level to 3.3V, which should be safe for most microcontrollers.


SCS transmit circuit

SCS transmit circuit

We directly connect the gate of a mosfet transistor to a GPIO pin of our microcontroller, so that when the microcontroller drives the pin high, we use the 100Ω resistor to attach a load to the SCS bus.

For comparison, the KNX bus, which is similar to the SCS bus, uses a 68Ω resistor here.


SCS lab setup

Use a lab power supply to generate 28V DC. I’m using the Velleman LABPS3005SM because it was in stock at Galaxus, but any power supply rated for at least 30V DC will do.

As the DIY home automation blog entry “A minimal KNX setup” describes, you’ll need to place a 47Ω resistor between the power line and your components.

Afterwards, just connect your components to the bus. The supply/ground line of a breadboard will work nicely.

SCS lab setup

Micro Controller choice

In this blog post, I’m using a Teensy 4 development board that is widely available for ≈20 USD:

Teensy 4

With its 600 MHz, the Teensy 4 has enough sheer clock frequency to allow for sloppier coding while still achieving high quality input/output.

The teensy tiny form factor (3.5 x 1.7 cm) works well for this project and will allow me to store the microcontroller in an existing intercom case.

The biggest downside is that NXP’s own MCUXpresso IDE cannot target the Teensy 4!

The only officially supported development environment for the Teensy 4 is Teensyduino, which is a board support package for the Arduino IDE. Having Arduino support is great, but let’s compare:

I also have NXP’s MIMXRT1060-EVK eval kit, which uses the same i.MX RT1060 micro controller family as the Teensy 4, but is much larger and comes with all the bells and whistles; notably:

  1. The MCUXpresso IDE works with the eval kit’s built-in debugger out of the box! Being able to inspect a stack trace, set breakpoints and look at register contents are invaluable tools when doing micro controller development.
  2. The MCUXpresso IDE comes with convenient graphical Pin and Clock config tools. Setting a pin’s alternate function becomes a few clicks instead of hours of fumbling around.
  3. The NXP SDK contains a number of drivers and examples that are tested on the eval kit. That makes it really easy to get started!

Each of these points is very attractive on their own, but together they make the whole experience so different!

Being able to deploy to the Teensy from MCUXpresso would be a killer feature! So many NXP SDK examples would suddenly become available, filling the Teensy community’s gaps.

Signal Setup

On a high level, this is how we are going to connect the various signals:

Step 1. We start with the SCS intercom bus signal (28V high, 22V low):

Step 2. Our SCS receive circuit takes the bus signal and divides it down to 2V:

voltage-divided SCS signal

Step 3. We convert the voltage-divided analog signal into a digital SCSRXOUT signal:

Analog Comparator output signal

Step 4. We modify our SCSRXOUT signal so that it can be sampled at 50%:

modified SCS signal

Step 5. We decode the signal using our micro controller’s UART:

Teensy 4 UART decodes SCS

Micro Controller firmware

Once I complete the next revision of the SCS interface PCB, I plan to release all design files, schematics, sources, etc. in full.

Until then, the following sections describe how the most important parts work, but skip over the implementation-specific glue code that wires everything together.

Analog Comparator

The Analog Comparator in our microcontroller lets us know whether a voltage is above or below a configured threshold voltage by raising an interrupt. A good threshold is 1.65V in my case.

In response to the voltage change, we set GPIO pin 15 to a digital high (3.3V) or low (0V) level:

volatile uint32_t cmpflags;

// ISR (Interrupt Service Routine), called by the Analog Comparator:
void acmp1_isr() {
  cmpflags = CMP1_SCR;

  { // clear interrupt status flags:
    uint8_t scr = (CMP1_SCR & ~(CMP_SCR_CFR_MASK | CMP_SCR_CFF_MASK));

  if (cmpflags & CMP_SCR_CFR_MASK) {
    // See below! This line will be modified:
    digitalWrite(15, HIGH);

  if (cmpflags & CMP_SCR_CFF_MASK) {
    digitalWrite(15, LOW);

This signal can easily be verified by attaching an oscilloscope probe each to the SCSRX voltage-regulated bus signal input and to the SCSRXOUT GPIO pin output:

Analog Comparator output signal

Analog Comparator Modification

There is one crucial difference between SCS and UART:

To transmit a 0 (or start bit):

  • SCS is low 34μs, then high 70μs
  • UART is low the entire 104μs

UART implementations typically sample at 50%, the middle of the bit period.

For SCS, we would need to sample at 20%, because the signal returns to high so quickly.

While setting a custom sample point is possible in e.g. sigrok’s UART decoder, neither software nor hardware serial implementations on micro controllers typically support it.

On a micro controller it is much easier to just modify the signal so that it can be sampled at 50%.

In practical terms, this means modifying the acmp1_isr function to return to high later than the Analog Comparator indicates:

volatile uint32_t cmpflags;

// ISR (Interrupt Service Routine), called by the Analog Comparator:
void acmp1_isr() {
  cmpflags = CMP1_SCR;

  { // clear interrupt status flags:
    uint8_t scr = (CMP1_SCR & ~(CMP_SCR_CFR_MASK | CMP_SCR_CFF_MASK));

  if (cmpflags & CMP_SCR_CFR_MASK) {
    // Instead of setting our output pin high immediately,
    // we delay going up by approx. 40us,
    // turning the SCS signal into a UART signal:
    digitalWrite(15, HIGH);

  if (cmpflags & CMP_SCR_CFF_MASK) {
    digitalWrite(15, LOW);

You can now read this signal using your laptop and a USB-to-serial adapter!

On a micro controller, we now feed this signal back into a UART decoder. For prototyping, this can literally mean a jumper wire connecting the output GPIO pin with a serial RX pin. Some micro controllers also support internal wiring of peripherals, allowing you to get rid of that cable.

SCS RX (receive)

With the SCS intercom bus signal bytes now available through the UART decoder, we can design a streaming SCS decoder. The decoder self-synchronizes and skips invalid SCS telegrams by checking their checksum. We start with a ring buffer and a convenience working copy:

constexpr int telegramLen = 7;

typedef struct {
  // circular buffer for incoming bytes, indexed using cur
  uint8_t buf[telegramLen];
  int cur;

  uint8_t tbuf[telegramLen];
} scsfilter;

Each byte we receive from the UART, we store in our ring buffer:

void sf_WriteByte(scsfilter *sf, uint8_t b) {
  sf->buf[sf->cur] = b;
  sf->cur = (sf->cur + 1) % telegramLen;

After every byte, we can check if the ring buffer decodes to a valid ring signal SCS bus telegram:

bool sf_completeAndValid(scsfilter *sf) {
  const uint8_t prev = sf->buf[(sf->cur+(telegramLen-1))%telegramLen];
  if (prev != 0xa3) {
    return false; // incomplete: previous byte not a telegram termination

  // Copy the whole telegram into tbuf; makes working with it easier:
  for (int i = 0; i < telegramLen; i++) {
    sf->tbuf[i] = sf->buf[(sf->cur+i)%telegramLen];

  const uint8_t stored = sf->tbuf[5];
  const uint8_t computed = sf->tbuf[1] ^
    sf->tbuf[2] ^
	sf->tbuf[3] ^
  if (stored != computed) {
    return false; // corrupt? checksum mismatch

  return true;

int sf_ringForApartment(scsfilter *sf) {
  if (!sf_completeAndValid(sf)) {
    return -1;

  if (sf->tbuf[3] != 0x60) {
    return -1; // not a ring command

  if (sf->tbuf[1] != 0x91) {
    return -1; // not sent by the intercom house station

  return (int)(sf->tbuf[2]); // apartment id

SCS TX (send)

Conceptually, writing serial data to a GPIO output from software is done with e.g. the Arduino SoftwareSerial library, but there are plenty of implementations for different micro controllers. This technique is also sometimes called “Bit banging”.

I started with the the Teensy SoftwareSerial::write implementation and modified it to:

  1. Invert the output to drive the SCS transmit circuit’s Mosfet transistor gate, i.e. low on idle and high on transmitting a 0 bit.

  2. Return to idle 70μs earlier than the signal would, i.e. after ≈34μs already.

The modified write function looks like this:

#define V27 LOW
#define V22 HIGH

#define scs0() do { \
  while (ARM_DWT_CYCCNT - begin_cycle < (target-43750/*70us*/)) ; \
  digitalWriteFast(11, V27); \
} while (0)

size_t SCSSerial::write(uint8_t b)
  elapsedMicros elapsed;
  uint32_t target;
  uint8_t mask;
  uint32_t begin_cycle;


  // start bit
  target = cycles_per_bit;
  begin_cycle = ARM_DWT_CYCCNT;
  digitalWriteFast(11, V22);
  wait_for_target(begin_cycle, target);

  // 8 data bits
  for (mask = 1; mask; mask <<= 1) {
    if (b&mask) {
      digitalWriteFast(11, V27);
    } else {
      digitalWriteFast(11, V22);
    target += cycles_per_bit;
    wait_for_target(begin_cycle, target);

  // stop bit
  digitalWriteFast(11, V27);
  target += cycles_per_bit;
  while (ARM_DWT_CYCCNT - begin_cycle < target) ; // wait
  return 1;

It works!

With the approach described above, I now have a micro controller that recognizes doorbell rings for my apartment and ignores doorbell rings for my neighbors. The micro controller can unlock the door, too, and both features are available through the Nuki Opener.

How is the Nuki Opener?

It took over 2 months before I saw the Nuki Opener working correctly for the first time.

I really hope the Nuki developers can work with what I described above and improve their product’s reliability for all customers with an SCS intercom system!

The device itself seems useful and usable, but time will tell how reliable it turns out in practice. I think I noticed push notifications when the door rang coming in rather late (many seconds later).

I’ll keep an eye on this and explore the various Nuki APIs more.

Appendix: Project Journal

  • 2020-09-26: I buy a Nuki Opener (Nuki Opener #1), but despite connecting it correctly, it never successfully opens the door. I start learning about the SCS home automation bus system that our intercom uses.
  • 2020-09-28: I publish an SCS bus decoder for sigrok and contact the Nuki Support.
  • 2020-10-15: I buy another Nuki Opener (Nuki Opener #2) to test their old firmware version, because downgrading firmware versions is impossible. Opener #2 actually opens the door, so I assume we are dealing with a firmware problem [turns out incorrect later].
  • 2020-10-16: I publish a detailed analysis of the Nuki Opener not sending the correct signal for the Nuki developers to go through.
  • 2020-11-03: I update my new Nuki Opener #2 to the latest firmware and realize that my old Nuki Opener #1 most likely just has some sort of hardware defect. However, Opener #2 has trouble detecting the ring signal: either it doesn’t detect any rings at all, or it detects all rings, including those for my neighbors!
  • 2020-11-16: In their 13th (!) email reply, Nuki Support confirms that the Opener firmware is capturing and matching the incoming ring signal, if I understand their developers correctly.
  • 2020-11-18: I suggest to Nuki developers (via Nuki Support) to decode the SCS signal with a UART decoder instead of comparing waveforms. This should be a lot more reliable!
  • 2020-11-23: My self-designed SCS receiver/transmitter/power supply PCB arrives. The schematics are based on existing SCS DIY work, but I created my own KiCad files because I was only interested in the SCS bus interface, not the PIC microcontroller they used.
  • 2020-11-25: Working on the intercom, I assume some wire touched an unlucky spot, and my BTicino intercom went up in smoke. We enabled the Nuki Opener’s ring sound and started using it as our main door bell. This meant we now started hearing the ring sound for (some) of our neighbors as well.
  • 2020-11-26: My Teensy 4 microcontroller successfully decodes the SCS bus signal with its Analog Comparator and UART decoder.
  • 2020-11-28: My Teensy 4 microcontroller is deployed to filter the SCS bus ring signal and drive the Nuki Opener in analogue mode.

at 2020-11-30 07:12



Hurra, wir (k)leben weiter! Aktion zur Remote Chaos Experience (rc3)

Auch wenn ohne Mateflaschenumfallgeklirr, Einlassbändchenkratzrandertastung, Bratnudelstandfettdampfklamottengeruch und Messeglaswurstecho sicher einiges an Congressfeeling fehlen wird – (Aufkleber-)Goldschatzauffindungsimpressionen sollen trotzdem nicht zu kurz kommen.

Hierfür haben wir die Aktion „Schicke Sticker von den Sticker-Schickern“ ins Leben gerufen.

Wenn ihr Lust auf eine klebrige Überraschung habt, könnt ihr uns bis zum 4. Dezember 2020 einen adressierten und frankierten Rückumschlag (am besten C5) an unsere neue Adresse senden und wir schicken euch Aufcccleber und andere Goodies zurück.

Die Aktion wird – außer der Umschläge – kostenlos sein. Dennoch freuen wir uns natürlich über allgemeine Spenden auf unser Konto oder einen Beitrag via PayPal, um alle Kosten zu decken und den möglichen Rest in unseren neuen Space zu investieren.

Bei Fragen könnt ihr euch auf Twitter und Mastodon an uns wenden.

at 2020-11-14 00:00



Achievement unlocked, Umzug geglückt

Einen Tag vor Ablauf unserer Umzugsfrist haben wir die allerletzten Reste aus den alten Räumlichkeiten rausgekehrt und die Schlüssel unserem ehemaligen Vermieter übergeben. Die Ära Boveristraße ist somit endgültig Geschichte.

Unser Elektroniklabor, die Holzwerkstatt, das FabLab und unsere Küche haben in der Weinheimer Straße ein neues Zuhause gefunden haben. Auch unser Olymp wird in anderer Form bei den Heidelberger Breidenbach Studios weiterleben.

Wir freuen uns auf die nächsten 10(0) Jahre RaumZeitLabor! Auf abgeschlossene und verworfene Ideen und Projekte, Vorträge, Feiern, Ess- und Mottopartys, Nerd am Herd, Bits & Bites und Stick-Nachmittage. Auf 3D-Druck- und Lasercut-Sessions, Programmier-Workshops, Agenda Aktion, GnoPN, Large Hackerspace Conventions, Film- und Analogspieleabende, Mario-Kart-Turniere, GameJams, Exkursionen und Museumsbesuche, Ausflüge zu Veranstaltungen und vor allem auf ganz, ganz viel Popcorn!

by flederrattie at 2020-11-13 00:00


Challenges and prospects of a posteriori error estimation in density-functional theory

Last week Wednesday I was invited to give a talk at the group seminar of the AG Christoph Jacob at TU Braunschweig, Germany. Christoph was especially interested in our recent publication on a posteriori error estimation in Kohn-Sham problems and so I decided to use the opportunity to give a broad introduction into the topic. Since the main audience for my talk were chemists I motivated our work from the context of high-throughput density-functional theory calculations, which are becoming more and more of interest in practice. In the second part of my talk I tried to lay out the basic ideas and challenges of a posteriori error estimation and what are the key aspects to understand and overcome if one wants to provide a useful error bound for a particular problem (see also this article for more details). In the last part of the talk I turned the attention specifically to our recent contribution, discussing error estimates in the context of simple Kohn-Sham problems. Many of the delicate details of our work I did not touch upon, but nevertheless this last section of my talk gives a very good overview of our approach, our main underlying assumptions and our results. While we have focused solely on plane-wave basis sets in our work, I briefly hinted whether extensions to other basis sets with similar methods can be achieved.

