What software do you run your cluster with? SGE?
Peace,
Matt.
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stuart Traxel
Sent: Wednesday, January 12, 2011 3:16 PM
To: [log in to unmask]
Subject: Re: [FSL] bedpostx - qsub flag error
Hi,
I am not able to run Bedpostx on the cluster we have in our department. I have tried running FEEDS, but get the output listed below when running the Bedpostx portion of the test suite. I have also attached the associated FSL error report file by copying it into a text file.
Starting FDT (bedpost) at Wed Jan 12 14:08:49 CST 2011
checking error on bedpost output:
No output image created
Warning - test failed!
HERE
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
No output image created
Warning - test failed!
Warning - not all tests passed
end time = Wed Jan 12 14:08:50 CST 2011
2690.74user 30.75system 45:20.17elapsed 100%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+13913293minor)pagefaults 0swaps
I have also tried running the bedpostx command but receive an error associated with qsub. An excerpt of the output is listed below. For now, I would like to just be able to run Bedpostx on the head node of our cluster. I would later like to set up the fsl_sub file so that we use other nodes on our cluster.
Making bedpostx directory structure
Queuing preprocessing stages
qsub: illegal -c value
qsub: illegal option -- s
usage: qsub [-a date_time] [-A account_string] [-b secs]
[-c { c[=<INTERVAL>] | s | n }] [-C directive_prefix] [-d path] [-D path]
[-e path] [-h] [-I] [-j oe] [-k {oe}] [-l resource_list] [-m {abe}]
[-M user_list] [-N jobname] [-o path] [-p priority] [-q queue] [-r y|n]
[-S path] [-u user_list] [-X] [-W otherattributes=value...] [-v variable_list]
[-V ] [-z] [script]
Queuing parallel processing stage
slice 0 has already been processed
qsub: illegal -c value
qsub: illegal option -- s
usage: qsub [-a date_time] [-A account_string] [-b secs]
[-c { c[=<INTERVAL>] | s | n }] [-C directive_prefix] [-d path] [-D path]
[-e path] [-h] [-I] [-j oe] [-k {oe}] [-l resource_list] [-m {abe}]
[-M user_list] [-N jobname] [-o path] [-p priority] [-q queue] [-r y|n]
[-S path] [-u user_list] [-X] [-W otherattributes=value...] [-v variable_list]
[-V ] [-z] [script]
Queuing post processing stage
qsub: illegal -c value
qsub: illegal option -- s
usage: qsub [-a date_time] [-A account_string] [-b secs]
[-c { c[=<INTERVAL>] | s | n }] [-C directive_prefix] [-d path] [-D path]
[-e path] [-h] [-I] [-j oe] [-k {oe}] [-l resource_list] [-m {abe}]
[-M user_list] [-N jobname] [-o path] [-p priority] [-q queue] [-r y|n]
[-S path] [-u user_list] [-X] [-W otherattributes=value...] [-v variable_list]
[-V ] [-z] [script]
Let me know if you need any other information.
Thanks,
Stuart Traxel