Dissertation: Lattice Boltzmann methods for microswimmers in complex environments

My dissertation has been published by the university:

Lattice Boltzmann methods for microswimmers in complex environments
Michael Kuron
PhD thesis, Universität Stuttgart
DOI: 10.18419/opus-11926

Printed copies are available at the university library and at the national library in Frankfurt and Leipzig. I also have a few spare ones, so if you think you really need one, let me know. The SHA1 hash of the PDF file I submitted to the library is 45f8b26dc10c04a5221d79fa3a2c42478a2b89b6, which matches the file available online as of today.

Abstract

This dissertation introduces, validates, and applies various models for the study of microswimmers, predominantly focusing on the development of lattice algorithms. The models are applicable to biological swimmers like bacteria, but also to artificial ones propelled via chemical reactions. The unifying theme is a complex fluidic environment, ranging from Newtonian single-component fluids, to electrolyte solutions, to viscoelastic media flowing through arbitrary geometries. A particular focus is placed on resolving each swimmer’s surface since the propulsion, or phoresis, originates from a small layer of fluid around it. Resolving the propulsion mechanism is necessary to accurately study hydrodynamic interactions with obstacles and other swimmers. It is also a prerequisite for the study of taxis, that is, alignment with an external field such as a nutrient gradient. Similarly, phoretic interactions can be investigated, like when a swimmer senses and avoids the trail where another swimmer has already depleted the fuel.

Novation Launchkey 61 MK3 and MainStage 3.5

Santa got me a Novation Launchkey 61 MK3 this year. I learned playing piano as a kid on a Yamaha PSR-340 and have been wanting to get back into music for a while now. These days, good low-priced MIDI keyboards and great-sounding virtual instruments are available for low prices, so the up-front investment is much smaller than back then.

I wanted a MIDI keyboard with a display and a couple of buttons and faders so I could select and control virtual pianos, synths, and organs on my computer. I also wanted integration of the controls with Apple Logic Pro. Some older MIDI devices used binary plugins for this purpose (which get installed into /Library/Application Support/MIDI Device Plug-ins), but with Apple recently having switched from Intel to its own custom Arm processors and many manufacturers not providing updates in a timely manner, the better way going forward is using Lua scripts.

Browsing through the Thomann store, I found that my criteria are met by the Akai MPK 261, Nektar Panorama P6, Novation Launchkey 61 MK3, and Roland A-800 Pro. (The Nektar Panorama T6 might also be okay once the manufacturer delivers the update promised. Same might go for the Novation SL MKIII if it gets an update.) The Nektar Panorama P series only has a binary plugin for Logic Pro, but a Lua script for MainStage. The Novation MK3 has a downloadable Lua script for Logic. The Roland A-PRO series and Akai MPK series are apparently supported out of the box through Lua scripts. Finally, there is the Studiologic Mixface SL, which is a controller with faders, knobs and buttons that magnetically attached to the Studiologic SL series of MIDI keyboards and which has a Lua script for Logic. There is also the Roland Fantom 6, a high-end synthesizer, that has a binary plugin for Logic and a Lua script for MainStage.

When you are not recording, but just playing virtual instruments, a DAW like Logic Pro is overkill. That’s what Apple MainStage is for — it hosts Audio Units (virtual instruments and effects), but unlike a DAW it has no concept of recording or timeline. After seeing Roland’s and Nektar’s documentation on their support of MainStage (they display all the on-screen controls on the keyboard display and allow you to interact with them via the knobs, buttons and faders), I wanted to see how much I could do with the Launchkey. It has special MIDI messages for all kinds of things and should thus be able to do most of the same. The Lua scripts that configure MIDI devices are installed into ~/Music/Audio Music Apps/MIDI Device Scripts (for Logic) and ~/Music/Audio Music Apps/MainStage Devices (for MainStage). The Lua API is not documented publicly, but can easily be deduced by poking through Apple’s own scripts, which are in /Applications/MainStage 3.app/Contents/Frameworks/MACore.framework/Versions/A/Resources/MIDI Device Scripts. The basic API is identical between MainStage and Logic, but Logic uses a different parameter feedback mechanism and supports multiple layers (or “modes”), both of which are not used by any of Apple’s scripts.