Unfortunately the whole "visit" to Braunschweig was completely virtual, which really was a shame as I would have loved to return to the city and spend a day with the group. Despite these circumstances though the discussions with Christoph and his group did not not really fall short. During the day I had many video call sessions where I had ample opportunity to discuss with PhD students about their projects and in this way get a good idea of the interesting research going on in Braunschweig. As that's typically my favourite part about visiting a group I'm very happy this worked out so well (thanks to everyone who I managed to talk to!) and I already look forward to properly meeting everyone in person when the usual conference schedules are back in place.

The slides from my talk are attached below.

Link Licence
Challenges and prospects of a posteriori error estimation in density-functional theory (Slides) Creative Commons License

by Michael F. Herbst at 2020-10-21 16:00 under talk, electronic structure theory, Julia, DFTK, theoretical chemistry, error estimates, numerical analysis, Kohn-Sham, high-throughput, invited talk


Moansi: Inhomogeneous preconditioning for density-functional theory

Last week (24th and 25th September) I attended the 4th annual meeting of the Moansi (Modelling, analysis and simulation of Molecular Systems) work group of the GAMM. I already attended the Moansi meeting last year, where I very much enjoyed both the broad range of talks at the interdisciplinary border of maths, chemistry and physics as well as the familial atmosphere with lively and stimulating discussions. In the same spirit I was looking forward to this year's addition, where in light of the global pandemic, however, the workshop had to be virtual. Nevertheless I was able to take away many stimulating impressions from the two days of the meeting and I already look forward to next year, where we hopefully meet again in person.

During the meeting I myself presented our recently published work on an LDOS-based SCF preconditioner, which is especially suitable for DFT calculations in inhomogeneous systems (metallic slabs or clusters). See this blog article and my slides for details.

Link Licence
Black-box inhomogeneous preconditioning for density-functional theory (Slides) Creative Commons License

by Michael F. Herbst at 2020-09-30 20:00 under talk, electronic structure theory, Julia, DFTK, theoretical chemistry, SCF, high-throughput


sECuREs website

Nuki Opener with an SCS bus intercom (bTicino 344212)

I have long been looking for a way to make my intercom a little more pleasant.

Recently, a friend made me aware of the Nuki Opener, which promises to make existing intercom systems smart, and claims to be compatible with the specific intercom I have!

So I got one and tried setting it up, but could not get it to work.

This post documents how I have analyzed what goes over the intercom’s SCS bus. Perhaps the technique is interesting, or perhaps you want to learn more about SCS :)

Note that I have not yet used the Nuki Opener, so I can’t say anything about it yet. What I have seen so far makes a good impression, but it just does not seem to work at all with my intercom. I will update this article after working with the Nuki support to fix this.

Connecting the Nuki Opener to the bTicino 344212

First, I identified which wires are used for the bus: between BUS- and BUS+, the internet tells me that I would expect to measure ≈27V, and indeed a multimeter shows:

BTicino multimeter

I then connected the Nuki Opener as described in “Connect the Nuki Opener to an unknown intercom”, Page 8, Bus intercoms → Basic setup without doorbell suppression:

Nuki wire Intercom Signal
black BUS- GND
red BUS+ SCS (+27V)
orange BUS+ SCS (+27V)
BTicino wiring

I had previously tried the enhanced setup with doorbell suppression, as the Nuki app recommends, but switched to the simplest setup possible when capturing the signal.

Configuring the Nuki Opener

With the Nuki app, I configured the Opener either as:

  • bTicino → 344212
  • Generic → Bus (SCS)
  • Unknown intercom

Unfortunately, with all configurations:

  1. The app says it learned the door open signal successfully.
  2. The device/app does react to door rings.
  3. The device never successfully opens the door.

Capturing the SCS bus with sigrok

The logic analyzer that I have at home only works with signals under 5V. As the SCS bus is running at 27V, I’m capturing the signal with my Hantek 6022BE USB oscilloscope.

sigrok is a portable, cross-platform, free open source signal analysis software suite and supports the Hantek 6022BE out of the box, provided you have at least version 0.1.4 of the the sigrok fx2lafw package installed.

Check out sigrok’s “Getting started with a logic analyzer” if you’re new to sigrok!

The Nuki Opener has 3 different pin headers you can use, depending on where you want to attach it on your wall. These are connected straight through, so I used them to conveniently grab BUS+ and BUS- just like the Nuki sees it:

BTicino capture

I set the oscilloscope probe head to its 10X divider setting, so that I had the full value range available, then started sampling 5M samples at 500 kHz:

sigrok PulseView screenshot

You can see 10s worth of signal. The three bursts are transmissions on the SCS bus.

The labeling didn’t quite match for me: it shows e.g. 3.2V instead of 27V, but as long as the signal comes in clearly, it doesn’t matter if it is offset or scaled.

SCS bus decoding with sigrok: voltage levels

Let’s tell sigrok what voltage level corresponds to a low or high signal:

  1. left-click on channel CH1
  2. set “conversion” to “to logic via threshold”
  3. set “conversion threshold” to 3.0V

Now you’ll see not only the captured signal, but also the logical signal below in green:

sigrok PulseView screenshot

SCS bus decoding with sigrok: SCS decoder

Now that we have obtained a logical/digital signal (low/high), we can write a sigrok decoder for the SCS bus. See sigrok’s Protocol decoder HOWTO for an introduction.

In general, I strongly recommend investing into tooling, in particular when decoding protocols. Spending a few minutes to an hour at this stage will minimize mistakes and save lots of time later, and—when you contribute your tooling—enable others to do more interesting work!

I found it easy to write a sigrok decoder, having never used their API before. It was quick to get something onto the screen, mistakes were easy to correct, and the whole process was nicely iterative.

Until it is merged and released with a new version of libsigrokdecode, you can find my SCS decoder on GitHub.

The decoder looks at every layer of an SCS telegram: the start/stop bits, the data bits, the value and the value’s logical position/function in the SCS telegram.

SCS full

Our SCS decoder displays the 3 bursts on the SCS bus when we ring the doorbell:

SCS bus door ring SCS bus door ring SCS bus door ring

Only the middle burst sets a destination address of 0x3, the configured number of my intercom system. I am not sure what the first and last burst indicate!

The SCS bus activity when opening the door seems more clear:

SCS bus door open SCS bus door open

These 2 bursts are sent one second apart, and only differ in the request parameter field: my guess is that 0xa4 means “start buzzing the door open” and 0xa0 means “stop buzzing the door open”.

I’m not sure why all these bursts repeat their SCS telegrams 3 times. My understanding was that SCS telegrams are repeated only when they are not acknowledged, and I indeed see no acknowledgement telegrams in my captures. Does that mean something is wrong with our intercom and it only works due to retransmissions?

SCS bus decoding with sigrok git: UART+SCS decoder

As Gerhard Sittig pointed out, in the git version of libsigrokdecode, one can use the existing UART decoder to decode SCS:

  1. Set Baud rate to 9600
  2. Set Sample point to 20%

This seems a little more robust than my cobbled-together SCS decoder from above :)

In addition to the UART decoder, we can still use a custom SCS decoder to label individual bytes within an SCS telegram according to their function, and do CRC checks.

Captured SCS telegrams

You can find my most recent captures in

  • 2020-09-27-anlern-01-open-PUR-filtered.srzip is the door buzzer
  • 2020-09-27-anlern-02-klingel-PUR-filtered.srzip is the bell ringing

To extract the interesting parts from the sigrok files, I:

  1. Click the Show Cursors icon in PulseView’s toolbar.
  2. Position the left and right cursor edges such that the signal of interest is selected.
  3. Click the drop-down next to the Save icon and select Save Selected Range As.

Further reading

I used the following sources; please let me know of any others!

at 2020-09-28 06:43


Faraday Discussions: New horizons in density functional theory

Following the submission of our paper on a posteriori error estimation in the Kohn-Sham equations a few months ago I was recently invited to present our work at the Faraday Discussions on New horizons in density functional theory. Being amongst speakers such as Kieron Burke, Andreas Savin or Weitao Yang this was truly a great honour.

Even though the conference had to be virtual, I enjoyed it very much, especially because of its very unusual format. Unlike most other conferences where the presenting author typically does his thing for like 30 minutes, followed by just a few questions, the situation is completely reversed for the Faraday discussions. Since we had to submit our paper already months in advance (and this was shared with the other participants) the content of my talk was already known to the audience. The main chunk of the time at the conference was therefore allocated to the discussion and not to the presentation. My few slides therefore only briefly recap our work and hint at the general motivation and outlook. As I hoped our work did indeed stimulate an intense discussion with interested and stimulating questions, which I really appreciated (thanks to everyone who asked or commented). As far as I understand both the paper as well a transcript of the discussion will be part of the official Faraday Discussions conference proceedings, which will be published by the Royal Society of Chemistry soon. As per usual my slides are attached below.

Link Licence
A posteriori error estimation for the non-self-consistent Kohn-Sham equations (Slides) Creative Commons License

by Michael F. Herbst at 2020-09-15 13:00 under talk, electronic structure theory, Julia, DFTK, theoretical chemistry, error estimates, numerical analysis, Kohn-Sham, high-throughput



Käfertal bleibt Käfertal bleibt Käfertal

Kaum zu glauben, aber wahr: Die Suche nach einem neuen Standort ist beendet! Das RaumZeitLabor bleibt in Käfertal und zieht 1,3 Luftlinienkilometer weiter in die Weinheimer Straße 58–60.

Hier gibt es noch einiges tun. Wände müssen versetzt, beziehungsweise gestellt werden, der Keller gehört renoviert und werkstatttauglich hergerichtet, die neue Aufteilung aller Räume muss durchdacht werden. Aber auch das “alte” RZL und die eigentliche Umzugsplanung sollten vor lauter Vorfreude auf die neue Location nicht vernachlässigt werden. 

Wir freuen uns weiterhin über Beteiligung aller Art. Wie es die kommenden Wochen weitergeht, erfahrt ihr auf der Mailingliste und sicher auch über Twitter/Mastodon.

by flederrattie at 2020-09-06 00:00


Black-box inhomogeneous preconditioning for self-consistent field iterations in density-functional theory

For the past half a year or so Antoine Levitt and myself have been looking at a particular tricky busyness for solid-state density-functional theory (DFT) calculations, namely how to design efficient self-consistent field (SCF) schemes for large inhomogeneous systems. I have already previously reported on this matter in a short talk at the seminar of our interdisciplinary working group, but now our results have reached a stage suitable for publication.

The underlying problem we are tackling in our work is that for large systems, meaning increased sizes of the unit cell, the SCF iterations become harder and harder to solve. Mathematically speaking the (spectral) condition number of the fixed point iterations underlying the SCF procedure increase rather drastically in such cases, leading to very slow convergence. For example in aluminium the number of iterations required to converge an SCF with a damped iteration scheme (the most simple one) increases quadratically with the system size. This quickly makes calculations intractable and multiple more sophisticated approaches have therefore been developed over the years. As is detailed in our work there are mainly two orthogonal directions of attack. The first is to black-box "accelerate" the convergence by using the so-called Anderson (or Pulay or DIIS) scheme. This reduces the growth of iterations with system size from quadratic to linear (in the aluminium example), which is a good start. The second approach is to use a carefully designed preconditioner for the SCF in order to tame the SCF iterations. Figuratively speaking this approach makes use of known physics to prevents the SCF from looking in the wrong direction for the solution. If done right, meaning that the physics modelled by the preconditioner fits the system at hand, this allows the SCF iteration count to become independent of system size. This latter approach is clearly the more important route to cure the problem, but both approaches are orthogonal and are therefore typically combined in order to get the fastest convergence.

Now what does it mean the preconditioner has to fit the system? As we detail in the paper, the convergence of an SCF is intimately linked to the dielectric behaviour of the material one models with the SCF. For homogeneous cases (i.e. bulk insulators, metals and semiconductors) people have devised very good models for their dielectric behaviour and have used them to construct preconditioners. As is well known (and confirmed by our study) these models show exactly the desirable property of a size-independent iteration count. The caveat is only that metals, insulators and semiconductors have deviating dielectric properties, meaning that each of these calls for a different preconditioning strategy. In return this means that heterogeneous cases where multiple of these materials are combined are difficult to treat in practice because none of the bulk recipes fully fit.

The main aim of our work was therefore to design a preconditioner which automatically and locally adapts to the system at hand, meaning that for heterogeneous cases it treats metallic regions like metals, insulating regions like insulators and so on. As we demonstrate with a number of test cases our preconditioner is able to do this completely black-box and parameter-free and performs well also for large heterogeneous systems. This is in contrast to previous approaches to tackle this problem, which were not as general as our approach and sometimes required complex hand-tuning of the involved parameters.

While our preconditioner solves the problem of efficiently treating cases like metallic slabs, metal clusters and basically any combination of metallic parts, insulators and vacuum, it is not fully capable of distinguishing insulators and semiconductors. We show that this can be cured at the expense of introducing another parameter to our algorithm. This works, but is not completely satisfactory to us. Part of our ongoing work is therefore to extend our scheme to treat mixed systems involving semiconductors as well. Another aspect we have so far neglected is spin, which is a constant annoyance for converging SCFs. Having a solid dielectric model as we propose it, also opens way to adapt preconditioning to each spin component differently. We hope to use this in the future to tackle convergence issues with spin in a hopefully more rigorous way than this is done to date.

The full abstract of our paper reads

We propose a new preconditioner for computing the self-consistent problem in Kohn-Sham density functional theory, based on the local density of states. This preconditioner is inexpensive and able to cure the long-range charge sloshing known to hamper convergence in large, inhomogeneous systems such as clusters and surfaces. It is based on a parameter-free and physically motivated approximation to the independent-particle susceptibility operator, appropriate for both metals and insulators. It can be extended to semiconductors by using the macroscopic electronic dielectric constant as a parameter in the model. We test our preconditioner successfully on inhomogeneous systems containing metals, insulators, semiconductors and vacuum.

by Michael F. Herbst at 2020-09-03 22:30 under electronic structure theory, theoretical chemistry, DFTK, Julia, dft, numerical analysis, Kohn-Sham


sECuREs website

Adding a fiber link to my home network


Despite using a FTTH internet connection since 2014, aside from the one fiber uplink, I had always used network gear with 1 Gbit/s links over regular old rj45 cat5(e) cables.

I liked the simplicity and uniformity of that setup, but decided it’s time to add at least one fiber connection, to get rid of a temporary ethernet cable that connected my kitchen with the rest of my network that is largely in the living room and office.

The temporary ethernet cable was an experiment to verify that running a server or two in my kitchen actually works (it does!). I used a flat ethernet cable, which is great for test setups like that, as you can often tape it onto the walls and still close the doors.

So, we will replace one ethernet cable with one fiber cable and converters at each end:

0.9mm thin fiber cables

Why is it good to switch from copper ethernet cables to fiber in this case? Fiber cables are smaller and hence easier to fit into existing cable ducts. While regular ethernet cable is way too thick to fit into any of the existing ducts in my flat, I was hoping that fiber might fit!

