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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