I am happy to report that I managed to create a complete MainStage integration for the Launchkey that pretty much matches what Roland (Fantom) and Nektar managed to do. Of course, due to lack of a graphical display, it’s not as nice, but it only costs half as much as the Nektar and a tenth of the Roland Fantom. Automatic mapping of knobs, faders, buttons, and drum pads works perfectly. The LEDs of the buttons mirror the state of the UI. The display shows parameter feedback (name and value) when you move a knob or fader. This goes beyond what the Roland A-800 or Akai MPK261 do, which have a similar price as the Launchkey, but cannot display parameter information.

Note that MainStage’s automatic mapping of controls has a few bugs. My device script cannot work around these, but you can manually re-map these controls if you need them:

  • The Keyboard quick-start project does not map Smart Drawbars to MIDI faders. The Tonewheel organ project template does however. You can manually map the Smart Drawbar controls though.
  • Smart Faders are not mapped to MIDI faders. You can manually map the Smart Fader controls.
  • Instruments that have Smart Controls spread across multiple pages only have their first page’s controls mapped. You can manually map the Tab 2 Smart Knobs though.
  • Drumpads on the keyboard trigger notes in the C6-B7 range and are mapped to MainStage’s Drum Pad controls. However, the virtual instruments expect notes in the C1-B2 range. You can manually change the trigger notes on all 24 drum channels.

Check out https://github.com/mkuron/launchkey-mk3-mainstage if you want to use your own Launchkey MK3 with MainStage. The versions for the smaller (25-key, 37-key, 49-key) models are untested, but should work just as well.

Update February 2022: The Novation SL MKIII got its promised Logic Pro integration. MainStage integration could be done in a similar way as I did for the Launchkey MK3. The Novation SL MKIII seems quite comparable to the Nektar Panorama P6, but a bit more modern.

Update March 2022: I uploaded a video to YouTube and tweeted about this, hoping to get it out to more people. Novation even liked my tweet:

Update April 2022: Downloadable installer packages (.pkg files) are now available for release versions at https://github.com/mkuron/launchkey-mk3-mainstage/releases. You will need to right-click to install the package as it is not signed.

Scientific Article: An extensible lattice Boltzmann method for viscoelastic flows: complex and moving boundaries in Oldroyd-B fluids

I’ve published a scientific article in the European Physical Journal E.

An extensible lattice Boltzmann method for viscoelastic flows: complex and moving boundaries in Oldroyd-B fluids
Michael Kuron, Cameron Stewart, Joost de Graaf, and Christian Holm
European Physical Journal E 44, 1 (2021)
DOI:
10.1140/epje/s10189-020-00005-6

The article is available as open-access from the publisher, thanks to Projekt DEAL. One of my pictures even made it onto the cover of the January 2021 issue:

Scientific Article: waLBerla: A block-structured high-performance framework for multiphysics simulations

I co-authored a scientific article in Computesr & Mathematics with Applications:

waLBerla: A block-structured high-performance framework for multiphysics simulations
Martin Bauer, Sebastian Eibl, Christian Godenschwager, Nils Kohl, Michael Kuron, Christoph Rettinger, Florian Schornbaum, Christoph Schwarzmeier, Dominik Thönnes, Harald Köstler, and Ulrich Rüde
Comp. Math. Appl. 81, 478 (2021)
DOI:
10.1016/j.camwa.2020.01.007

The journal does not provide open access to the article, but you can download it for free from arXiv: arXiv:1909.13772.

Ubuntu 20.04: OpenMPI bind-to NUMA is broken when running without mpiexec

I tend to set the CPU pinning for my OpenMPI programs to the NUMA node. That way, they always access fast local memory without having to cross between processors. Some recent CPUs like the AMD Ryzen Threadripper have multiple NUMA nodes per socket, so pinning to the socket is not the same thing.