When I actually received the cables, I was surprised how much thinner fiber cables actually can be: there are 0.9mm cables, which are so thin, they can be hidden in plain sight! I had only ever seen 2mm fiber cables before, and the 0.9mm cables are incredibly light, flexible and thin! Even pasta is typically thicker:

Preparing a delicious pot of glass noodles ;)

Preparing a delicious pot of glass noodles ;)

The cable shown above comes from the fiber store FS.COM, which different people have praised on multiple occasions, so naturally I was curious to give them a shot myself.

Also, for the longest time, it was my understanding that fiber connectors can only be put onto fiber cables using expensive (≫2000 CHF) machines. A while ago I heard about field assembly connectors so I wanted to verify that those indeed work.

Aside from practical reasons, playing around with fiber networking also makes for a good hobby during a pandemic :)

Hardware Selection

I ordered all my fiber equipment at FS.COM: everything they have is very affordable, and products in stock at their German warehouse arrive in Switzerland (and presumably other European countries) within the same week.

If you are in the luxurious position to have enough physical space and agility to pull through an entire fiber cable, without having to remove any connectors, you can make a new network connection with just a few parts:

amt price total article note
2x 36 CHF 72 CHF #17237 1 Gbit/s media converter RJ45/SFP
1x 8.5 CHF 8.5 CHF #39135 1 Gbit/s BiDi SFP 1310nm-TX/1550nm-RX
1x 11 CHF 11 CHF #39138 1 Gbit/s BiDi SFP 1550nm-TX/1310nm-RX
1x 2.3 CHF 2.3 CHF #12285 fiber cable, 0.9mm LC UPC/LC UPC simplex

I recommend buying an extra fiber cable or two so that you can accidentally damage a cable and still have enough spares.

Total cost thus far: just under 100 CHF. If you have existing switches with a free SFP slot, you can use those instead of the media converters and save most of the cost.

If you need to temporarily remove one or both of the fiber cable connector(s), you also need field assembly connectors and a few tools in addition:

amt price total article note
2x 4 CHF 8 CHF #35165 LC/UPC 0.9mm pre-polished field assembly connector
1x 110 CHF 110 CHF #14341 High Precision Fibre Optic Cleaver FS-08C
1x 26 CHF 26 CHF #14346 Fibre Optic Kevlar Cutter
1x 14 CHF 14 CHF #72812 Fibre Optical Stripper

I recommend buying twice the number of field assembly connectors, for practicing.

Personally, I screwed up two connectors before figuring out how the process goes.

Total cost: about 160 CHF for the field assembly equipment, so 260 CHF in total.

To boost your confidence in the resulting fiber, the following items are nice to have, but you can get by without, if you’re on a budget.

price article note
18 CHF #35388 FVFL-204 Visual Fault Locator
9.40 CHF #82730 2.5mm to 1.25mm adapter for Visual Fault Locator
4.10 CHF #14010 1.25mm fiber clean swabs (100pcs)

With the visual fault locator, you can shine a light through your fiber. You can verify correct connector assembly by looking at how the light comes out of the connector.

The fiber cleaning swabs are good to have in general, but for the field assembly connector, you need to use alcohol-soaked wipes anyway (which FS.COM does not stock).

The total cost for everything is just under 300 CHF.

Hardware Selection Process

The large selection at FS.COM can be overwhelming to navigate at first. My selection process went something like this:

My first constraint is using bi-directional (BiDi) fiber optics modules so that I only need to lay a single fiber cable, as opposed to two fiber cables.

The second constraint is to use field assembly connectors.

If possible, I wanted to use bend-insensitive fiber so that I wouldn’t need to pay so much attention to the bend radius and have more flexibility in where and how I can lay fiber.

With these constraints, there aren’t too many products left to combine. An obvious and good choice are 0.9mm fiber cable using LC/UPC connectors.

FS.COM details

As of 2020-08-05, FS.COM states they have 5 warehouses in 4 locations:

  • Delaware (US)
  • Munich (Germany)
  • Melbourne (Australia)
  • Shenzhen (China)

They recently built another, bigger (7 km²) warehouse in Shenzhen, and now produce inventory for the whole year.

By 2019, FS.COM had over 300,000 registered corporate customers, reaching nearly 200 million USD yearly sales.

Delivery times

As mentioned before, delivery times are quick when the products are in stock at FS.COM’s German warehouse.

In my case, I put in my order on 2020-Jun-26.

The items that shipped from the German warehouse arrived on 2020-Jul-01.

Some items had to be manufactured and/or shipped from Asia. Those items arrived after 3 more weeks, on 2020-Jul-24.

Unfortunately, FS.COM doesn’t stock any 0.9mm fiber cables in their German warehouse right now, so be prepared for a few weeks of waiting time.

Laying The Fiber

Use a cable puller to pull the fiber through existing cable ducts where possible.

  • In general, buy the thinnest one you can find. I have this 4mm diameter cable puller, but a 3mm or even 2mm one would work in more situations.

  • I found it worthwhile to buy a brand one. It is distinctly better to handle (less stiff, i.e. more flexible) than the cheap one I got, and thinner, too, which is always good.

In my experience, it generally did not work well to push the fiber into an existing duct or alongside an existing cable. I really needed a cable puller.

If you’re lucky and have enough space in your duct(s), you can leave the existing connectors on the fiber. I have successfully just used a piece of tape to fix the fiber connector on the cable puller, pushing down the nose temporarily:

fiber cable taped to cable puller

Where there are no existing ducts, you may need to lay the fiber on top of the wall. Obviously, this is tricky as soon as you need to make a connection going through a wall: whereas copper ethernet cables can be bent and squeezed into door frames, you quickly risk breaking fiber cables.

Luckily, the fiber is very light, so it’s very easy to fix to the wall with a piece of tape:

fiber cables on the wall

You can see the upstream internet fiber in the top right corner, which is rather thick in comparison to my 0.9mm yellow fiber that’s barely visible in the middle of the picture.

Note how the fiber entirely disappears behind the existing duct atop the door!

Above, you can see the flat ethernet cable I have been using as a temporary experiment.

Where there is an existing cable that you can temporarily remove, it might be possible to remove it, put the fiber in, and put the old cable back in, too. This is possible because the 0.9mm fiber cable is so thin!

I’m using this technique to cross another wall where the existing cable duct is too full, but there is a cable that can be removed and put back after pulling the fiber through:

fiber cable next to existing cable

…and on the other side of the wall:

fiber cable next to existing socket

Note how the fiber is thin enough to fit between the socket and duct!

Note: despite measuring how long a fiber cable I would need, my cable turned out too short! While the cable was just as long as I had measured, with distances exceeding 10m, it is a good idea to add a few meters spare on each side of the connection.

Field assembly connectors

To give you an overview, these are the required steps at a high level:

  1. Cut the fiber with the Fibre Optic Kevlar Cutter
  2. Strip the fiber with the Fibre Optical Stripper
  3. Put the field assembly jacket onto the fiber
  4. Cut the stripped fiber cleanly with the High Precision Fibre Optic Cleaver FS-08C
  5. Put the field assembly connector onto the fiber

I thought the following resources were useful:

  1. Pictograms: PDF: FS.COM LC UPC field assembley connectors quick start guide
  2. Pictures: Installation Procedure on FS.COM
  3. Video: YouTube: Terminate Fiber in 5 Minutes: this video shows a different product, but I found it helpful to see any field assembly connector on video, and this is one of the better videos I could find.

Beware: the little paper booklet that comes with the field assembly connector contains measurements which are not to scale. I have suggested to FS.COM that they fix this, but until then, you’ll need to use e.g. a tape measure.

For establishing an intuition of their different sizes, here are the different connectors:

fiber cable connectors

From left to right:

  • 2.0mm fiber cable
  • cat6 ethernet cable
  • 0.9mm fiber cable (LC/UPC factory)
  • 0.9mm fiber cable (LC/UPC field assembly connector)

The 0.9mm fiber cables come with smaller connectors than the 2.0mm fiber cables, and that alone might be a reason to prefer them in some situations.

The field assembly connectors are pretty bulky in comparison, but since you can attach them yourself after pulling only the cable through the walls and/or ducts, you usually don’t care too much about their size.


Modern fiber cables available at FS.COM are:

  • thinner than I expected
  • more robust than I expected
  • cheaper than I expected
  • survive tighter bend radiuses than I expected

Replacing this particular connection with a fiber connection was a smooth process overall, and I would recommend it in other situations as well.

I would claim that it is totally feasible for anyone with an hour of patience to learn how to put a field assembly connector onto a fiber cable.

If labor cost is expensive in your country or you just like doing things yourself, I can definitely recommend this approach. In case you mess the connector up and don’t want to fix it yourself, you can always call an electrician!

Stay tuned for the next part, where I upgrade the 1G link to a 10G link!

at 2020-08-09 12:53


DFTK: A Julian approach for simulating electrons in solids

Since last Friday I have been attending JuliaCon, the annual conference for the Julia language. Naturally given the current situation the event did not take place "on location", but was instead converted into a virtual event. Albeit the different feel compared to a real-life conference the organisers did a very good job to maintain the social component into the event. Talks were pre-recorded and speakers available in a chat room to discuss during and after the presentation in written form. Birds of feather brainstorming sessions took place using audio discussions and at the end of every day there was a Gather Town virtual social, where one could videochat with fellow attendees by meeting up in a beautifully animated world, where each attendee was represented by a tiny avatar.

Apart from attending and listing to the great talks about the Julia language and its plenty of applications, I also had the chance to actively participate by giving a lecture about our package DFTK.jl. While I have presented on DFTK a few times before in front of expert audiences of the field, it was really the first time I presented DFTK as a released package to the broader Julia audience. That meant that I could, for once, give up on my usual storyline where I try and convince people into using Julia and instead focus on providing insight into the fascinating challenges of electronic-structure theory and how DFTK and Julia are ideal tools to tackle these.

In my talk I start easy by a general introduction into electronic-structure theory illustrating why an exact solution for electronic structures in molecules or solids is just not possible in realistic timeframes. Therefore one needs to live with approximate models, one example being density-functional theory (DFT), which we use in DFTK. As I detail in the talk an almost immediate consequence of the complexity of the problem is that advances in electronic-structure theory can typically only be realised if multiple disciplines join forces. An interdisciplinary project, however, brings some practical problems just quite frankly due to the fact that different fields have different approaches when tackling a problem. Being able to support such multidisciplinary motions in a common software platform for DFT, is one of the key aims of DFTK.

Related to this point we wanted DFTK to have a low entrance barrier for novel researchers. As time and money in research is tight programs should be easy to use and code simple and self-explanatory, such that new PhD students or researchers from foreign fields do not have a tough time to get started. In my talk I mention a few recent projects (an undergrad internship and a master project), where a noteworthy result could be achieved albeit students had little prior experience with neither Julia nor electronic-structure theory. A similar success story emphasising our ability to rapidly realise novel ideas in DFTK includes our recently published Faraday paper, where it only took 10 weeks from starting the project to submitting the paper.

Lastly, I discussed challenges arising from the so-called high-throughput screening methods, which are recently gaining popularity in computational materials design. In this particular research direction algorithms need to be particularly robust and tunable to find a sweet spot between accuracy and computational cost. This demands extremely stable and reliable algorithms, which poses interesting mathematical problems in numerical analysis and e.g. with respect to designing estimators for discretisation error. Especially in this area of application-oriented mathematical research we expect DFTK to be a handy tool in the future.

If you are interested in the full story a recording of the talk is available on youtube.

Link Licence
DFTK: A Julian approach for simulating electrons in solids (Slides) Creative Commons License
Youtube recording of the talk

by Michael F. Herbst at 2020-07-31 20:00 under talk, electronic structure theory, Julia, HPC, DFTK, theoretical chemistry, SCF, high-throughput


Mero’s Blog

Parametric context

tl;dr: Go's Context.Value is controversial because of a lack of type-safety. I design a solution for that based on the new generics design draft.

If you are following what's happening with Go, you are aware that recently an updated design draft for generics has dropped. What makes this particularly notable is that it comes with an actual prototype implementation of the draft, including a playground. This means for the first time, people get to actually try out how a Go with generics might feel, once they get in. It is a good opportunity to look at common Go code lacking type-safety and evaluate if and how generics can help address them.

One area I'd like to look at here is Context.Value. It is often criticized for not being explicit enough about the dependencies a function has and some people even go so far as to discourage its use altogether. On the other hand, I'm on record saying that it is too useful to ignore. Generics might be a way to bring together these viewpoints.

We want to be able to declare dependency on a functionality in context.Context via a function's signature and make it impossible to call it without providing that functionality, while also preserving the ability to pass it through APIs that don't know anything about it. As an example of such functionality, I will use logging. Let's start by creating a fictional little library to do that (the names are not ideal, but let's not worry about that):

package logctx

import (

type LogContext interface {
    // We embed a context.Context, to say that we are augmenting it with
    // additional functionality.

    // Logf logs the given values in the given format.
    Logf(format string, values ...interface{})

func WithLog(ctx context.Context, l *log.Logger) LogContext {
    return logContext{ctx, l}

// logContext is unexported, to ensure it can't be modified.
type logContext struct {
    l *log.Logger

func (ctx logContext) Logf(format string, values ...interface{}) {
    ctx.l.Printf(format, values...)

You might notice that we are not actually using Value() here. This is fundamental to the idea of getting compiler-checks - we need some compiler-known way to "tag" functionality and that can't be Value. However, we provide the same functionality, by essentially adding an optional interface to context.Context.

If we want to use this, we could write

func Foo(ctx logctx.LogContext, v int) {
    ctx.Logf("Foo(%v)", v)

func main() {
    ctx := logctx.WithLog(context.Background(), log.New(os.Stderr, "", log.LstdFlags))
    Foo(ctx, 42)

However, this has a huge problem: What if we want more than one functionality (each not knowing about the other)? We might try the same trick, say

package tracectx

import (


type TraceContext interface {
    Tracer() opentracing.Tracer

func WithTracer(ctx context.Context, t opentracing.Tracer) TraceContext {
    return traceContext{ctx, t}

type traceContext struct {
    t opentracing.Tracer

func (ctx traceContext) Tracer() opentracing.Tracer {
    return ctx.t

But because a context.Context is embedded, only those methods explicitly mentioned in that interface are added to traceContext. The Logf method is erased. After all, that is the trouble with optional interfaces.

