Hi,
I had the same problem on OS X too. I showed it to my system
administrator and he modified the fdt.tcl by changing the "exec batch
-q all.q ${filebase}_script.sh" to "exec qsub -q all.q ${filebase}
_script.sh". Now it works fine for me.
-Merry
On Oct 10, 2007, at 2:36 PM, Lokke Highstein wrote:
> hi matthew,
>
> we don't have a long.q (or a short.q, veryshort.q, or verylong.q)
> we only are currently using the all.q
>
> so i went and changed all the references to "long.q" in the fdt.tcl
> file and edited them to all.q instead. i think that is what you
> are getting at. if you were suggesting that i remove any
> references to long.q by commenting out the whole line, i can do
> that but it seems like it would guarantee that the job wouldn't get
> submitted to the cluster then.
>
> unfortunately changing that didn't help with the GUI error, and
> even under command line use, the job still just ran on the head
> node (didn't get submitted to the SGE)
>
> here's the error output 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 all.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)
>
> On Oct 10, 2007, at 6:42 AM, Matthew Webster wrote:
>
>> 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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