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pelkmanslab / iBRAIN_BRUTUS

A version of canonical iBRAIN (2015) deployed on BRUTUS cluster
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Strange warning / possibly wrong pathdef #19

Closed tstoeger closed 9 years ago

tstoeger commented 9 years ago

I have just been (seemingly successfully) applying an SVM to a plate via iBrain (that called SVM_Classify_with_Probabilities_iBRAIN.m according to log/results file)

In contrast to the past, the results file lists several warnings. Since they have not been there in the past, I am not sure, if they indicate some potentially relevant change.

My first thought is that I have seen similar warnings, if the pathdef.m of MATLAB was outdated.

Sender: LSF System lsfadmin@a6078 Subject: Job 92170235: <matlab -singleCompThread -nodisplay << M_PROG;SVM_Classify_with_Probabilities_iBRAIN('/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/SVM_corrsegc01.mat','/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/BATCH/'); M_PROG> Done

Job <matlab -singleCompThread -nodisplay << M_PROG;SVM_Classify_with_Probabilities_iBRAIN('/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/SVM_corrsegc01.mat','/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/BATCH/'); M_PROG> was submitted from host by user in cluster . Job was executed on host(s) , in queue , as user in cluster . </cluster/home/biol/yyauhen> was used as the home directory. </cluster/home/biol/yyauhen/iBRAIN> was used as the working directory. Started at Tue Jun 30 11:22:43 2015 Results reported at Tue Jun 30 11:33:56 2015

Your job looked like:

LSBATCH: User input

matlab -singleCompThread -nodisplay << M_PROG SVM_Classify_with_Probabilities_iBRAIN('/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/SVM_corrsegc01.mat','/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/BATCH/');

M_PROG

Successfully completed.

Resource usage summary:

CPU time   :    617.71 sec.
Max Memory :       282 MB
Max Swap   :      2216 MB

Max Processes  :         3
Max Threads    :        18

The output (if any) follows:

Opening log file: /cluster/home/biol/yyauhen/java.log.7590

                        < M A T L A B (R) >
              Copyright 1984-2013 The MathWorks, Inc.
                R2013a (8.1.0.604) 64-bit (glnxa64)
                         February 15, 2013

[Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/physmod/simscape_language/simscape_language] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/target/extensions/processor/blackfin/blackfindemos] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/simrf/simrfmasks] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/simrf/simrfdemos] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/physmod/simulation/base/m] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/physmod/gl/mli/m] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/idelink/extensions/adivdsp/vdspdemos] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/sam/m3i] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/physmod/logging/mli/m] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/idelink/extensions/adivdsp/mdlinfo] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/idelink/extensions/adivdsp/tfl] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/idelink/extensions/adivdsp/vdspblks] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/idelink/extensions/adivdsp/rtw] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/physmod/gl/sli/m] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/physmod/pmir/pmir] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/physmod/gl/core/m] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/target/extensions/processor/blackfin] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/target/extensions/processor/blackfin/blks] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/target/extensions/processor/blackfin/blks/mex] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/target/extensions/processor/blackfin/blks/masks] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/physmod/logging/base/m] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/rtw/coder_foundation/tfl] [Warning: Name is nonexistent or not a directory: /cluster/apps/matlab/8.1/toolbox/rtw/coder_foundation/build]

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/cluster/home/biol/yyauhen/iBRAIN/startup.m: randomizing rand initial state /cluster/home/biol/yyauhen/iBRAIN/startup.m: 16 CPUs detected, using 1 threads

SVM_Classify_iBRAIN: PERFORMING CLASSIFICATION /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/SVM_corrsegc01.mat ON /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Thomas/150625-RBPoverexpression/BATCH/

SVM output name is corrsegc01

Loading.. field: Cells_AreaShape Loading.. field: Cells_Intensity_CorrFarRed Loading.. field: Cells_Texture_5_CorrFarRed

Classifying... PROCESSING IMAGE 1 OF 1848 PROCESSING IMAGE 2 OF 1848 PROCESSING IMAGE 3 OF 1848 ... (and so on)

ewiger commented 9 years ago

Indeed. Since today's switch to 2013a the pathdef was not updated. Thnx for reporting. Those warnings are solved now.