This is where generics come in. We can change our wrapper-types and -functions like this:

type LogContext(type parent context.Context) struct {
    // the type-parameter is lower case, so the field is not exported.
    l *log.Logger

func WithLog(type Parent context.Context) (ctx Parent, l *log.Logger) LogContext(Parent) {
    return LogContext(parent){ctx, l}

By adding a type-parameter and embedding it, we actually get all methods of the parent context on LogContext. We are no longer erasing them. After giving the tracectx package the same treatment, we can use them like this:

// FooContext encapsulates all the dependencies of Foo in a context.Context.
type FooContext interface {
    Logf(format string, values ...interface{})
    Tracer() opentracing.Tracer

func Foo(ctx FooContext, v int) {
    span := ctx.Tracer().StartSpan("Foo")
    defer span.Finish()

    ctx.Logf("Foo(%v)", v)

func main() {
    l := log.New(os.Stderr, "", log.LstdFlags)
    t := opentracing.GlobalTracer()
    // ctx has type TraceContext(LogContext(context.Context)),
    //    which embeds a LogContext(context.Context),
    //    which embeds a context.Context
    // So it has all the required methods
    ctx := tracectx.WithTracer(logctx.WithLog(context.Background(), l), t)
    Foo(ctx, 42)

Foo has now fully declared its dependencies on a logger and a tracectx, without requiring any type-assertions or runtime-checks. The logging- and tracing-libraries don't know about each other and yet are able to wrap each other without loss of type-information. Constructing the context is not particularly ergonomic though. We require a long chained function call, because the values returned by the functions have no longer a unified type context.Context (so the ctx variable can't be re-used).

Another thing to note is that we exported LogContext as a struct, instead of an interface. This is necessary, because we can't embed type-parameters into interfaces, but we can embed them as struct-fields. So this is the only way we can express that the returned type has all the methods the parameter type has. The downside is that we are making this a concrete type, which isn't always what we want¹.

We have now succeeded in annotating context.Context with dependencies, but this alone is not super useful of course. We also need to be able to pass it through agnostic APIs (the fundamental problem Context.Value solves). However, this is easy enough to do.

First, let's change the context API to use the same form of generic wrappers. This isn't backwards compatible, of course, but this entire blog post is a thought experiment, so we are ignoring that. I don't provide the full code here, for brevity's sake, but the basic API would change into this:

package context

// CancelContext is the generic version of the currently unexported cancelCtx.
type CancelContext(type parent context.Context) struct {
    // other fields

func WithCancel(type Parent context.Context) (ctx Parent) (ctx CancelContext(Parent), cancel CancelFunc) {
    // ...

This change is necessary to enable WithCancel to also preserve methods of the parent context. We can now use this in an API that passes through a parametric context. For example, say we want to have an errgroup package, that passes the context through to the argument to (*Group).Go, instead of returning it from WithContext:

// Derived from the current errgroup code.

// A Group is a collection of goroutines working on subtasks that are part of the same overall task.
// A zero Group is invalid (as opposed to the original errgroup).
type Group(type Context context.Context) struct {
    ctx    Context
    cancel func()

    wg sync.WaitGroup

    errOnce sync.Once
    err     error

func WithContext(type C context.Context) (ctx C) *Group(C) {
    ctx, cancel := context.WithCancel(ctx)
    return &Group(C){ctx: ctx, cancel: cancel}

func (g *Group(Context)) Wait() error {
    return g.err

func (g *Group(Context)) Go(f func(Context) error) {

    go func() {
        defer g.wg.Done()

        if err := f(g.ctx); err != nil {
            g.errOnce.Do(func() {
                g.err = err

Note that the code here has barely changed. It can be used as

func Foo(ctx FooContext) error {
    span := ctx.Tracer().StartSpan("Foo")
    defer span.Finish()
    ctx.Logf("Foo was called")

func main() {
    var ctx FooContext = newFooContext()
    eg := errgroup.WithContext(ctx)
    for i := 0; i < 20; i++ {
    if err := eg.Wait(); err != nil {

After playing around with this for a couple of days, I feel pretty confident that these patterns make it possible to get a fully type-safe version of context.Context, while preserving the ability to have APIs that pass it through untouched or augmented.

A completely different question, of course, is whether all of this is a good idea. Personally, I am on the fence about it. It is definitely valuable, to have a type-safe version of context.Context. And I think it is impressive how small the impact of it is on the users of APIs written this way. The type-argument can almost always be inferred and writing code to make use of this is very natural - you just declare a suitable context-interface and take it as an argument. You can also freely pass it to functions taking a pure context.Context unimpeded.

On the other hand, I am not completely convinced the cost is worth it. As soon as you do non-trivial things with a context, it becomes a pretty "infectious" change. For example, I played around with a mock gRPC API to allow interceptors to take a parametric context and it requires almost all types and functions involved to take a type-parameter. And this doesn't even touch on the fact that gRPC itself might want to add annotations to the context, which adds even more types. I am not sure if the additional machinery is really worth the benefit of some type-safety - especially as it's not always super intuitive and easily understandable. And even more so, if it needs to be combined with other type-parameters, to achieve other goals.

I think this is an example of what I tend to dislike about generics and powerful type-systems in general. They tempt you to write a lot of extra machinery and types in a way that isn't necessarily semantically meaningful, but only used to encode some invariant in a way the compiler understands.

[1] One upside however, is that this could actually address the other criticism of context.Value: Its performance. If we consequently embed the parent-context as values in struct fields, the final context will be a flat struct. The interface-table of all the extra methods we add will point at the concrete implementations. There's no longer any need for a linear search to find a context value.

I don't actually think there is much of a performance problem with context.Value in practice, but if there is, this could solve that.

at 2020-07-20 00:00


sECuREs website

Introducing the kinT kinesis keyboard controller

Kinesis Advantage ergonomic keyboard

Back in 2013, I published a replacement controller for the Kinesis Advantage ergonomic keyboard. In the community, it is often referred to simply as the “stapelberg”, and became quite popular.

Many people like to use the feature-rich QMK firmware, which supports my replacement controller out of the box.

kinesis pcb mounted

On eBay, you can frequently find complete stapelberg kits or even already-modified Kinesis keyboards including the stapelberg board for sale.

In 2017, Kinesis released the Kinesis Advantage 2, which uses a different connector (an FPC connector) for connecting the two thumb pad PCBs to the controller PCB, instead of the soldered cable the older Kinesis Advantage used. Aside from the change in connector and cable type, the newer keyboard uses the same pinout as the old one.

I wanted to at least update my project to support the Kinesis Advantage 2. While doing so, I decided to also make a bunch of improvements to make the project more approachable and usable for beginners. Among many other improvements, the project switched from Eagle to KiCad, which is FOSS and means no more costly license fees!

kinT (T for Teensy!)

I am hereby announcing the kinT kinesis keyboard controller: a replacement keyboard controller for your Kinesis Advantage or Advantage 2 ergonomic keyboards.

kinT keyboard controller

The Teensy footprint looks a bit odd, but it’s a combined footprint so that you can use the same board with many different Teensy microcontrollers, giving you full flexibility regarding cost and features. See “Compatibility: which Teensy to use?” for more details.

I originally replaced the controller of my Kinesis Advantage to work around a bug, but these days I do most of it just because I enjoy tinkering with keyboards.

You might consider to replace your keyboard controller for example…

Building your own kinT keyboard controller

  1. Follow “Buying the board and components (Bill of materials)”. When ordering from OSH Park (board) and Digi-Key (components), you’ll get the minimum quantity of 3 boards for 72 USD (24 USD per board), and one set of components for 49 USD.

    • If you have any special requirements regarding which Teensy microcontroller to use, this is the step where you would replace the Teensy 3.6 with your choice.
  2. Wait for the components to arrive. When ordering from big shops like Digi-Key or Mouser, this typically takes 2 days to many places in the world.

  3. Wait for the boards to arrive. This takes 6 days in the best case when ordering from OSH Park with their Super Swift Service option. In general, the longer you are willing to wait, the cheaper it is going to get.

  4. Follow the soldering guide. This will take about an hour.

  5. Install the firmware

Improvements over the older replacement board

In case you’re familiar with the older replacement board and are wondering what changed, here is a complete list:

  • The kinT supports both, the older Kinesis Advantage (KB500) and the newer Kinesis Advantage 2 (KB600) keyboards. They differ in how the thumb pads are connected. See the soldering instructions below.

  • The kinT is made for the newer Teensy 3.x and 4.x series, which will remain widely available for years to come, whereas the future of the Teensy++ 2.0 is not as certain.

  • The kinT is a smaller PCB (4.25 x 3.39 inches, or 108.0 x 86.1 mm), which makes it:

    • more compact: can be inserted/removed without having to unscrew a key well.

    • cheaper: 72 USD for 3 boards at oshpark, instead of 81 USD.

  • The kinT silkscreen (front, back) and schematic are much much clearer, making assembly a breeze.

  • The kinT is a good starting point for your own project:

    • kinT was designed in the open source KiCad program, meaning you do not need any license subscriptions.

    • The clear silkscreen and schematic make development and debugging easier.

  • On the kinT, the Teensy no longer has to be soldered onto the board upside down.

  • On the kinT, the FPC connectors have been moved for less strain on the cables.

  • The kinT makes possible lower-cost builds: if you don’t need the scroll lock, num lock and keypad LEDs, you can use a Teensy LC for merely 11 USD.


I’m very excited to release this new keyboard controller, and I can’t wait to see all the custom builds and modifications!

By the way, there is also a (4-hour!) stream recording in case you are interested in some more history and context, and want to see me solder a kinT controller live on stream!

at 2020-07-09 07:25



Will hack for space

Das Jahr 2020 und seine schlechten Neuigkeiten hören nicht auf. Zu allem Übel sind uns jetzt auch noch unsere Räumlichkeiten zum 31. Oktober 2020 gekündigt worden.

Damit wir passend zu Halloween eine Einweihungsparty feiern können, brauchen wir eure Mithilfe bei der Suche nach einem neuen Zuhause für den Verein und seinen Maschinenpark.

Was wir uns für ein zukünftiges RaumZeitLabor wünschen würden:

  • Büro- und Werkstatt-/Hallen-Kombination (wir brauchen wieder Arbeitsbereich und Platz für unsere Werkstätten)
  • Mindestens 200m², besser ein paar mehr m² Platz oder eine Option auf später Erweiterung
  • Küche oder Anschlüsse, um eine aufstellen zu können
  • Sanitäre Anlagen und Heizung
  • Einigermaßen guter ÖPNV-Anschluss, Parkmöglichkeiten in der Nähe
  • Internet, schnell


  • provisionsfrei
  • wenige Nachbarn, oder Nachbarn, die nur tagsüber vor Ort sind
  • barrierearmer Zugang

Solltet ihr einen Hinweis auf eine solche Immobilie haben, lasst es uns wissen und schreibt uns gern unter an.

Die kommenden vier Monate heißt es jetzt „Auf die Kartons, fertig, los!“. Kommt bitte vorbei, nehmt eure privaten Sachen mit nach Hause und helft uns, alles umzugssicher zu verpacken.

Vielen Dank!

by flederrattie at 2020-07-01 00:00


Insanity Industries

Socket activating arbitrary services

Socket activation is the idea of activating a daemon or service not by manually starting it, but by merely pre-exposing the socket that is used for communication with that service. This has several advantages:

  • system boot speeds up as less things need to actually be started at boot time
  • system resource usage is reduced as less services actually run1
  • you can restart services behind the socket invisible to the client (if the service gracefully takes up the connection on the socket again) without loosing messages2

The two requirements for this are:

  • a daemon that manages these sockets and activates the corresponding process once communication happens
  • the socket-activated daemon being able to work with a preestablished socket-connection

For the first part, systemd got us covered. The second part must be implemented in the daemon code, but we can regardless activate any socket based service, even if they don’t implement socket activation themselves with a little help. Let’s take a look at how things work in this order.

Systemd socket activation: The principle

This will be a brief rundown on how systemd’s socket activation works (see here for all the details):

To activate a service via its socket, we need to define two units: the service and the socket. A socket can be a network socket, a unix socket and several other connection types. In this post, however, we will exemplarily focus on network sockets. We place the service file of our socket-activatable service (we will come back to what this means in a moment) as /etc/systemd/system/myservice.service:

Description=Socket-activatable example service


and we place the corresponding socket unit (in this case a TCP-network-socket) as /etc/systemd/system/myservice.socket:

Description=Socket for example service

# In this example we only listen on localhost


Note that the service does not require an install section, only the socket does3. We then enable our socket via systemctl enable --now myservice.socket.

Now we have an inactive service unit, but an active socket which is set up by systemd. The moment any activity occurs on this socket, systemd will start myservice.service and hand over the socket, buffering what is already written to it until the service takes over.

Leveraging socket activation in practice

In practice, we can distinguish three different cases:

1. Socket activation natively supported already

If the service in question already natively supports socket activation, simply activate the corresponding socket unit (or create one if it doesn’t exist yet). See systemctl list-units | grep socket for socket-units already available on the system.

2. Fault tolerance and boot time optimization desired only

If our service is intended to be started at boot and socket activation is intended only to provide transparent restarts and boot parallelization, we can simply use systemd’s systemd-socket-proxyd. See man systemd-socket-proxyd or here for details and usage examples.

Make sure you add an [Install]-section to the service file and enable the service itself as well then as systemd-socket-proxyd merely decouples the service unit from its socket, but doesn’t start it automatically.

3. On-demand starting and stopping of arbitrary services

If our service does not support socket activation natively and we want it to start not at boot time, but on-demand, we can use the tool socket-activate. For this, configure actual.service to listen on localhost on a different port such as and create two units: socket-activate-actual.service containing

Description=Socket-activate proxy for example service

ExecStart=/usr/bin/socket-activate -u "actual.service" -a ""

as well as a corresponding socket-activate-actual.socket as noted above, listening on the actual desired port. On the first connection to the socket, socket-activate-actual.service will be started and in turn start actual.service, proxying all traffic to it.

If socket-activate is invoked with an additional -t <timeout>, then both socket-activate-actual.service as well as actual.service are stopped again when no activity is detected for the specified timeout.

  1. Especially as socket-activated services can terminate once their job is done, as they simply get reactivated next time someone connects to their communication socket again. ↩︎

  2. This includes crashes or upgrades of the service, no further data written to the socket will be lost, only the data the service has already read from it before it crashed or was restarted. ↩︎

  3. The service may still have an [Install] section to be started conventionally or already being started even if no one has yet connected to its socket. In the latter case the socket activation would primarily serve as restart resilience and boot parallelization. ↩︎

by Jonas Große Sundrup at 2020-06-28 15:23


SCF preconditioning for mixed systems

Fortunately the general lockdown due to the Corona pandemic slowly starts to ease around Paris as well. While basically all seminars are only virtual it is good to see old procedures and habits to slowly return. From my end I gave the first talk after the forced break today in the EMC2 group meeting.

Since it was the first time discussing DFTK in the EMC2 synergy group I decided to talk about it taking the angle of tackling an actual research problem. After presenting briefly DFT methods and DFTK in the first half of the talk, I therefore focused on one of my ongoing projects with Antoine Levitt, namely constructing better preconditioners for the self-consistent field (SCF) iterations in mixed systems. What is meant by mixed systems are systems where locally differing dielectric properties are found, i.e. where some parts of the material are insulating, others may be metallic or semiconductors. Since the dielectric properties are closely related to the spectrum of the SCF fixed-point map, they therefore also control the convergence properties of SCF procedures. For metals and (to a minor extent) semiconductors simple SCF procedures, where one just applies the SCF cycle over and over require extremely small step sizes (i.e. small damping values). As a result the SCF converges only very slowly. The remedy is to precondition the spectrum of the SCF map itself by using so-called mixing techniques. In state-of-the-art approaches these are usually material-specific, i.e. different mixings are used for insulators, metals or semiconductors. This is fine for bulk materials, but fails in case of mixed systems, since one has to globally select a single approach. Our recent work has been to investigate the spectrum of the SCF map and to try and construct a preconditioner which locally adapts and as a result is able to properly treat mixed systems as well. The results I presented today are, however, not yet final and more investigations are to be underdone for our approach to work as reliable as we want.

