Hi,
It looks like the problem is with the batch call - the "-q"
option doesn't seem to be available for the osx batch command. If you
remove "-q long.q" from the batch command in fdt.tcl, I think it
should batch correctly.
Matthew
> hello list,
>
> sorry to keep bugging you all, but we are making a lot of progress
> with our cluster, thanks to this list, and we are almost fully
> functional which is very exciting, as we are seeing some very
> impressive speeds on the larger jobs (especially bedpost!)
>
> i implemented the symbolic links which were suggested to me in
> earlier posts, and now we can run bedpostx jobs and FEAT jobs fine
> from the gui, however we seem to have hit a snag with probtrackx.
> here is the information i got from the user in question, please
> advise what the problem could be, as it works fine from the command
> line (although for some reason this job gets run on the head node
> only and never gets submitted through the qsub process to the
> cluster.)
>
> Running probtrackx from the GUI creates the appropriate output
> directory, but only contains fdt_log.tcl and fdt_script.sh
>
> If I open fdt_script.sh and paste only the probtrackx command into
> the terminal command line, the job runs perfectly. This is the
> command that I paste:
>
> /common/fsl/bin/probtrackx --mode=seedmask -x /Volumes/Clinical/
> homes/tyanagihara/sweat/DTI/mask-dump/seed-internalCapsule-
> mask.hdr -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --stop=/
> Volumes/Clinical/homes/tyanagihara/sweat/DTI/mask-dump/target1-
> mask.hdr --forcedir --opd -s
>
> This is the error I get when running from the GUI:
> usage: at [-q x] [-f file] [-m] time
> at -c job [job ...]
> at [-f file] -t [[CC]YY]MMDDhhmm[.SS]
> at -r job [job ...]
> at -l -q queuename
> at -l [job ...]
> atq [-q x] [-v]
> atrm job [job ...]
> batch [-f file] [-m]
> usage: at [-q x] [-f file] [-m] time
> at -c job [job ...]
> at [-f file] -t [[CC]YY]MMDDhhmm[.SS]
> at -r job [job ...]
> at -l -q queuename
> at -l [job ...]
> atq [-q x] [-v]
> atrm job [job ...]
> batch [-f file] [-m]
> while executing
> "exec batch -q long.q ${filebase}_script.sh"
> ("probtrackx" arm line 144)
> invoked from within
> "switch -- $probtrack(tool) {
> eddy_current {
> global eddy
>
> set errorStr ""
> if { $eddy(input) == "" } { set errorStr "You need to specify..."
> (procedure "fdt:apply" line 5)
> invoked from within
> "fdt:apply .fdt keep"
> invoked from within
> ".fdt.apply invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .fdt.apply"
> (command bound to event)
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