Since upgrading to Ubuntu 20.04, we were seeing error messages like this:

$ python3 -m mpi4py.bench helloworld
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

 Setting processor affinity failed failed
 --> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------

Launching through mpiexec/mpirun, even if it was with just one MPI rank, did not show the error:

$ mpiexec -n 1 python3 -m mpi4py.bench helloworld
Hello, World! I am process 0 of 1 on host1.
$ mpirun -n 1 python3 -m mpi4py.bench helloworld
Hello, World! I am process 0 of 1 on host1.
$ mpiexec -n 4 python3 -m mpi4py.bench helloworld
Hello, World! I am process 3 of 4 on host1.
Hello, World! I am process 0 of 4 on host1.
Hello, World! I am process 1 of 4 on host1.
Hello, World! I am process 2 of 4 on host1.

If you look through the OpenMPI code, you can see that CPU pinning is done by different code depending on whether you run standalone (called singleton mode) or through mpiexec. The relevant bit for the former is in ess_base_fns.c. It searches for a hwloc object of type HWLOC_OBJ_NODE (which is deprecated on the hwloc side and identical to the newer HWLOC_OBJ_NUMANODE). Since hwloc 2.0, NUMA nodes are no longer containers for CPU cores, but exist besides them inside a HWLOC_OBJ_GROUP.

$ lstopo --version
lstopo 1.11.9
$ lstopo --output-format console
Machine (31GB total) + Package L#0
  NUMANode L#0 (P#0 16GB)
    L3 L#0 (8192KB)
      L2 L#0 (512KB) + L1d L#0 (32KB) + L1i L#0 (64KB) + Core L#0
        PU L#0 (P#0)
        PU L#1 (P#12)
[...]
$ lstopo --version
lstopo 2.1.0
$ lstopo --output-format console
Machine (31GB total) + Package L#0
  Group0 L#0
    NUMANode L#0 (P#0 16GB)
    L3 L#0 (8192KB)
      L2 L#0 (512KB) + L1d L#0 (32KB) + L1i L#0 (64KB) + Core L#0
        PU L#0 (P#0)
        PU L#1 (P#12)
[...]

The current OpenMPI master (i.e. versions beyond the 4.1.x series) don’t bind through hwloc anymore, so the issue is fixed upstream (if only by accident). However, we’re stuck with Ubuntu 20.04 for the next two years, so let’s fix it ourselves. We load up the incriminating file, /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-rte.so.40.20.3, in Hopper and jump to orte_ess_base_proc_binding. Comparing it to its C code quickly reveals the instruction we need to change:

0x3 is OPAL_BIND_TO_NUMA and 0xd is HWLOC_OBJ_NODE. Looking at the hex code tells us that we need to make this change:

- 66 83 F8 03 0F 85 70 02 00 00 BA 0D 00 00 00
+ 66 83 F8 03 0F 85 70 02 00 00 BA 0C 00 00 00

Here’s a bit of Python code to do that:

import mmap
with open("/usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-rte.so.40.20.3", 'r+b') as f:
m = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_WRITE)
m.seek(m.find(bytes.fromhex("66 83 F8 03 0F 85 70 02 00 00 BA 0D 00 00 00")))
m.write( bytes.fromhex("66 83 F8 03 0F 85 70 02 00 00 BA 0C 00 00 00"))

Update 2021-02-26

The recent kernel update from 5.4.0.65 to 5.4.0.66 switched us from HWLOC_OBJ_GROUP to HWLOC_OBJ_DIE. lstopo now reports

$ lstopo --output-format console
 Machine (31GB total) + Package L#0
   Die L#0
     NUMANode L#0 (P#0 16GB)
     L3 L#0 (8192KB)
       L2 L#0 (512KB) + L1d L#0 (32KB) + L1i L#0 (64KB) + Core L#0
         PU L#0 (P#0)
         PU L#1 (P#16)
[...]

So the patch needs to be modified to have 0x13 in its fourth-to-last byte now.

Update 2021-05-07

The AMD Epyc still uses HWLOC_OBJ_GROUP instead of HWLOC_OBJ_DIE and thus needs the previous patch:

Machine (252GB total)
   Package L#0
     Group0 L#0
       NUMANode L#0 (P#0 31GB)
       L3 L#0 (16MB)
         L2 L#0 (512KB) + L1d L#0 (32KB) + L1i L#0 (32KB) + Core L#0
           PU L#0 (P#0)
           PU L#1 (P#48)
[...]

