SRIM in Docker — Python 3.11 Edition

A reproducible Docker environment that runs SRIM 2013 and PySRIM on modern Python 3.11.
It follows the same idea as Christopher Ostrouchov’s original costrouc/pysrim image, but:

• starts from a slim Debian 12 / Python 3.11 base instead of Ubuntu 16.04 / Python 3.6;
• installs the VB 6 runtime (winetricks vb6run) in a fresh 32-bit Wine prefix, letting SRIM’s Visual-Basic executables run without crashing;
• wraps Wine with xvfb-run automatically so SRIM can run head-less;
• patches PySRIM’s deprecated yaml.load() call for compatibility with PyYAML ≥ 6.0.

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Repository layout

File	Purpose
Dockerfile	Builds the complete SRIM + PySRIM stack (see below).
my_srim.py	Slow TRIM benchmark: 50 MeV range in 4 cm water & 60 MeV exit energy after 1 cm water.
fast_srim.py	Tiny SR sanity check: 10 MeV proton residual energy after 0.2 cm water; finishes fast.

(Add your own scripts in the same directory—/workspace in the container maps to your current host folder.)

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Building the image

docker build -t srim_pysrim:latest .

What happens during the build

1. System packages – installs Wine 8 (x86 + x64), Winetricks, cabextract, unzip, xvfb, xauth, and helper tools on Debian 12 slim.

2. Head-less Wine wrapper – replaces /usr/bin/wine with a tiny script that runs
   xvfb-run -a wine-bin …, so every Wine/Winetricks call has a dummy X-server.

3. 32-bit Wine prefix + VB6 runtime – deletes any old prefix, creates a fresh WINEARCH=win32 prefix, and runs winetricks -q vb6run to install MSVBVM60.DLL and the common VB6 OCXs SRIM needs.

4. SRIM 2013 extraction – downloads SRIM-2013-Std.e from srim.org, unpacks it silently with 7z, and stores everything in /opt/srim.

5. Python layer – installs NumPy 2.3.1 and PySRIM 0.5.10 on Python 3.11, then patches a deprecated yaml.load() call to yaml.safe_load() for PyYAML ≥ 6.

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Running scripts

# quick SR sanity check (seconds)
docker run --rm -v ${PWD}:/workspace srim_pysrim:latest python /workspace/fast_srim.py

# full TRIM benchmark (minutes)
docker run --rm -v ${PWD}:/workspace srim_pysrim:latest python /workspace/example_trim.py

/opt/srim is on the container’s PATH; the default working directory inside the container is /workspace.

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Notes & caveats

• Layer-width limit – SRIM’s deterministic SR tables can only handle layers
  ≤ 21.47 cm (2 147 483 648 Å). Use multiple thin slabs or TRIM for thicker water phantoms.
• Root warnings – Wine/Winetricks complain about running as root; inside a Docker container this is safe and expected.
• Performance tips – For faster TRIM runs, lower number_ions in your scripts or spin up multiple containers in parallel and merge the outputs.

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What went wrong

SRIM’s executables are launched successfully, but from the wrong working directory. PySRIM writes its inputs under <SRIM_DIR>/SR Module/... and then starts SRModule.exe; that executable expects to read its control file (e.g., SR.IN) and write outputs inside the SRIM program folder. When the process CWD isn’t <SRIM_DIR>/SR Module (for SR) or <SRIM_DIR> (for TRIM), the VB6 app aborts with Runtime error 53 (File not found) — exactly the failure observed under Wine. The “X connection to :99 broken” line is a side-effect of xvfb-run tearing down the virtual display after the Windows app exits, not the root cause.

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References

• SRIM home page – http://www.srim.org
• costrouc/pysrim Docker image – https://github.com/costrouc/pysrim
• WineHQ FAQ on running as root – https://wiki.winehq.org/FAQ
• Winetricks documentation – https://github.com/Winetricks/winetricks
• PySRIM documentation – https://pysrim.readthedocs.io