open-discussion > PSOM in sh & tcsh
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Jun 17, 2012 08:06 AM | Zaixu Cui
PSOM in sh & tcsh
Dear Pierre:
I am using /bin/bash all the time ans PSOM works well.
How about PSOM in /bin/tcsh & /bin/csh environment?
Have you tested before?
Best Regards
Zaixu
I am using /bin/bash all the time ans PSOM works well.
How about PSOM in /bin/tcsh & /bin/csh environment?
Have you tested before?
Best Regards
Zaixu
Jun 17, 2012 06:06 PM | Pierre Bellec
RE: PSOM in sh & tcsh
Hi Zaixu,
Good question. I have used PSOM for years on a csh system, but I haven't made much tests recently (since 0.9). I don't see any major potential issues, as I have been quite careful to keep all scripts explicitely #!/bin/bash , but I am not 100% sure it will work. If you run into any issue let me know (remember to run psom_config) and we'll fix it right away. Those additional tests would be really helpful as we're aiming at releasing PSOM 1.0 in the coming weeks.
Best,
Pierre
Good question. I have used PSOM for years on a csh system, but I haven't made much tests recently (since 0.9). I don't see any major potential issues, as I have been quite careful to keep all scripts explicitely #!/bin/bash , but I am not 100% sure it will work. If you run into any issue let me know (remember to run psom_config) and we'll fix it right away. Those additional tests would be really helpful as we're aiming at releasing PSOM 1.0 in the coming weeks.
Best,
Pierre
Jun 18, 2012 12:06 AM | Zaixu Cui
RE: PSOM in sh & tcsh
Dear Pierre:
In fact, I have run into error in /bin/tcsh environment.
I define a job named 'dcm2nii_dwi_00001', then PSOM created a script named 'dcm2nii_dwi_00001.sh'.
The command in this script is:
"/opt/software/matlabR2010b/bin/matlab" -nosplash -nodesktop -r "load('/data/node1/Zaixu/225/logs//PIPE.mat','path_work'), if ~ismember(path_work,{'gb_niak_omitted','gb_psom_omitted'}), path(path_work), end, psom_run_job('/data/node1/Zaixu/225/logs//dcm2nii_dwi_00001.mat'),exit" >"/data/node1/Zaixu/225/logs//dcm2nii_dwi_00001.log" 2>&1
This command cannot work in /bin/tcsh & /bin/csh environment.
The error is 'Ambiguous output redirect.'
It seemd the error is in '>"/data/node1/Zaixu/225/logs//dcm2nii_dwi_00001.log" 2>&1'.
Thanks very much.
Best Regards.
Zaixu
In fact, I have run into error in /bin/tcsh environment.
I define a job named 'dcm2nii_dwi_00001', then PSOM created a script named 'dcm2nii_dwi_00001.sh'.
The command in this script is:
"/opt/software/matlabR2010b/bin/matlab" -nosplash -nodesktop -r "load('/data/node1/Zaixu/225/logs//PIPE.mat','path_work'), if ~ismember(path_work,{'gb_niak_omitted','gb_psom_omitted'}), path(path_work), end, psom_run_job('/data/node1/Zaixu/225/logs//dcm2nii_dwi_00001.mat'),exit" >"/data/node1/Zaixu/225/logs//dcm2nii_dwi_00001.log" 2>&1
This command cannot work in /bin/tcsh & /bin/csh environment.
The error is 'Ambiguous output redirect.'
It seemd the error is in '>"/data/node1/Zaixu/225/logs//dcm2nii_dwi_00001.log" 2>&1'.
Thanks very much.
Best Regards.
Zaixu
Jun 18, 2012 01:06 AM | Zaixu Cui
RE: PSOM in sh & tcsh
Dear Pierre:
I'm sorry.
PSOM work well in /bin/tcsh.
It's my fault.
PSOM is powerful, I should modify my code now.
Thanks very much.
Zaixu
I'm sorry.
PSOM work well in /bin/tcsh.
It's my fault.
PSOM is powerful, I should modify my code now.
Thanks very much.
Zaixu
Jun 18, 2012 05:06 PM | Pierre Bellec
RE: PSOM in sh & tcsh
Dear Zaixu,
haha, I was running tests on tcsh and could not reproduce the errors. Thanks for all the feedback it's fantastic, it seems like we're close to being ready for PSOM 1.0
Best,
Pierre
haha, I was running tests on tcsh and could not reproduce the errors. Thanks for all the feedback it's fantastic, it seems like we're close to being ready for PSOM 1.0
Best,
Pierre