Update 2022

Unfortunately, OpenMPI 5 was still not released and Ubuntu 22.04 thus retains this problem. My binary-patching trick does not work anymore either because the compiler makes some complex optimizations. Therefore, I suggest you use

OMPI_MCA_rmaps_base_mapping_policy=l3cache OMPI_MCA_hwloc_base_binding_policy=l3cache

instead of

OMPI_MCA_rmaps_base_mapping_policy=numa OMPI_MCA_hwloc_base_binding_policy=numa

This still gives you the benefit of pinning to more than a single core, which gives the kernel some scheduling flexibility.

What to do when Mathematica’s ParallelMap/ParallelTable takes a long time to start up

I have a Mathematica notebook that derives some rather massive expressions. I wanted to do some transformations on them in parallel using ParallelMap or ParallelTable, but noticed that these commands were only running on a single CPU core for hours before actually starting to run in parallel and occupy all CPU cores. While it was running on only that single CPU core, I could not even abort the evaluation using Alt-. like one usually can: it simply seemed stuck.

make_massive_expression[x_] := ...;
process[x_] := Simplify[x];
a1 = simple_expression;
a2 = make_massive_expression[a1];
a3 = make_massive_expression[a2];
as = {a1,a2,a3};

b = ParallelTable[process[as[[i]]], {i,Length[as]}];

As it turns out, during the startup phase Mathematica copies all definitions from the main kernel to the parallel kernels. And that seems to be a rather inefficient procedure. So let’s transfer the needed definitions manually.

make_massive_expression[x_] := ...;
process[x_] := Simplify[x];
a1 = simple_expression;
a2 = make_massive_expression[a1];
a3 = make_massive_expression[a2];
as = {a1,a2,a3};

DistributeDefinitions[as, process];
b = ParallelTable[process[as[[i]]], {i,Length[as]}, DistributedContexts -> None];

Now DistributeDefinitions is slow, but ParallelTable immediately starts running in parallel on multiple kernels. We haven’t gained anything by splitting things like this, but at least we can now tell exactly where the problem lies. So instead of transferring the massive expressions to the parallel kernels, let’s only transfer the simple expression and have the parallel kernels derive the massive expression themselves:

make_massive_expression[x_] := ...;
process[x_] := Simplify[x];
a1 = simple_expression;

DistributeDefinitions[a1, make_massive_expression, process];

ParallelEvaluate[(
   a2 = make_massive_expression[a1];
   a3 = make_massive_expression[a2];
   as = {a1,a2,a3}
), DistributedContexts -> None];

b = ParallelTable[process[as[[i]]], {i,Length[as]}, DistributedContexts -> None];

Leserbrief “Corona-Einschränkungen”

Im November 2020 beschlossen die Landesregierungen, einen großen Teil der Maßnahmen wiederherzustellen, die sie bereits im Frühjahr gegen die Ausbreitung des Coronavirus ergriffen hatten. Am 4. November 2020 druckte die Süddeutsche Zeitung dazu einen von mir verfassten Leserbrief:

Zu viel Optimismus

Der zweite Quasi-Lockdown zeigt, dass der erste keinen bleibenden Nutzen gestiftet hat, sondern lediglich das Unvermeidliche um einige Monate verzögerte. Auch der dritte oder vierte wird uns nicht nah genug an ein Heilmittel bringen, so sehr wir uns das auch wünschen mögen. Gleichzeitig setzt sich immer mehr die Erkenntnis durch, dass die in die Impfstoffentwicklung gesetzte Hoffnung viel zu optimistisch war und ein Impfstoff voraussichtlich die Eindämmungsmaßnahmen nicht obsolet machen wird. Man muss also durchaus die Frage stellen, ob das Ziel, das wir zu erreichen suchen, überhaupt erreichbar ist. Auch für die rechtliche Bewertung ist diese Frage elementar: Ist eine Maßnahme ungeeignet, ihr Ziel zu erreichen, so ist sie unverhältnismäßig. An einem übermächtigen Gegner wie einer Naturkatastrophe zu scheitern, ist jedenfalls keine Schande. Im Gegenteil, es zeigt, dass wir immer noch Menschen und keine Götter sind. Leider sind Politiker nicht bekannt dafür, eigene Fehler eingestehen zu können. Dies wird aber nötig sein, da es mit der aktuellen Strategie wohl kein „nach Corona“ geben wird – wenn man bloßes Wunschdenken überhaupt als Strategie bezeichnen kann.

