Allpix2 on lxplus

1

Hi there,
I am trying to run a test file [0] on lxplus [1,2] and I get an out of memory error:

> allpix -c exercise2-config.conf 
> |03:22:38.315| =140104232206080=  (STATUS) <Allpix.cpp/load:L117> Welcome to Allpix^2 v3.2.0
> |03:22:38.315| =140104232206080=  (STATUS) <Allpix.cpp/load:L137> Initialized PRNG with system entropy seed 2177663960827033228
> |03:22:39.699| =140104232206080= (WARNING) <ModuleManager.cpp/load:L78> Main ROOT file "/afs/cern.ch/work/c/cvernier/HandsOn_A-AllpixSquared/workdir/output/exercise2.root" exists and will be overwritten.
> |03:22:39.742| =140104232206080=  (STATUS) <ModuleManager.cpp/load:L273> Loaded 7 modules                   
> |03:22:39.742| =140104232206080=  (STATUS) <ModuleManager.cpp/initialize:L597> Multithreading disabled
> |03:22:39.742| =140104232206080=  (STATUS) <ModuleManager.cpp/initialize:L620> Initializing 7 module instantiations
> |03:22:40.072| =140104232206080= (WARNING) [I:SimpleTransfer:detector1] <SimpleTransferModule.cpp/initialize:L75> Detector detector1 of type exercise2-mimosis1 has implants defined but collecting charge carriers from full sensor surface
> |03:22:40.072| =140104232206080= (WARNING) [I:DetectorHistogrammer:detector1] <DetectorHistogrammerModule.cpp/initialize:L71> Selected plotting granularity of (26899,30199) bins creates very large histograms.
>                                                                                                                               Consider reducing the number of bins using the granularity parameter.
> 
> Message from root@lxplus909.cern.ch on <no tty> at 03:22 ...
> Dear LxPlus User cvernier
> 
> The process (allpix) has been killed as the CGroup of all
> your processes has reached your memory allocation.
> 
> Memory cgroup out of memory: Killed process 3193009 (allpix) total-vm:39273432kB, anon-rss:35906880kB, file-rss:7168kB, shmem-rss:0kB, UID:32644 pgtables:71296kB oom_score_adj:0
> 
> To check your memory limits of your CGroup and current usage:
> 
> systemctl status user-0.slice
> EOF
> Killed

any suggestion?
thanks
Caterina

[0] Files · master · Elio Sacchetti / MAPS Academy 2025 - Allpix Squared Hands-on · GitLab
[1]

> [cvernier@lxplus909 cvernier]$ cat /etc/os-release
> 
> NAME="Red Hat Enterprise Linux"
> 
> VERSION="9.6 (Plow)"
> 
> ID="rhel"
> 
> ID_LIKE="fedora"
> 
> VERSION_ID="9.6"
> 
> PLATFORM_ID="platform:el9"
> 
> PRETTY_NAME="Red Hat Enterprise Linux 9.6 (Plow)"
> 
> ANSI_COLOR="0;31"
> 
> LOGO="fedora-logo-icon"
> 
> CPE_NAME="cpe:/o:redhat:enterprise_linux:9::baseos"
> 
> HOME_URL="https://www.redhat.com/"
> 
> DOCUMENTATION_URL="https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/9"
> 
> BUG_REPORT_URL="https://issues.redhat.com/"
> 
> REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 9"
> 
> REDHAT_BUGZILLA_PRODUCT_VERSION=9.6
> 
> REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
> 
> REDHAT_SUPPORT_PRODUCT_VERSION="9.6"

[2] source /cvmfs/clicdp.cern.ch/software/allpix-squared/3.2.0/x86_64-el9-gcc12-opt/setup.sh

2

Hi @cvernier ,

I think the problem is hinted at in the warning message; the granularity in [DetectorHistogrammer] is very fine, so the in-pixel histograms become memory-hungry.
If you didn’t manually set the granularity parameter, I recommend checking that you provide a unit to the pixel size in the exercise2-mimosis1 model. It looks like you maybe don’t give a unit, and the granularity defaults to the pixel size in µm. As the internal unit in Allpix Squared is mm, you might be off in pixel size and thus granularity by a factor 1000

Hope this helps! Let me know if not, and I’ll try to dig a bit deeper

Kind regards,
Håkan

3

That was the culprit - I overlooked that ! thanks a lot!

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