Link Licence
SCF preconditioning for mixed systems: A DFTK case study (Slides) Creative Commons License
A few DFTK examples (Jupyter notebook) GNU GPL v3
SCF preconditioners in 1D (Jupyter notebook) GNU GPL v3

by Michael F. Herbst at 2020-06-26 16:00 under talk, electronic structure theory, Julia, DFTK, theoretical chemistry, SCF


sECuREs website

Using the iPhone camera as a Linux webcam with v4l2loopback

iPhone camera setup

For my programming stream at, I wanted to add an additional camera to show test devices, electronics projects, etc. I couldn’t find my old webcam, and new ones are hard to come by currently, so I figured I would try to include a phone camera somehow.

The setup that I ended up with is:

iPhone camera
→ Instant Webcam
→ WiFi
→ gstreamer
→ v4l2loopback

Disclaimer: I was only interested in a video stream! I don’t think this setup would be helpful for video conferencing, due to lacking audio/video synchronization.

iPhone Software: Instant Webcam app

I’m using the PhobosLab Instant Webcam (install from the Apple App Store) app on an old iPhone 8 that I bought used.

There are three interesting related blog posts by app author Dominic Szablewski:

  1. MPEG1 Video Decoder in JavaScript (2013-May)
  2. HTML5 Live Video Streaming via WebSockets (2013-Sep)
  3. Decode it like it’s 1999 (2017-Feb)

As hinted at in the blog posts, the way the app works is by streaming MPEG1 video from the iPhone (presumably via ffmpeg?) to the jsmpeg JavaScript library via WebSockets.

After some git archeology, I figured out that jsmpeg was rewritten in commit 7bf420fd just after v0.2. You can browse the old version on GitHub.

Notably, the Instant Webcam app seems to still use the older v0.2 version, which starts WebSocket streams with a custom 8-byte header that we need to strip.

Linux Software

Install the v4l2loopback kernel module, e.g. community/v4l2loopback-dkms on Arch Linux or v4l2loopback-dkms on Debian. I used version 0.12.5-1 at the time of writing.

Then, install gstreamer and required plugins. I used version 1.16.2 for all of these:

Lastly, install either websocat or wsta for accessing WebSockets. I successfully tested with websocat 1.5.0 and wsta 0.5.0.


First, load the v4l2loopback kernel module:

% sudo modprobe v4l2loopback video_nr=10 card_label=v4l2-iphone

Then, we’re going to use gstreamer to decode the WebSocket MPEG1 stream (after stripping the custom 8-byte header) and send it into the /dev/video10 V4L2 device, to the v4l2loopback kernel module:

% websocat --binary ws://iPhone.lan/ws | \
  dd bs=8 skip=1 | \
  gst-launch-1.0 \
    fdsrc \
    ! queue \
    ! mpegvideoparse \
    ! avdec_mpeg2video \
    ! videoconvert \
    ! videorate \
    ! 'video/x-raw, format=YUY2, framerate=30/1' \
    ! v4l2sink device=/dev/video10 sync=false

Here are a couple of notes about individual parts of this pipeline:

  • You must set websocat (or the alternative wsta) into binary mode, otherwise they will garble the output stream with newline characters, resulting in a seemingly kinda working stream that just displays garbage. Ask me how I know.

  • The queue element uncouples decoding from reading from the network socket, which should help in case the network has intermittent troubles.

  • Without enforcing framerate=30/1, you cannot cancel and restart the gstreamer pipeline: subsequent invocations will fail with streaming stopped, reason not-negotiated (-4)

  • Setting format YUY2 allows ffmpeg-based decoders to play the stream. Without this setting, e.g. ffplay will fail with [ffmpeg/demuxer] video4linux2,v4l2: Dequeued v4l2 buffer contains 462848 bytes, but 460800 were expected. Flags: 0x00000001.

  • The sync=false property on v4l2sink plays frames as quickly as possible without trying to do any synchronization.

Now, consumers such as OBS (Open Broadcaster Software), ffplay or mpv can capture from /dev/video10:

% ffplay /dev/video10
% mpv av://v4l2:/dev/video10 --profile=low-latency


Hopefully the instructions above just work for you, but in case things go wrong, maybe the following notes are helpful.

To debug issues, I used the GST_DEBUG_DUMP_DOT_DIR environment variable as described on Debugging tools: Getting pipeline graphs. In these graphs, you can quickly see which pipeline elements negotiate which caps.

I also used the PL_MPEG example program to play the supplied MPEG test file. PL_MPEG is written by Dominic Szablewski as well, and you can read more about it in Dominic’s blog post MPEG1 Single file C library. I figured the codec and parameters might be similar between the different projects of the same author and used this to gain more confidence into the stream parameters.

I also used Wireshark to look at the stream traffic to discover that websocat and wsta garble the stream output by default unless the --binary flag is used.

at 2020-06-06 09:18


First release of the density-functional toolkit (DFTK)

After we released a preliminary snapshot of DFTK last year our focus in the first half of this year was on using it for some new science. Recently, however, we got back into polishing our code base and our documentation in order to get DFTK ready for a wider audience. Today I am proud to announce that DFTK 0.1.0 has been accepted into the Julia Package repository, such that the package can now be readily installed within the Julia ecosystem.

Let me take this opportunity to recapitulate on DFTK: I started the code with Antoine Levitt about a year ago when I moved to Paris. What we had in mind was to create a simple platform for methodological developments in density functional theory (DFT). Clearly our code should support the interdisciplinary requirements of the field, where advances are often the result from devising chemically and physically sound models, using mathematical insight for suggesting stable algorithms and then scaling them up to the high-performance regime. This means that we would need both (a) the flexibility to mix and match models and numerical approaches by keeping the code high-level and similar to a scripting language and (b) access to the usual tricks (vectorisation, GPUs, threading, distributed computing) to tweak performance down to the metal.

In Julia we found a language which suits these aims perfectly. This is illustrated by the fact that after only a good year of development we already support a sizable number of features in only about 5k lines of source code. Right now the focus of DFTK is on DFT ground-state simulations for solids (LDA/GGA in a plane-wave basis with GTH pseudopotentials) with more to come. Special care is taken to have a simple and clean codebase, well-commented and suitable for teaching or extensions (other models, basis, etc.). DFT is not hard-coded, and other similar models can be computed with DFTK (for instance, the 2D Gross-Pitaevskii equation with a magnetic field). Nevertheless, the performance is comparable with that of established plane-wave DFT codes, usually within a factor of 2. DFTK is fully multithreaded, although not distributed (yet). We also include interfaces with various codes (ASE, pymatgen, abipy...) for easy workflows and to integrate to the world beyond the Julia ecosystem. See for example the asedftk python package, which integrates DFTK into the atomistic simulation environment.

The code is of course fully open source and installation is easy. Since it is intended as a platform for multidisciplinary collaboration, we welcome any question, suggestion or addition. Feel free to get in touch by opening an issue at any time.

by Michael F. Herbst at 2020-06-05 08:00 under programming and scripting, DFTK, dft, electronic structure theory, Julia


Recent developments in adcc

Since the publication of the adcc paper a few months back, there are a few updates to report briefly:

  • adcc can now be interactively tried in the browser at using the infrastructure from the binder project.
  • Binary installation of adcc is now available via conda for Linux and MacOS, see the adcc documentation.
  • Calculation of rotatory strengths at all ADC levels.
  • adcc is now fully integrated into the Psi4 quantum chemistry package. This means that ADC calculations in adcc can now be directly started from within the Psi4 ecosystem, including Psi4's python frontend and input files. This effectively equips Psi4 with all ADC capabilities adcc offers. See some details in the recent Psi4 paper.
  • Tensor evaluations in adcc are now lazy, which means that complex tensor evaluation expressions can be coded up in python without being evaluated. Only once results are needed the complete expression is evaluated in a batch using the underlying linear algebra frameworks.

by Michael F. Herbst at 2020-06-03 17:00 under electronic structure theory, theoretical chemistry, adcc, algebraic-diagrammatic construction


sECuREs website

stapelberg uses this: my 2020 desk setup

Desk setup

I generally enjoy reading the uses this blog, and recently people have been talking about desk setups in my bubble (and on my Twitch stream), so I figured I’d write a post about my current setup!

Desk setup

I’m using a desk I bought at IKEA well over 10 years ago. I’m not using a standing desk: while I have one at work, I never change its height. Just never could get into the habit.

I was using an IKEA chair as well for many years.

Currently, I’m using a Haworth Comforto 89 chair that I bought second-hand. Unfortunately, the arm rests are literally crumbling apart and the lumbar back support and back rest in general are not as comfortable as I would like.

Hence, I recently ordered a Vitra ID Mesh chair, which I have used for a couple of years at the office before moving office buildings. It will take a few weeks before the chair arrives.

Full Vitra ID Mesh chair configuration details
  • ID Mesh
  • Chair type: office swivel chair
  • Backrest: ID Mesh
  • Colours and materials
  • - Cover material: seat and backrest Silk Mesh
  • - Colour of back cover: dim grey/ like frame colour
  • - Colour of seat cover: dim grey
  • - Frame colour: soft grey
  • Armrests: 2D armrests
  • Base: five-star base, polished aluminium
  • Base on: castors hard, braked for carpet
  • Ergonomics
  • Seat and seat depth adjustment: seat with seat depth adjustment
  • Forward tilt: with forward tilt

The most important aspect of the desk/chair setup for me are the arm rests. I align them with the desk height so that I can place my arms at a 90 degree angle, eliminating strain.


Note: all of my peripherals are Plug & Play under Linux and generally work with standard drivers across Windows, macOS and Linux.

Monitor: Dell 8K4K monitor (UP3218K)

The most important peripheral of a computer is the monitor: you stare at it all the time. Even when you’re not using your keyboard or mouse, you’re still looking at your monitor.

Ever since I first used a MacBook Pro with Retina display back in 2013, I’ve been madly in love with hi-DPI displays, and have gradually replaced all displays in my day-to-day with hi-DPI displays.

My current monitor is the Dell UP3218K, an 8K4K monitor (blog post).

Dell introduced the UP3218K in January 2017. It is the world’s first available 8K monitor, meaning it has a resolution of 7680x4320 pixels at a refresh rate of 60 Hz. The display’s dimensions are 698.1mm by 392.7mm (80cm diagonal, or 31.5 inches), meaning the display shows 280 dpi.

I run it in 300% scaling mode (Xft.dpi: 288), resulting in incredibly crisp text.

Years ago, I used multiple monitors (sometimes 3, usually 2). I stopped doing that in 2011/2012, when I lived in Dublin for half a year and decided to get only one external monitor for practical and cost reasons.

I found that using only one monitor allows me to focus more on what I’m doing, and I don’t miss anything about a multi-monitor setup.

Keyboard: Kinesis advantage keyboard

Kinesis advantage keyboard

The Kinesis is my preferred commercially available ergonomic keyboard. I like its matrix layout, ergonomic key bowls, thumb pads and split hands.

I find typing on it much more comfortable than regular keyboards, and I value the Kinesis enough to usually carry one with me when I travel. When I need to use a laptop keyboard for longer periods of time, my hands and arms get tired.

I bought my first one in 2008 for ≈250 EUR, but have since cleaned up and repaired two more Kinesis keyboards that were about to be trashed. Now I have one for home, one for work, and one for traveling (or keyboard development).

Over the years, I have modified my Kinesis keyboards in various ways:

The first modification I did was to put in Cherry MX blue key switches (tactile and audible), replacing the default Cherry MX browns. I like the quick feedback of the blues better, possibly because I was used to them from my previous keyboards. Without tons of patience and good equipment, it’s virtually impossible to unsolder the key switches, so I reached out to Kinesis, and they agreed to send me unpopulated PCBs into which I could solder my preferred key switches! Thank you, Kinesis.

I later replaced the keyboard controller to address a stuck modifier bug. The PCB I made for this remains popular in the Kinesis modification community to this day.

In 2018, I got interested in keyboard input latency and developed kinX, a new version of my replacement keyboard controller. With this controller, the keyboard has an input latency of merely 0.225ms in the worst case.

Aside from the keyboard hardware itself, I’m using the NEO Ergonomically Optimized keyboard layout. It’s optimized for German, English, Programming and Math, in that order. Especially its upper layers are really useful: hover over “Ebene 3” to see.

I used to remap keys in hardware, but that doesn’t cover the upper layers, so nowadays I prefer just enabling the NEO layout included in operating systems.

Pointing device: Logitech MX Ergo

During my student years (2008 to 2013), I carried a ThinkPad X200 and used its TrackPoint (“red dot”) in combination with trying to use lots of keyboard shortcuts.

The concept of relative inputs for mouse movement made sense to me, so I switched from a mouse to a trackball on the desktop, specifically the Logitech Trackball M570.

I was using the M570 for many years, but have switched to the Logitech MX Ergo a few months ago. It is more comfortable to me, so I replaced all 3 trackballs (home, office, travel) with the MX Ergo.

In terms of precision, a trackball will not be as good as a mouse can be. To me, it more than makes up for the fact by reducing the strain on my hands and wrists.

For comparison: a few years ago, I was playing a shooter with a regular mouse for one evening (mostly due to nostalgia), and I could feel pain from that for weeks afterwards.

Microphone: RØDE Podcaster

To record screencasts for the i3 window manager with decent audio, I bought a RØDE Podcaster USB Broadcast Mic in 2012 and have been using it ever since.

The big plus is that the setup couldn’t be easier: you connect it via USB, and it is Plug & Play on Linux. This is much easier than getting a working setup with XLR audio gear.

The audio quality is good: much better than headsets or cheap mics, but probably not quite as good as a more expensive studio mic. For my usage, this is fine: I don’t record radio broadcasts regularly, so I don’t need the absolutely highest quality, and for video conferences or the occasional podcast, the RØDE Podcaster is superb.

Webcam: Logitech C920

In the past, I have upgraded my webcam every so often because higher resolutions at higher frame rates became available for a reasonably low price.

I’m currently using the Logitech HD Pro Webcam C920, and I’m pretty happy with it. The picture quality is good, the device is Plug & Play under Linux and the picture quality is good out of the box. No fumbling with UVC parameters or drivers required :-)

Note: to capture at 30 fps at the highest resolution, you may need to specify the pixel format

Headphones: Sony WH-1000XM3

At work, I have been using the Bose QuietComfort 15 Noise Cancelling headphones for many years, as they were considered the gold standard for noise cancelling headphones.

I decided to do some research and give bluetooth headphones a try, in the hope that the technology has matured enough.

I went with the Sony WH-1000XM3 bluetooth headphones, and am overall quite happy with them. The lack of a cable is very convenient indeed, and the audio quality and noise cancellation are both superb. A single charge lasts me for multiple days.

