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czimaginginstitute / MotionCor3

Anisotropic correction of beam induced sample motion for cryo-electron microscopy and tomography
BSD 3-Clause "New" or "Revised" License
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MotionCor3 1.0.1, with option "-Serial 1" process holds excessive memory. #13

Closed larsonmattr closed 5 months ago

larsonmattr commented 5 months ago

When running with -Serial option turned on, this version of MotionCor3 appears to be using excessive memory when iterating over a datasets of 1000 micrographs:

~ 500 micrographs processed:

    PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND                                                                                                                  
 113220 1111471+  20   0  363.5g 328.2g 874640 S 294.1  65.2  59:56.75 MotionCor3

~ 750 micrographs processed:

     PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND                                                                     
 113220 1111471+  20   0  491.0g 453.5g 953284 S 278.2  90.1  83:10.06 MotionCor3

After about 750 micrographs the process had allocated over 450GB of memory, and this is possibly a memory leak that could kill the process eventually.

apeck12 commented 5 months ago

What resources are you requesting? We often use:

--cpus-per-task=16
--mem-per-cpu=196G

when running in -Serial mode for larger datasets. Did you find that you needed fewer compute resources when running MotionCor2 for similarly sized datasets?