Michael Kuron, Frickenhausen

Setting up BigBlueButton

Like so many other people, me and most of my two dozen colleagues are currently working from home full-time. While even before the current situation we have always had people work at home for individual days, we didn’t have the infrastructure to replace physical person-to-person communication. The first day was full of phone calls and emails, while our usual video conferencing system DFNconf, provided by the German research network, was struggling to keep up with growing demand. Microsoft Teams was also collapsing under the unexpected load, and I suspect other services like WebEx and Zoom had similar problems. As we might be stuck in this situation for months, we decided to take things into our own hands. For privacy reasons, we wouldn’t be able to use any of these commercial services anyway.

The first step was a chat system. We already have a self-hosted GitLab instance, so switching on Mattermost, an open-source competitor to Slack or Microsoft Teams, was a matter of minutes. Create a DNS record, wait for it to propagate, edit one GitLab config file, and restart GitLab twice.

Next step was video. This is what this article is going to be about. Unlike Microsoft Teams, Mattermost does not have a built-in video conferencing solution. It does have an API that allows third-party software and services to integrate with it. There is a list of video integrations. Our requirements were that it be self-hosted, free, straight forward to set up, and well maintained. That basically led us to BigBlueButton, which can interface to Mattermost via a plugin.

Prerequisites

You need two Linux machines. We have access to an OpenStack cloud provided by the state (bwCloud), so that was easy. The first one, called turn.example.com, has 2 GB RAM, 2 CPU cores, and Ubuntu 18.04. The second one, called video.example.com, has 8 GB RAM, 4 CPU cores and Ubuntu 16.04 (no, that is not a typo). Once the machines are running, set up DNS records for IPv4 and IPv6 and wait until they propagate. Then, SSH into each of them and get them prepared:

sudo hostnamectl set-hostname XXX.example.com
sudo apt-get update
sudo apt-get install language-pack-en
sudo systemctl set-environment LANG=en_US.UTF-8
sudo apt-get upgrade
sudo apt-get dist-upgrade
sudo reboot

While that is running, configure your cloud provider’s firewall rules. turn.example.com needs incoming IPv4 and IPv6 access for tcp/80, tcpudp/3478, tcpudp/443, udp/49152-65535, while video.example.com needs tcp/80, tcp/443, udp/16384-32768.

Setting up the TURN server

SSH into turn.example.com and run

wget -qO- https://ubuntu.bigbluebutton.org/bbb-install.sh | sudo bash -s -- \
  -c turn.example.com:YYYYYYYY -e you@example.com

Instead of the placeholder YYYYYYYY, you should use a random token. You’ll need it again in the next section to connect BigBlueButton to your TURN server.

Setting up BigBlueButton

SSH into video.example.com and run

wget -qO- https://ubuntu.bigbluebutton.org/bbb-install.sh | sudo bash -s -- \
  -v xenial-22 -s video.example.com -e you@example.com \
  -c turn.example.com:YYYYYYYY
sudo apt-get install bbb-webhooks
sudo bbb-conf --stop
sudo sed -i 's/allowStartStopRecording=./allowStartStopRecording=false/g' \
  /usr/share/bbb-web/WEB-INF/classes/bigbluebutton.properties
sudo sed -i 's/disableRecordingDefault=./disableRecordingDefault=true/g' \
  /usr/share/bbb-web/WEB-INF/classes/bigbluebutton.properties
sudo bbb-conf --start
sudo bbb-conf --secret

The last command will print out a URL and a secret. Save these for later; you’ll need them to integrate with Mattermost. If you don’t have Mattermost, add -g to the third line and the installer will install the Greenlight management UI for you.