Switching devices is a bit cumbersome: when I have the headphones connected to my phone and want to switch to my computer, I need to explicitly disconnect on my phone, then explicitly connect on my computer. I guess this is just how bluetooth works.

One issue I ran into is that when the headphones re-connected to my computer, they would not select the high-quality audio profile until you explicitly disconnect and re-connect again. This was fixed in BlueZ 5.51, so make sure you run at least that version.

USB memory stick: Sandisk Extreme PRO SSD USB 3.1

USB memory sticks are useful for all sorts of tasks, but I mostly use them to boot Linux distributions on my laptop or computer, for development, recovery, updates, etc.

A year ago, I was annoyed by my USB memory sticks being slow, and I found the Sandisk Extreme PRO SSD USB 3.1 which is essentially a little SSD in USB memory stick form factor. It is spec'd at ≈400 MB/s read and write speed, and I do reach about ≈350 MB/s in practice, which is a welcome upgrade from the < 10 MB/s my previous sticks did.

A quick USB memory stick lowers the hurdle for testing distri images on real hardware.

Audio: teufel sound system

My computer is connected to a Teufel Motiv 2 stereo sound system I bought in 2009.

The audio quality is superb, and when I tried to replace them with the Q Acoustics 3020 Speakers (Pair) I ended up selling the Q Acoustics and going back to the Teufel. Maybe I’m just very used to its sound at this point :-)

Physical paper notebook for sketches

I also keep a paper notebook on my desk, but don’t use it a lot. It is good to have it for ordering my thoughts when the subject at hand is more visual rather than textual. For example, my analysis of the TurboPFor integer compression scheme started out on a bunch of notebook pages.

I don’t get much out of hand writing into a notebook (e.g. for task lists), so I tend to do that in Emacs Org mode files instead (1 per project). I’m only a very light Org mode user.

Laptop: TBD

I’m writing a separate article about my current laptop and will reference the post here once published.

I will say that I mostly use laptops for traveling (to conferences or events) these days, and there is not much travel happening right now due to COVID-19.

Having a separate computer is handy for some debugging activities, e.g. single-stepping X11 applications in a debugger, which needs to be done via SSH.

Internet router and WiFi: router7 and UniFi AP HD

Mostly for fun, I decided to write router7, a highly reliabile, automatically updating internet router entirely in Go, primarily targeting the fiber7 internet service.

While the router could go underneath my desk, I currently keep it on top of my desk. Originally, I placed it in reach to lower the hurdle for debugging, but after the initial development phase, I never had to physically power cycle it.

These days, I only keep it on top of my desk because I like the physical reminder of what I accomplished :-)

For WiFi, I use a UniFi AP HD access point from Ubiquiti. My apartment is small enough that this single access point covers all corners with great WiFi. I’m configuring the access point with the mobile app so that I don’t need to run the controller app somewhere.

In general, I try to connect most devices via ethernet to remove WiFi-related issues from the picture entirely, and reduce load on the WiFi.

Switching peripherals between home and work computer

Like many, I am currently working from home due to COVID-19.

Because I only have space for one 32" monitor and peripherals on my desk, I decided to share them between my personal computer and my work computer.

To make this easy, I got an active Anker 10-port USB3 hub and two USB 3 cables for it: one connected to my personal computer, one to my work computer. Whenever I need to switch, I just re-plug the one cable.

Software setup


I have been using Linux as my primary operating system since 2005. The first Linux distribution that I installed in 2005 was Ubuntu-based. Later, I switched to Gentoo, then to Debian, which I used and contributed to until quitting the project in March 2019.

I had briefly tried Fedora before, and decided to give Arch Linux a shot now, so that’s what I’m running on my desktop computer right now. My servers remain on Flatcar Container Linux (the successor to CoreOS) or Debian, depending on their purpose.

For me, all Linux package managers are too slow, which is why I started distri: a Linux distribution to research fast package management. I’m testing distri on my laptop, and I’m using distri for a number of development tasks. I don’t want to run it on my desktop computer, though, because of its experimental nature.

Window Manager: i3

It won’t be a surprise that I am using the i3 tiling window manager, which I created in 2009 and still maintain.

My i3 configuration file is pretty close to the i3 default config, with only two major modifications: I use workspace_layout stacked and usually arrange two stacked containers next to each other on every workspace. Also, I configured a volume mode which allows for easily changing the default sink’s volume.

One way in which my usage might be a little unusual is that I always have at least 10 workspaces open.


Over time, I have moved all new development work to Go, which is by far my favorite programming language. See the article for details, but in summary, Go’s values align well with my own: the tooling is quick and high-quality, the language well thought-out and operating at roughly my preferred level of abstraction vs. clarity.

Here is a quick description of a few notable Go projects I started:

Debian Code Search is a regular expression source code search engine covering all software available in Debian.

RobustIRC is an IRC network without netsplits, based on the Raft consensus algorithm.

gokrazy is a pure-Go userland for your Raspberry Pi 3 appliances. It allows you to overwrite an SD card with a Linux kernel, Raspberry Pi firmware and Go programs of your chosing with just one command.

router7 is a pure-Go small home internet router.

debiman generates a static manpage HTML repository out of a Debian archive and powers

The distri research linux distribution project was started in 2019 to research whether a few architectural changes could enable drastically faster package management. While the package managers in common Linux distributions (e.g. apt, dnf, …) top out at data rates of only a few MB/s, distri effortlessly saturates 1 Gbit, 10 Gbit and even 40 Gbit connections, resulting in superior installation and update speeds.

Editor: Emacs

In my social circle, everyone used Vim, so that’s what I learnt. I used it for many years, but eventually gave Emacs a shot so that I could try the best notmuch frontend.

Emacs didn’t immediately click, and I haven’t used notmuch in many years, but it got me curious enough that I tried getting into the habit of using Emacs a few years ago, and now I prefer it over Vim and other editors.

Here is a non-exhaustive list of things I like about Emacs:

  1. Emacs is not a modal editor. You don’t need to switch into insert mode before you can modify the text. This might sound like a small thing, but I feel more of a direct connection to the text this way.

  2. I like Emacs’s built-in buffer management. I could never get used to using multiple tabs or otherwise arranging my Vim editor window, but with Emacs, juggling multiple things at the same time feels very natural.
    I make heavy use of Emacs’s compile mode (similar to Vim’s quick fix window): I will compile not only programs, but also config files (e.g. M-x compile i3 reload) or grep commands, allowing me to go through matches via M-g M-n.

  3. The Magit package is by far my most favorite Git user interface. Staging individual lines or words comes very naturally, and many operations are much quicker to accomplish compared to using Git in a terminal.

  4. The eglot package is a good LSP client, making available tons of powerful cross-referencing and refactoring features.

  5. The possible customization is impressive, including the development experience: Emacs’s built-in help system is really good, and allows jumping to the definition of variables or functions out of the box. Emacs is the only place in my day-to-day where I get a little glimpse into what it must have been like to use a Lisp machine

Of course, not everything is great about Emacs. Here are a few annoyances:

  1. The Emacs default configuration is very old, and a number of settings need to be changed to make it more modern. I have been tweaking my Emacs config since 2012 and still feel like I’m barely scratching the surface. Many beginners find their way into Emacs by using a pre-configured version of it such as Doom Emacs or Spacemacs.

  2. Even after going through great lengths to keep startup fast, Emacs definitely starts much more slowly than e.g. Vim. This makes it not a great fit for trivial editing tasks, such as commenting out a line of configuration on a server via SSH.

For consistency, I eventually switched my shell and readline config from vi key bindings to the default Emacs key bindings. This turned out to be a great move: the Emacs key bindings are generally better tested and more closely resemble the behavior of the editor. With vi key bindings, sooner or later I always ran into frustrating feature gaps (e.g. zsh didn’t support the delete-until-next-x-character Vim command) or similar.

Hardware setup: desktop computer

I should probably publish a separate blog post with PC hardware recommendation, so let me focus on the most important points here only:

I’m using an Intel i9-9900K CPU. I briefly switched to an AMD Ryzen 3900X based on tech news sites declaring it faster. I eventually found out that the Intel i9-9900K actually benchmarks better in browser performance and incremental Go compilation, so I switched back.

To be able to drive the Dell 8K4K monitor, I’m using a nVidia GeForce RTX 2070. I don’t care for its 3D performance, but more video RAM and memory bandwidth make a noticeable difference in how many Chrome tabs I can work with.

To avoid running out of memory, I usually max out memory based on mainboard support and what is priced reasonably. Currently, I’m using 64 GB of Corsair RAM.

For storage, I currently use a Phison Force MP600 PCIe 4 NVMe disk, back from when I tried the Ryzen 3900X. When I’m not trying out PCIe 4, I usually go with the latest Samsung Consumer SSD PRO, e.g. the Samsung SSD 970 PRO. Having a lot of bandwidth and IOPS available is great in general, but especially valuable when e.g. re-generating all manpages or compiling a new distri version from scratch.

I’m a fan of Fractal Design’s Define case series (e.g. the Define R6) and have been using them for many years in many different builds. They are great to work with: no sharp edges, convenient screws and mechanisms, and they result in a quiet computer.

For fans, my choice is Noctua. Specifically, their NH-U14S makes for a great CPU fan, and their NF-A12x25 are great case fans. They cool well and are super quiet!

Network storage

For redundancy, I am backing up my computers to 2 separate network storage devices.

My devices are built from PC Hardware and run Flatcar Linux (previously CoreOS) for automated updates. I put in one hard disk per device for maximum redundancy: any hardware component can fail and I can just use the other device.

The software setup is intentionally kept very simple: I use rsync (with hardlinks) over SSH for backups, and serve files using Samba. That way, backups are just files, immediately available, and accessible from another computer if everything else fails.


I hope this was interesting! If you have any detail questions, feel free to reach out via email or twitter.

If you’re looking for more product recommendations (tech or otherwise), one of my favorite places is the wirecutter.

at 2020-05-23 13:22


sECuREs website

a new distri linux (fast package management) release

I just released a new version of distri.

The focus of this release lies on:

  • a better developer experience, allowing users to debug any installed package without extra setup steps

  • performance improvements in all areas (starting programs, building distri packages, generating distri images)

  • better tooling for keeping track of upstream versions

See the release notes for more details.

The distri research linux distribution project was started in 2019 to research whether a few architectural changes could enable drastically faster package management.

While the package managers in common Linux distributions (e.g. apt, dnf, …) top out at data rates of only a few MB/s, distri effortlessly saturates 1 Gbit, 10 Gbit and even 40 Gbit connections, resulting in fast installation and update speeds.

at 2020-05-16 07:13


Quantifying the error of the core-valence separation approximation

After only a few months of publishing our adcc paper, which introduces the novel algebraic-diagrammatic construction (ADC) code adcc, the package has already found mention in a number of related articles. One example is a manuscript on updates in the Psi4 quantum chemistry package, which features adcc as one of the highlighted community modules. As the paper discusses, the close integration of adcc into the Psi4 ecosystem now allows to start ADC calculations in adcc directly form Psi4's python frontend and its input files. This effectively extends Psi4 by all ADC capabilities adcc offers. Another example is a paper on computing complex polarisabilities for excited states, which especially emphasises the importance adcc has played for simplifying the implementation of the method.

On my end, I recently conducted a study with Thomas Fransson on the error of the core-valence separation (CVS) approximation. This approximation is very important for the simulation of X-ray absorption spectra using accurate wave-function methods like coupled-cluster or ADC. In the literature the error of the CVS approximation is widely accepted to be negligible compared to the error with respect to experiment. This statement is, however, based on previous investigations of the CVS error, which were limited by the methodologies to only small, non-representative basis sets.

In our work we present an iterative post-processing scheme in the ADC context, which is able to undo the CVS approximation and remove the CVS error. Our procedure is still basic (essentially just Rayleigh-Quotient iteration), but it allowed us to study the CVS error for a much larger range of systems and basis sets. This includes augmented and/or core-polarised triple-zeta basis sets as well as other bases prominent in the community to carry out simulations of core-excitations and X-ray spectra (read 6-311++G** and variants). Based on a representative compounds from elements of the second and third period we managed to confirm that the CVS error is not only small compared to experiment but additionally the spread across elements and compounds is even smaller, such that the impact on energy differences is small, too. This is an important finding, since most aspects of chemistry (spectroscopy, reaction barrier heights, thermochemistry) are dominated by energy differences and while relative errors in energies might be small, relative errors in energy differences can be much larger if the error spread across compounds is not uniform.

In particular our work identified the main contributions to the CVS error to originate from two classes of couplings, which are neglected by the CVS approximation and which moreover contribute with opposite sign. We demonstrate that basis sets providing a balanced description of core and valence regions of the electron density are also capable of describing these neglected couplings in a balanced fashion, thus providing not only a good description of the core-excitation process, but also a small CVS error in terms of absolute value and spread. Based on these findings we were able to conclude that especially tight polarising functions are key for describing core-excitations. Along our study we suggest appropriate modifications for the popular 6-311++G** basis to reduce its CVS error. The full abstract of our paper reads

For the calculation of core-excited states probed through X-ray absorption spectroscopy, the core-valence separation (CVS) scheme has become a vital tool. This approach allows to target such states with high specificity, albeit introducing an error. We report the implementation of a post-processing step for CVS excitations obtained within the algebraic-diagrammatic construction scheme for the polarisation propagator (ADC), which removes this error. Based on this we provide a detailed analysis of the CVS scheme, identifying its accuracy to be dominated by an error balance between two neglected couplings, one between core and valence single excitations and one between single and double core excitations. The selection of the basis set is shown to be vital for a proper description of both couplings, with tight polarising functions being necessary for a good balance of errors. The CVS error is confirmed to be stable across multiple systems, with an element-specific spread of only about ±0.02 eV. A systematic lowering of the CVS error by 0.02-0.03 eV is noted when considering excitations to extremely diffuse states, emulating ionisation.

by Michael F. Herbst at 2020-05-12 22:30 under electronic structure theory, theoretical chemistry, adcc, algebraic-diagrammatic construction, core-valence separation


sECuREs website

Hermetic packages (in distri)

In distri, packages (e.g. emacs) are hermetic. By hermetic, I mean that the dependencies a package uses (e.g. libusb) don’t change, even when newer versions are installed.

For example, if package libusb-amd64-1.0.22-7 is available at build time, the package will always use that same version, even after the newer libusb-amd64-1.0.23-8 will be installed into the package store.

Another way of saying the same thing is: packages in distri are always co-installable.

This makes the package store more robust: additions to it will not break the system. On a technical level, the package store is implemented as a directory containing distri SquashFS images and metadata files, into which packages are installed in an atomic way.

Out of scope: plugins are not hermetic by design

One exception where hermeticity is not desired are plugin mechanisms: optionally loading out-of-tree code at runtime obviously is not hermetic.

As an example, consider glibc’s Name Service Switch (NSS) mechanism. Page 29.4.1 Adding another Service to NSS describes how glibc searches $prefix/lib for shared libraries at runtime.

Debian ships about a dozen NSS libraries for a variety of purposes, and enterprise setups might add their own into the mix.

systemd (as of v245) accounts for 4 NSS libraries, e.g. nss-systemd for user/group name resolution for users allocated through systemd’s DynamicUser= option.

