JObs stopped


#1

Hello,

I am running Cellprofiler 2.1.1(rev 4e6ec2c) on cluster and for unknown reasons some jobs are not completeted. Error message is always the same

‘assertion !pthread_create(&thr->thrH, &attr, rout, arg) failed, line 113 of file /scratch/jeronimo/final/tmp/ATLAS/amd64/…//src/threads/ATL_thread_start.c’

Do you have suggection what it could be? Complete log file is below.
Thanks a lot,
Best,
Milan

Version: 2014-06-14T17:02:06 4e6ec2c / 20140614170206
Plugin directory doesn’t point to valid folder: /mnt/storage-jihlava1-cerit.ib/home/esner/plugins
ilastik import: failed to import the ilastik. Please follow the instructions on
"http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
File “/afs/ics.muni.cz/software/cellprofiler/2.1.0/CellProfiler/cellprofiler/modules/classifypixels.py”, line 82, in
from ilastik.core.dataMgr import DataMgr, DataItemImage
ImportError: No module named ilastik.core.dataMgr
ilastik import: failed to import the ilastik. Please follow the instructions on
"http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
File “/afs/ics.muni.cz/software/cellprofiler/2.1.0/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py”, line 81, in
import ilastik_main
ImportError: No module named ilastik_main
Times reported are CPU times for each module, not wall-clock time
Wed Jul 22 08:39:41 2015: Image # 2051, module Images # 1: 0.00 sec
Wed Jul 22 08:39:41 2015: Image # 2051, module Metadata # 2: 0.00 sec
Wed Jul 22 08:39:41 2015: Image # 2051, module NamesAndTypes # 3: 1.86 sec
Wed Jul 22 08:39:43 2015: Image # 2051, module Groups # 4: 0.00 sec
Wed Jul 22 08:39:43 2015: Image # 2051, module MeasureImageIntensity # 5: 6.06 sec
Wed Jul 22 08:39:49 2015: Image # 2051, module ImageMath # 6: 0.02 sec
Wed Jul 22 08:39:49 2015: Image # 2051, module ImageMath # 7: 0.02 sec
Wed Jul 22 08:39:49 2015: Image # 2051, module ApplyThreshold # 8: 5.71 sec
Wed Jul 22 08:39:55 2015: Image # 2051, module ApplyThreshold # 9: 5.98 sec
Wed Jul 22 08:40:01 2015: Image # 2051, module Smooth # 10: 0.99 sec
Wed Jul 22 08:40:02 2015: Image # 2051, module IdentifyPrimaryObjects # 11: 9.01 sec
Wed Jul 22 08:40:11 2015: Image # 2051, module EnhanceOrSuppressFeatures # 12: 0.86 sec
Wed Jul 22 08:40:12 2015: Image # 2051, module EnhanceOrSuppressFeatures # 13: 0.49 sec
Wed Jul 22 08:40:12 2015: Image # 2051, module IdentifyPrimaryObjects # 14: 24.30 sec
Wed Jul 22 08:40:37 2015: Image # 2051, module IdentifyPrimaryObjects # 15: 10.29 sec
Wed Jul 22 08:40:47 2015: Image # 2051, module EnhanceOrSuppressFeatures # 16: 0.49 sec
Wed Jul 22 08:40:47 2015: Image # 2051, module IdentifyPrimaryObjects # 17: 6.83 sec
assertion !pthread_create(&thr->thrH, &attr, rout, arg) failed, line 113 of file /scratch/jeronimo/final/tmp/ATLAS/amd64/…//src/threads/ATL_thread_start.c


#2

Hi,

I don’t have direct experience with ATLAS clusters, but I don’t think this error is fro within CellProfiler, per se. It seems to have to do with threading on ATLAS, it seems? (sourceforge.net/p/math-atlas/sup … uests/873/). Are you running the headless version of CellProfiler, which should run with a very few threads? (Mostly one, but I believe BioFormats and others might open another thread).

Can you limit the number of threads on ATLAS somehow?

Regards,
David


#3

Hi David,

thanks a lot. I will check that with our IT administrator as I don’t understand all those details and let you know.

Thanks. Best regards,

Milan