Integrating Mattermost and BigBlueButton

Download the latest release from the GitHub repo. Go to your Mattermost system console, go to Plugin Management and upload the file. Refresh the page and go to the plugin’s settings. Make sure the plugin is disabled, paste the URL (https://video.example.com/bigbluebutton/api) and secret from the previous step, and click Save. Then, enable the plugin and click Save again.

That’s it, you now have a video button at the top of every Mattermost conversation. Click it in a direct message or channel and it will post an invitation link. Everyone can click it to join. The plugin will always show the names of the people that have joined a conference. There’s an end meeting button, but the conference will automatically end a few minutes after the last person has left.

Configuring Phone Dial-in

On video.example.com, configure FreeSWITCH to route incoming calls by creating /opt/freeswitch/etc/freeswitch/dialplan/public/dialin.xml with the following contents:

<extension name="from_my_provider">
  <condition field="destination_number" expression="^ZZZZZZZZZZ">
    <action application="answer"/>
    <action application="sleep" data="500"/>
    <action application="play_and_get_digits" data="5 5 3 7000 # conference/conf-pin.wav ivr/ivr-that_was_an_invalid_entry.wav pin \d+"/>
    <action application="transfer" data="SEND_TO_CONFERENCE XML public"/>
  </condition>
 </extension>
 <extension name="check_if_conference_active">
  <condition field="${conference ${pin} list}" expression="/sofia/g" />
  <condition field="destination_number" expression="^SEND_TO_CONFERENCE$">
    <action application="set" data="bbb_authorized=true"/>
    <action application="transfer" data="${pin} XML default"/>
  </condition>
 </extension>

Configure your SIP PBX/provider to route calls for your number (assumed to be +49 711 12345678 in the following) to sip:ZZZZZZZZZZ@video.example.com;transport=tcp without registration. ZZZZZZZZZZ is a secret token and you should pick a random one.

In /usr/share/bbb-web/WEB-INF/classes/bigbluebutton.properties on video.example.com, set

defaultDialAccessNumber=+49-711-12345678
defaultWelcomeMessageFooter=<br><br>To join this meeting by phone, dial:<br>  %%DIALNUM%%<br>Then enter %%CONFNUM%% as the conference PIN number.<br>Note that this will only work once at least one person has joined the audio bridge from their computer.<br>You can mute and unmute yourself by pushing 0.

and restart BigBlueButton (sudo bbb-conf --stop && sudo bbb-conf --start). Open tcp/5060 in the firewall and you are ready.

Using Greenlight

If you are using Greenlight instead of Mattermost to manage your conferences, it will be available at https://video.example.com. I have not tried it, so I am leaving you to read the documentation yourself.

Conclusion

We decided to do this on Monday around noon (day one of the semi-lockdown) and I sent out the announcement email to my colleagues just four hours later. In other words, BigBlueButton is really easy to set up, thanks to bbb-install.

Today is day four. So far all our meetings were small (< 5 people), but BigBlueButton is extremely light on server resources. Audio quality is great (though the noise gate is a bit aggressive sometimes). Screen sharing and webcam streaming work well, even from networks with firewalls that block all UDP traffic. Firefox, Chrome and Safari work equally well, the only thing that is currently missing is screen sharing from Safari. The server mainly expends CPU time for mixing the audio conferences (extrapolating suggests we can handle at least 20 participants, probably more), while all video is just relayed to the other participants. That means that your server needs enough bandwidth for every participant to exchange ~500 Kbit/s with every other participant if everyone has their camera enabled. Your clients need 500 Kbit/s upstream total and 500 Kbit/s downstream for every other participant.