Having packages be as hermetic as possible remains a worthwhile goal despite any exceptions: I will gladly use a 99% hermetic system over a 0% hermetic system any day.

Side note: Xorg’s driver model (which can be characterized as a plugin mechanism) does not fall under this category because of its tight API/ABI coupling! For this case, where drivers are only guaranteed to work with precisely the Xorg version for which they were compiled, distri uses per-package exchange directories.

Implementation of hermetic packages in distri

On a technical level, the requirement is: all paths used by the program must always result in the same contents. This is implemented in distri via the read-only package store mounted at /ro, e.g. files underneath /ro/emacs-amd64-26.3-15 never change.

To change all paths used by a program, in practice, three strategies cover most paths:

ELF interpreter and dynamic libraries

Programs on Linux use the ELF file format, which contains two kinds of references:

First, the ELF interpreter (PT_INTERP segment), which is used to start the program. For dynamically linked programs on 64-bit systems, this is typically

Many distributions use system-global paths such as /lib64/, but distri compiles programs with -Wl,--dynamic-linker=/ro/glibc-amd64-2.31-4/out/lib/ so that the full path ends up in the binary.

The ELF interpreter is shown by file(1), but you can also use readelf -a $BINARY | grep 'program interpreter' to display it.

And secondly, the rpath, a run-time search path for dynamic libraries. Instead of storing full references to all dynamic libraries, we set the rpath so that will find the correct dynamic libraries.

Originally, we used to just set a long rpath, containing one entry for each dynamic library dependency. However, we have since switched to using a single lib subdirectory per package as its rpath, and placing symlinks with full path references into that lib directory, e.g. using -Wl,-rpath=/ro/grep-amd64-3.4-4/lib. This is better for performance, as uses a per-directory cache.

Note that program load times are significantly influenced by how quickly you can locate the dynamic libraries. distri uses a FUSE file system to load programs from, so getting proper -ENOENT caching into place drastically sped up program load times.

Instead of compiling software with the -Wl,--dynamic-linker and -Wl,-rpath flags, one can also modify these fields after the fact using patchelf(1). For closed-source programs, this is the only possibility.

The rpath can be inspected by using e.g. readelf -a $BINARY | grep RPATH.

Environment variable setup wrapper programs

Many programs are influenced by environment variables: to start another program, said program is often found by checking each directory in the PATH environment variable.

Such search paths are prevalent in scripting languages, too, to find modules. Python has PYTHONPATH, Perl has PERL5LIB, and so on.

To set up these search path environment variables at run time, distri employs an indirection. Instead of e.g. teensy-loader-cli, you run a small wrapper program that calls precisely one execve system call with the desired environment variables.

Initially, I used shell scripts as wrapper programs because they are easily inspectable. This turned out to be too slow, so I switched to compiled programs. I’m linking them statically for fast startup, and I’m linking them against musl libc for significantly smaller file sizes than glibc (per-executable overhead adds up quickly in a distribution!).

Note that the wrapper programs prepend to the PATH environment variable, they don’t replace it in its entirely. This is important so that users have a way to extend the PATH (and other variables) if they so choose. This doesn’t hurt hermeticity because it is only relevant for programs that were not present at build time, i.e. plugin mechanisms which, by design, cannot be hermetic.

Shebang interpreter patching

The Shebang of scripts contains a path, too, and hence needs to be changed.

We don’t do this in distri yet (the number of packaged scripts is small), but we should.

Performance requirements

The performance improvements in the previous sections are not just good to have, but practically required when many processes are involved: without them, you’ll encounter second-long delays in magit which spawns many git processes under the covers, or in dracut, which spawns one cp(1) process per file.

Downside: rebuild of packages required to pick up changes

Linux distributions such as Debian consider it an advantage to roll out security fixes to the entire system by updating a single shared library package (e.g. openssl).

The flip side of that coin is that changes to a single critical package can break the entire system.

With hermetic packages, all reverse dependencies must be rebuilt when a library’s changes should be picked up by the whole system. E.g., when openssl changes, curl must be rebuilt to pick up the new version of openssl.

This approach trades off using more bandwidth and more disk space (temporarily) against reducing the blast radius of any individual package update.

Downside: long env variables are cumbersome to deal with

This can be partially mitigated by removing empty directories at build time, which will result in shorter variables.

In general, there is no getting around this. One little trick is to use tr : '\n', e.g.:

distri0# echo $PATH

distri0# echo $PATH | tr : '\n'

Edge cases

The implementation outlined above works well in hundreds of packages, and only a small handful exhibited problems of any kind. Here are some issues I encountered:

Issue: accidental ABI breakage in plugin mechanisms

NSS libraries built against glibc 2.28 and newer cannot be loaded by glibc 2.27. In all likelihood, such changes do not happen too often, but it does illustrate that glibc’s published interface spec is not sufficient for forwards and backwards compatibility.

In distri, we could likely use a per-package exchange directory for glibc’s NSS mechanism to prevent the above problem from happening in the future.

Issue: wrapper bypass when a program re-executes itself

Some programs try to arrange for themselves to be re-executed outside of their current process tree. For example, consider building a program with the meson build system:

  1. When meson first configures the build, it generates ninja files (think Makefiles) which contain command lines that run the meson --internal helper.

  2. Once meson returns, ninja is called as a separate process, so it will not have the environment which the meson wrapper sets up. ninja then runs the previously persisted meson command line. Since the command line uses the full path to meson (not to its wrapper), it bypasses the wrapper.

Luckily, not many programs try to arrange for other process trees to run them. Here is a table summarizing how affected programs might try to arrange for re-execution, whether the technique results in a wrapper bypass, and what we do about it in distri:

technique to execute itself uses wrapper mitigation
run-time: find own basename in PATH yes wrapper program
compile-time: embed expected path no; bypass! configure or patch
run-time: argv[0] or /proc/self/exe no; bypass! patch

One might think that setting argv[0] to the wrapper location seems like a way to side-step this problem. We tried doing this in distri, but had to revert and go the other way.

Misc smaller issues

Appendix: Could other distributions adopt hermetic packages?

At a very high level, adopting hermetic packages will require two steps:

  1. Using fully qualified paths whose contents don’t change (e.g. /ro/emacs-amd64-26.3-15) generally requires rebuilding programs, e.g. with --prefix set.

  2. Once you use fully qualified paths you need to make the packages able to exchange data. distri solves this with exchange directories, implemented in the /ro file system which is backed by a FUSE daemon.

The first step is pretty simple, whereas the second step is where I expect controversy around any suggested mechanism.

Appendix: demo (in distri)

This appendix contains commands and their outputs, run on upcoming distri version supersilverhaze, but verified to work on older versions, too.

Large outputs have been collapsed and can be expanded by clicking on the output.

The /bin directory contains symlinks for the union of all package’s bin subdirectories:

distri0# readlink -f /bin/teensy_loader_cli

The wrapper program in the bin subdirectory is small:

distri0# ls -lh $(readlink -f /bin/teensy_loader_cli)
-rwxr-xr-x 1 root root 46K Apr 21 21:56 /ro/teensy-loader-cli-amd64-2.1+g20180927-7/bin/teensy_loader_cli

Wrapper programs execute quickly:

distri0# strace -fvy /bin/teensy_loader_cli |& head | cat -n
     1  execve("/bin/teensy_loader_cli", ["/bin/teensy_loader_cli"], ["USER=root", "LOGNAME=root", "HOME=/root", "PATH=/ro/bash-amd64-5.0-4/bin:/r"..., "SHELL=/bin/zsh", "TERM=screen.xterm-256color", "XDG_SESSION_ID=c1", "XDG_RUNTIME_DIR=/run/user/0", "DBUS_SESSION_BUS_ADDRESS=unix:pa"..., "XDG_SESSION_TYPE=tty", "XDG_SESSION_CLASS=user", "SSH_CLIENT= 42556 22", "SSH_CONNECTION= 42556 10"..., "SSHTTY=/dev/pts/0", "SHLVL=1", "PWD=/root", "OLDPWD=/root", "=/usr/bin/strace", "LD_LIBRARY_PATH=/ro/bash-amd64-5"..., "PERL5LIB=/ro/bash-amd64-5.0-4/ou"..., "PYTHONPATH=/ro/bash-amd64-5.b0-4/"...]) = 0
     2  arch_prctl(ARCH_SET_FS, 0x40c878)       = 0
     3  set_tid_address(0x40ca9c)               = 715
     4  brk(NULL)                               = 0x15b9000
     5  brk(0x15ba000)                          = 0x15ba000
     6  brk(0x15bb000)                          = 0x15bb000
     7  brk(0x15bd000)                          = 0x15bd000
     8  brk(0x15bf000)                          = 0x15bf000
     9  brk(0x15c1000)                          = 0x15c1000
    10  execve("/ro/teensy-loader-cli-amd64-2.1+g20180927-7/out/bin/teensy_loader_cli", ["/ro/teensy-loader-cli-amd64-2.1+"...], ["USER=root", "LOGNAME=root", "HOME=/root", "PATH=/ro/bash-amd64-5.0-4/bin:/r"..., "SHELL=/bin/zsh", "TERM=screen.xterm-256color", "XDG_SESSION_ID=c1", "XDG_RUNTIME_DIR=/run/user/0", "DBUS_SESSION_BUS_ADDRESS=unix:pa"..., "XDG_SESSION_TYPE=tty", "XDG_SESSION_CLASS=user", "SSH_CLIENT= 42556 22", "SSH_CONNECTION= 42556 10"..., "SSHTTY=/dev/pts/0", "SHLVL=1", "PWD=/root", "OLDPWD=/root", "=/usr/bin/strace", "LD_LIBRARY_PATH=/ro/bash-amd64-5"..., "PERL5LIB=/ro/bash-amd64-5.0-4/ou"..., "PYTHONPATH=/ro/bash-amd64-5.0-4/"...]) = 0

Confirm which ELF interpreter is set for a binary using readelf(1):

distri0# readelf -a /ro/teensy-loader-cli-amd64-2.1+g20180927-7/out/bin/teensy_loader_cli | grep 'program interpreter'
[Requesting program interpreter: /ro/glibc-amd64-2.31-4/out/lib/]

Confirm the rpath is set to the package’s lib subdirectory using readelf(1):

distri0# readelf -a /ro/teensy-loader-cli-amd64-2.1+g20180927-7/out/bin/teensy_loader_cli | grep RPATH
 0x000000000000000f (RPATH)              Library rpath: [/ro/teensy-loader-cli-amd64-2.1+g20180927-7/lib]

…and verify the lib subdirectory has the expected symlinks and target versions:

distri0# find /ro/teensy-loader-cli-amd64-*/lib -type f -printf '%P -> %l\n' -> /ro/glibc-amd64-2.31-4/out/lib/ -> /ro/glibc-amd64-2.31-4/out/lib/ -> /ro/glibc-amd64-2.31-4/out/lib/ -> /ro/libudev-amd64-245-11/out/lib/ -> /ro/libusb-compat-amd64-0.1.5-7/out/lib/ -> /ro/libusb-amd64-1.0.23-8/out/lib/

To verify the correct libraries are actually loaded, you can set the LD_DEBUG environment variable for

distri0# LD_DEBUG=libs teensy_loader_cli
       678:     find [0]; searching
       678:      search path=/ro/teensy-loader-cli-amd64-2.1+g20180927-7/lib            (RPATH from file /ro/teensy-loader-cli-amd64-2.1+g20180927-7/out/bin/teensy_loader_cli)
       678:       trying file=/ro/teensy-loader-cli-amd64-2.1+g20180927-7/lib/

NSS libraries that distri ships:

find /lib/ -name "libnss_*.so.2" -type f -printf '%P -> %l\n' -> ../systemd-amd64-245-11/out/lib/ -> ../systemd-amd64-245-11/out/lib/ -> ../systemd-amd64-245-11/out/lib/ -> ../systemd-amd64-245-11/out/lib/ -> ../glibc-amd64-2.31-4/out/lib/ -> ../glibc-amd64-2.31-4/out/lib/ -> ../glibc-amd64-2.31-4/out/lib/ -> ../glibc-amd64-2.31-4/out/lib/ -> ../glibc-amd64-2.31-4/out/lib/

at 2020-05-09 16:48


A posteriori error estimation for the non-self-consistent Kohn-Sham equations

After about a year of work on the density-functional toolkit (DFTK) we finally started using the code for some new science. Given the mathematics background of the CERMICS the first two DFTK-related articles were not so much about large-scale applications, but rather deal some fundamental questions of Kohn-Sham density-functional theory (DFT). The first submission provides a detailed analysis of self-consistent iterations and direct-minimisation approaches for solving equations such as DFT. My main focus in the past weeks, however, was rather the second project, an invited submission for the Faraday discussions New horizons in density functional theory, which are to take place in September this year.

In this article we deal with numerical error in DFT calculations. More precisely we want to address the question: What is the remaining error in the result obtained by a particular DFT simulation, which has already been performed?

This is naturally a rather broad statement, which cannot realistically be addressed in the scope of a single article. As we detail we only address the question of bounding the error of a particular quantity of interest, namely band energies near the Fermi level. Other quantities, such as the forces or the response to an external perturbation, might benefit from our ideas, but will need extensions on top. Also one needs to keep in mind that there are plenty of sources for error in a DFT calculation, including:

  1. The model error due to replacing the (almost) exact model of the many-body Schrödinger equation by a reduced, but more feasible model like DFT.
  2. The discretisation error due to employing only finitely many basis functions instead of solving analytically in an infinite-dimensional Hilbert space.
  3. The algorithmic error resulting from using non-zero convergence tolerances in the eigensolvers as well as the SCF procedure.
  4. The arithmetic error obtained by doing computation only in finite-precision floating-point arithmetic.

Of course in practice people often have a good ballpark idea of the error of DFT as a method or the errors obtained from a particular basis cutoff. Rightfully one might ask, why one should go through the effort of deriving provable bounds to the error in a DFT result? While there are surely many takes on this question, I only want to highlight two aspects in this summary:

  • Educated guesses for convergence parameters taken from experience can fail. Typically they fail exactly when interesting things happen in a system and thus the usual heuristic breaks down. In other words converging a simulation to investigate what's going on becomes difficult when it's most needed. Detailed error analysis splitting up the error during an SCF iteration into contributions like the errors 1 to 4 (or even finer) can help to hint at the parameters worth tweaking or can provide insight into which error term behaves unusual in an SCF.
  • Thinking such aspects one step further, a good bound to the individual terms even allows to equilibrate sources of error during a running calculation. The outlook of this idea would be a fully black-box scheme for DFT calculations where typical convergence parameters are automatically while the calculation progresses in order to yield the cheapest path to a desired target accuracy.

With respect to the errors 1 to 4 mentioned above one would of course like to be able to provide an upper bound to each of them. Unfortunately especially obtaining an estimate for the model error is a rather difficult task. In our work we have therefore concentrated on the errors 2 to 4 and moreover we only focused on Kohn-Sham models without self-consistency, i.e. where none of the terms in the Hamiltonian depend on the density / orbitals. It goes without saying that especially this last restriction needs to be lifted to make our results useful in practice. This angle we have left for future work.

