thanks merry,
that was it, we are able to submit the probtrack jobs fine now.
just a few more types of jobs to test.
-lokke
On Oct 10, 2007, at 2:57 PM, Merry Mani wrote:
> 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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