Week 2 Update (2020-03-24)

Today we had our first bigger video meeting. Ten people with audio, five with video and the server was operating at around 50% of one CPU core. Three problems were discovered:

  • Safari cannot send video if it is behind a firewall that blocks UDP, producing an error 1020. Judging from packet captures, it does not appear to fall back to the TURN server.
    Solution: use Chrome or Firefox.
  • Firefox cannot send audio if ICE is disabled. uBlock and some other privacy addons might cause that. Go to about:config and check whether any of the media.peerconnection.* settings have been modified from their defaults (are displayed in boldface).
    Solution: disable the addons and return these settings to their default. If it works after that, you might re-enable the addons and whitelist your server.
  • Some people don’t have headsets. Their microphones pick up ambient noise, overdrive, feed back, etc. and make audio a pain to listen to.
    Solution: get a USB headset. I have a Plantronics Blackwire C320 (mainly because it is compatible with my desk phone), which is a few years old and no longer sold, but you can buy its successor, the Plantronics Blackwire 3220. It’s cheap (around 30 Euros) and good enough for someone like me who only needs it for an hour or two per day. Of course, they are sold out everywhere, so be prepared to wait for multiple weeks to get yours delivered. Until then, use your smartphone headset as it’s still better than your computer’s built-in microphone, or dial into the conference via telephone.

Week 6 Update (2020-04-23)

We have had a few minor complaints about audio quality, mainly in direct comparison to Webex and Zoom. These seem to do better echo cancellation, apply some kind of magic audio processing that makes built-in microphones not sound as terrible, and have (better) packet loss concealment. Still, considering its price, privacy, and ease of use, I prefer BBB.

There is a more significant audio issue in BBB (#7007) though where you get occasional drops and crackles for no apparent reason. I set use-dtx=0, jitterbuffer=60, and energy-level=50 as suggested there and it gets a bit better, but there is still room for improvement. Hopefully that will be resolved by the BBB developers soon.

Today I updated to the latest version of BigBlueButton. It is as simple as running bbb-install again and only takes a minute or two.

Exploring the MoneyMoney database

MoneyMoney is a convenient online banking application for macOS, most useful if you have accounts with multiple different German banks. I wanted to export some of the data I had stored there in a format that the app didn’t support by itself, so I was wondering if I could pull it straight from the database. You can go to the Help menu and click Show Database in Finder and will be led to ~/Library/Containers/com.moneymoney-app.retail/Data/Library/Application Support/MoneyMoney/Database/MoneyMoney.sqlite. If you go to MoneyMoney’s About screen, you’ll see that it attributes SQLCipher.

So, download and compile SQLCipher like this:

git clone https://github.com/sqlcipher/sqlcipher.git
cd sqlcipher
./configure --enable-tempstore=yes CFLAGS="-DSQLITE_HAS_CODEC" LDFLAGS="-L/opt/local/lib -lcrypto" CC=clang CXX=clang++
make -j 4

Now you can open the database using

./sqlcipher "file://$HOME/Library/Containers/com.moneymoney-app.retail/Data/Library/Application Support/MoneyMoney/Database/MoneyMoney.sqlite?mode=ro"

and decrypt and dump it by typing the following commands at the SQLite prompt:

PRAGMA key = '<your database password>';
PRAGMA cipher_compatibility = 3;
.dump

The database password is just what you set in MoneyMoney and I figured out the compatibility level by trial and error. It seems like MoneyMoney didn’t yet get around to upgrading to SQLCipher 4, which was released in late 2018. It’s entirely possible that some older versions of MoneyMoney require a lower compatibility level and that some future version may be using level 4.

Disclaimer: You should not attempt to modify the database as that may cause MoneyMoney’s data to become inconsistent or modified in ways the developer did not anticipate. That’s why I open the file in read-only mode above. If you do modify it, you’re on your own.

Debugging code-signed applications on macOS

To debug a code-signed application on macOS, you need to turn off System Integrity Protection. Some applications however explicitly forbid debugging them. This manifests itself in lldb error messages like

Process 12345 exited with status = 45 (0x0000002d) 

If you google that message, you’ll find that this happens if the application disallows attaching a debugger by calling

ptrace(PT_DENY_ATTACH, 0, 0, 0)

There are many workarounds described around the internet. The one I like using is the following lldb command:

breakpoint set --name ptrace --command "thread return" --command "continue"

It just causes the ptrace call to be skipped. Of course, some applications take more involved measures to prevent attaching a debugger, but often this is sufficient.