Already at the stage of the current reduced model, however, there are a few aspects to consider when finding an upper bound:

  • We wanted our bound to be fully-guaranteed, which means that we wanted to design a bound where we are able to prove that the exact answer must lie inside the bounds we give. This means when we provide error bars for band energies it is mathematically guaranteed to find the exact answer of the full-dimensional (complete-basis set limit) calculation at infinite accuracy and at zero convergence tolerances inside our bound.
  • To be useful our bound should be (cheaply) computable, because otherwise plainly checking the calculation at vastly increased precision might end up being the better option. Notice that our bound does require to use a finer discretisation for some terms, but this is only a one-shot a posteriori step and not an iterative one.
  • Ideally the bound should be sharp meaning that the upper bound to the error we report should not be too far off the true error. Even better would be an optimal bound, where we are as close to the true error as possible (given proposed structure in the error estimate). Such considerations are very important to not end up with completely correct but also useless statements like: "The error in the band energy is smaller than 10 million Hartree".

Finding a balance between these three aspects is not always easy and in our work we often take the pragmatic route to obtain a simpler, albeit less sharp error. Still, our bound is fully computable and allowed us, for the first time, to report band structure diagrams of silicon annotated with fully-guaranteed error bars of combined discretisation, algorithm and arithmetic errors. Details of our methodologies are given in the paper. Its full abstract reads

We address the problem of bounding rigorously the errors in the numerical solution of the Kohn-Sham equations due to (i) the finiteness of the basis set, (ii) the convergence thresholds in iterative procedures, (iii) the propagation of rounding errors in floating-point arithmetic. In this contribution, we compute fully-guaranteed bounds on the solution of the non-self-consistent equations in the pseudopotential approximation in a plane-wave basis set. We demonstrate our methodology by providing band structure diagrams of silicon annotated with error bars indicating the combined error.

by Michael F. Herbst at 2020-04-28 14:30 under electronic structure theory, theoretical chemistry, DFTK, Julia, dft, numerical analysis, Kohn-Sham, error estimates



Using Boundary Scan for PCB debugging

I did a seminar talk on JTAG and how to use it to check a PCB for errors. For this i designed a little board in order to simulate manufacturing errors. In this post I want to give you a short introduction to JTAG and how to use it.

What is Boundary-scan

Boundary-scan was developed to simplify testing of integrated circuits. To do this the Joint Test Action Group introduced the Boundary Scan architecture as a standard and today it has replaced the old testing methods because of its cost efficiency and speed up of test development and execution.

So how does this work?

I will be just covering the basics here. If you want a more detailed introduction, you can read the articles referenced at the end of this post.

Boundary-scan is a technology which places cells at the circuits boundary that can sample the circuit inputs and also drive its outputs. This can be done while the circuit is operating and it is controlled via the JTAG interface. With these cells in place we wan test the internal logic of the circuit as well as the interconnects between the devices on a board.

In the picture above you can see an overview of the boundary-scan architecture. This picture only shows one JTAG device, but on more complex PCB there are many such devices that are connected in a JTAG chain. This means that the data out of one chip is connected to the input of the next.

In order for us use this architecture, we need to connect to the four JTAG pins:

  • TDI Test Data In
  • TDO Test Data Out
  • TCK Test Clock
  • TMS Test Mode Select

Once connected we can control all of the devices in the JTAG chain. In general we can perform two different types of actions. We can either write/read data or we can write instructions. Testing a circuit involves both of theses actions. By writing instructions we can set the connected circuits into different modes. And by writing data we can set the pins to the desired levels as well as read the results.

There are three different instructions we are interested in when testing interconnects:


With the SAMPLE/PRELOAD instruction the boundary-scan cells will sample the inputs of the circuit, and when shifting in data we can read values received at the pins. We can also use this command to load data into the boundary-scan cells. The EXTEST instruction will set the output of the pins to the values provided in the boundary-scan cells and the BYPASS instruction lets us skip devices in the chain that are not of interest to the test currently performed.

With these instructions we can set pins of a device to a logic level and test at the receiving circuit if the correct logic level was received.

The Hardware

We need to connect to the JTAG pins of a devices. If they are exposed there probably is a connector on the board. If not it may be possible to solder wires directly to the pins. In any case we will need a JTAG adapter in order to connect them to a normal computer via USB. I am using a JLink adapter which features a 20 pin JTAG connector.

The PCB I am using for testing is a small circuit I designed myself, it also has a 20 pin connector which exposes the JTAG pins. Here is the layout:

It features two MAX V Altera CPLDs that implement the boundary-scan architecture and are connected in a JTAG chain. To test some connections between them I connected eight of their pins at the top and added a dip switch to simulate shorts between the wires as well as pull ups and pull downs.


Okay so we got a PCB and connected it to a computer with a JTAG adapter now what? How do get the tests running?

Well this is where it gets hard, because there is no nice open source software that does it all for us. We need to write the test ourselves and for that we need to know the details of the interconnects on our PCB and the details of how the boundary-scan architecture is implemented in the devices in our JTAG chain.

BSDL Files

The Boundary-scan standard does not tell manufacturers what bit codes to use to encode the instructions, but it does require them to publish the so called BSDL (Boundary Scan Description Language) files free of charge for their devices. These files use a dialect derived from VHDL a hardware description language and describe all information needed to use a devices boundary-scan architecture. For example:

  • Instruction register description
  • Boundary-scan cell description
  • Pin mappings
  • and more

Basically all information we might want to know about a specific device is in that file.

SVF Files

Most JTAG adapter tool chains support a file format called SVF (Serial Vector Format). These are plain text files that describe what data or instructions to write to the JTAG connection. It has no knowledge about the JTAG chain of devices or any of there properties. We can just specify what data/instructions to shift in and what results we expect to be shifted out.

Designing a simple test

Okay so putting it all together. Lets say we want to test two neighboring interconnects for a bridging fault.

On my example PCB two neighboring interconnects are connected as follows:

  1. CHIP 1 IO56 - CHIP 2 IO49
  2. CHIP 1 IO55 - CHIP 2 IO50

So if we set IO56 of the first chip to a logic 1 and IO55 to logic 0, we would expect to receive a logic 1 on IO49 and a logic 0 at IO50 on the second chip. If we receive a logic 1 at IO50 that means that there is a bridging fault between the interconnects.

To write a test for this we need to write an SVF file that we can run with the JTAG adapter tool chain. It needs to complete the following steps:

  1. Set first chip into SAMPLE/PRELOAD mode. (Shift in Instructions)
  2. Load Test pattern into first chip (Shift in Data)
  3. Set first chip to EXTEST and second chip to SAMPLE/PRELOAD mode (Shift in Instructions)
  4. Shift in dummy data to receive the data sampled from chip 2 and compare against the expected result (Shift in Data)

The following SVF files does exactly this:

FREQUENCY 10000000 HZ;
SIR 20 TDI (01405);
SDR 480 TDI (000000000000000000000000000000000000000000800000000000000
SIR 20 TDI (03c05);
SDR 480 TDI (0) TDO (000000000000000000000000000000000000000000000000
	0000000) MASK (00000000000000000000000000000000000000000000000000

Up until the first line starting with SIR all we are doing is making sure the boundary-scan circuit is in a known state and setting the speed at which we want to operate.

SIR means we want to write instruction data. We need to specify the length and since we have to chips with both 10 bit instruction registers we are writing 20 bits of data. The data we want to write is specified behind the TDI statement as a hex string surrounded by parenthesis.

SDR works the same as SIR but instead of instruction data we are just writing data. In this case we are writing 480 bits, since both chips have a boundary-scan register length of 240 bits. If we want to compare the shifted out data against the expected data we have to write the expected result as a hex string behind the TDO statement and we can even mask the result so that we only look at the bits we are interested in.

How do we know what data to write and what data to expect? Well for that we have to look at the BSDL files of the devices in our JTAG chain and figure out which pin is mapped to which bit in the data. Of course writing a SVF by hand is very tedious, so instead I created some python scripts to help me with the task. Feel free to use them for your own projects.


Using Boundary-scan for PCB testing is very nice when trying to automatically test PCBs. Sadly there is little to no open source software which makes it easy to design tests for your own layouts. Which means that you still have to do a lot of information gathering if you want to use this technology. But once the tests are implemented testing a PCB becomes a very easy and fast.

I hope this blog post gave you an idea of what you need to do, to get up and running with boundary-scan testing. If you have any feedback feel free to contact me.

Further Reading Material

by Felix Richter at 2020-03-29 00:00


Insanity Industries

Simple networking

It is time to revisit of the simple wifi setup as much has changed since. This time, however, we will not only cover wifi, but also wired connections as well as DNS.

Wired networking

This wired setup is based on systemd-networkd, which typically comes with systemd. If you use a systemd-based Linux, you should be ready to go right away. It further assumes that acquiring an IP address via DHCP once a cable is plugged in the typical usecase.1

Create the file /etc/systemd/network/cable.network2:

Name=<name of the wired network device> <second one if applicable> [<more ...>]



Then systemctl enable --now systemd-networkd and plug in a cable, wired networking with DHCP is up and running.

Wireless networking

The wireless setup is based on iwd, the currently vastly superior tool for wireless networking on Linux compared to existing alternatives such as wpa_supplicant (the effectively only other contender in this game) and software using it such as NetworkManager and netctl. It requires iwd as well as Linux >= 4.20 for full operation.

Create the file /etc/iwd/main.conf:

# uncomment for setting the wifi interface name yourself
# see

# enable builtin DHCP-client within iwd for wifi

# randomizes mac-address every time iwd starts or the hardware is initially detected

Then systemctl enable --now iwd, wireless networking with DHCP is up and running, blazingly fast and stable.

You might want to take a look at the previous post to deal with race conditions that might be introduced due to iwd being significantly faster than other wifi-solutions on Linux.


iwd stores its known networks in /var/lib/iwd. To add, modify or delete them, several options are available:


You can now connect to simple PSK wifi networks in the iwctl shell:

[iwctl] station <devicename> get-networks
[iwctl] station <devicename> connect <network-name>

iwctl will ask you for the password, iwd will memorize it for later connections and autoconnect the next time the network appears. Currently, iwctl only supports creating simple password-only network connections, for more complex network setups, instead of iwctl asking you all the nifty details of an enterprise connection, use the file-based config instead. For everything else, just type help within iwctl.

file-based config

If you have more complex wifi-setups, you can simply drop a network configuration file in /var/lib/iwd. The files must be named as networkname.protocol. You can find the protocol listed in the output of get-networks in the iwctl-shell. To fill the file, take a look to the network configuration settings in the iwd documentation or the manpage.

For example, to use the University Heidelberg’s eduroam network, create the file /var/lib/iwd/eduroam.8021x containing

EAP-TTLS-Phase2-Password=<your University account password>

For other institutions, the details in the method might vary, of course. See man for details. It also includes several examples for almost all possible configurations.

Network Manager

You can also use Network Manager for a more graphical experience, you just have to enable the iwd-backend for NetworkManager to use it. In addition to that, double check if you have the right NetworkManager version for your iwd version, just as a precaution.


For modern domain name resolution, you can use systemd-resolved, which provides statistics, automated caching of DNS requests, DNSSEC validation and much more. To use it, ensure systemd-resolved is installed3 and systemctl enable --now systemd-resolved. Ensure that /etc/resolv.conf is symlinked to /run/systemd/resolve/stub-resolv.conf, if not

ln -sf /run/systemd/resolve/stub-resolv.conf /etc/resolv.conf

takes care of it. Afterwards, you can change the default fallback DNS servers and other things in /etc/systemd/resolved.conf, if desired and otherwise enjoy resolvectl and resolvectl statistics.

Miscellaneous optimizations

Binding iwd to the wifi-device

To disable iwd when the wifi is not present (and iwd therefore not needed) create the file /etc/udev/rules.d/wifi.rules containing

# bind iwd to wifi
SUBSYSTEM=="rfkill", ENV{RFKILL_NAME}=="phy0", ENV{RFKILL_TYPE}=="wlan", ACTION=="change", ENV{RFKILL_STATE}=="1", RUN+="/usr/bin/systemctl --no-block start iwd.service"
SUBSYSTEM=="rfkill", ENV{RFKILL_NAME}=="phy0", ENV{RFKILL_TYPE}=="wlan", ACTION=="change", ENV{RFKILL_STATE}=="0", RUN+="/usr/bin/systemctl --no-block stop iwd.service"

If AddressRamdomization=once is set in the configuration, this udev rule has the nice side-effect that, as iwd starts nanew when the wifi is un-rfkilled, the MAC address of the interface is randomized again.

Persistent device naming

If you want to have persistent device names, for example for devices showing up in a status bar or something similar, this ist easiest achieved by creating a link-file4 /etc/systemd/network. To persistently name the wireless device wifi, create /etc/systemd/network/ containing

MACAddress=ab:cd:ef:12:34:56  # wifi's original MAC address

Name=wifi  # can be used for matching in the according *.network-file

If you do this for any device operated by iwd, ensure you have UseDefaultInterface=true set in section [General] in /etc/iwd/main.conf.

Setting specific MAC addresses for specific wifi networks and randomizing on every connect

In case you need to set a specific address for a specific wireless network, iwd>=1.6 allows using AddressOverride= inside a network configuration file. For this to take effect, however, AddressRandomization=once must be dropped from /etc/iwd/main.conf. This makes iwd generate persistent MAC addresses per network (generated from its SSID and real hardware address) by default and allows AddressOverride to take effect. Additionally, a network file can contain AlwaysRandomizeAddress=true, which randomizes the MAC address on each connect for this network (also only takes effect when AddressRandomization is not set or set do its default value in main.conf. However, due to kernel limitations, each change of a MAC address requires powercyling the card. This leads to (for iwd standards) singificantly prolonged connection times (by ≈300-400ms). Given that, as long as you do not require AddressOverride, AddressRandomization=once gives you fast connection times while still randomizing your card’s MAC address regularly enough.

Thanks to rixx for proofreading and helpful suggestions.

  1. Although this if of course an assumption, my personal statistics says that this setup has worked with 100% of all network cables I ever plugged into my laptop so far. ↩︎

  2. see man (preferrably, as it fits your version) or for the latest docs. ↩︎

  3. The simplest check is systemctl status systemd-resolved. ↩︎

  4. see man or ↩︎

by Jonas Große Sundrup at 2020-03-22 00:00


Insanity Industries

Mastodon and Twitter Feeds

This blog has had an RSS-feed from the very start. But from today on, this blog also officially has feeds on Mastodon and Twitter you can subscribe to if you do not like RSS or prefer these over RSS.

Let’s see where this goes, I’m curious if that’s something people will find useful. Retoots or -tweets encouraged!

by Jonas Große Sundrup at 2020-03-15 00:00




ACHTUNG: Aufgrund der aktuellen Lage und Vorgaben der Stadt Mannheim (siehe auch) bleibt das RaumZeitLabor bis auf weiteres geschlossen. Alle öffentlichen Veranstaltungen sind abgesagt.

Passt auf euch auf.

by tabascoeye at 2020-03-14 00:00