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Hi Michael,<br>
good your back from holiday ;) Here's the thread history.<br>
Cheers<br>
Stefan<br>
<br>
<br>
-> MESSAGE 1.<br>
Dear list,<br>
have installed a fresh Debian (debian-6.0.5-amd64) system + fsl and <br>
condor from the neurodebian repository. Ran fsl-feeds (i.e. <br>
fsl-selftest) without problems - though running parallelized FDT or
FEAT <br>
actually leads to longer processing times in comparison to setting <br>
FSLPARALLEL=0 (I think this is something Bertram Walter pointed out
some <br>
time ago (<a
href="http://web.archiveorange.com/archive/v/FQvMCazdbKoptd7PgAqu">http://web.archiveorange.com/archive/v/FQvMCazdbKoptd7PgAqu</a>)
<br>
-> there has been, however, no solution posted on the list...<br>
Here's the real problem: tbss_reg_2 -n invokes condor, but terminates <br>
(within a minute or so) without having done calculations. See the <br>
exerpts below.<br>
<br>
<br>
<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">stefan
at gehirne</a>:~$ condor_q<br>
<br>
-- Submitter: : <127.0.0.1:39795> : gehirne.fritz.box<br>
ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD<br>
44.140 stefan 5/15 08:06 0+00:00:00 R 0 0.1 sh <br>
/home/stefan/st<br>
44.141 stefan 5/15 08:06 0+00:00:00 R 0 0.1 sh <br>
/home/stefan/st<br>
44.142 stefan 5/15 08:06 0+00:00:00 R 0 0.1 sh <br>
/home/stefan/st<br>
44.143 stefan 5/15 08:06 0+00:00:00 R 0 0.1 sh <br>
/home/stefan/st<br>
[...]<br>
<br>
<br>
<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">stefan
at gehirne</a>:~$ condor_status<br>
<br>
Name OpSys Arch State Activity LoadAv Mem <br>
ActvtyTime<br>
<br>
<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">slot1
at gehirne.frit</a> LINUX X86_64 Claimed Busy 0.000 2001 <br>
0+00:00:01<br>
<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">slot2
at gehirne.frit</a> LINUX X86_64 Claimed Busy 0.000 2001 <br>
0+00:00:02<br>
<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">slot3
at gehirne.frit</a> LINUX X86_64 Claimed Busy 0.000 2001 <br>
0+00:00:01<br>
<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">slot4
at gehirne.frit</a> LINUX X86_64 Claimed Busy 0.510 2001 <br>
0+00:00:01<br>
Total Owner Claimed Unclaimed Matched Preempting <br>
Backfill<br>
<br>
X86_64/LINUX 4 0 4 0 0 <br>
0 0<br>
<br>
Total 4 0 4 0 0 <br>
0 0<br>
<br>
<br>
All the file operations are done - the log files in the /FA/tbss_logs <br>
directory all say "sed: can't read .commands: No such file or directory"<br>
Contrary to the instructions page <br>
(<a
href="http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html?highlight=fsl%20condor">http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html?highlight=fsl%20condor</a>)
<br>
I notice that I'm not the owner of the slots (no idea if this is of any
<br>
relevance...).<br>
<br>
Any ideas?<br>
<br>
Cheers<br>
<br>
Stefan<br>
<br>
<br>
<br>
-> MESSAGE 2.<br>
Sorry for the html-gibberish in the previous mail - here's another <br>
attempt...<br>
<br>
<br>
<br>
> Ahhhhhhhhhh! I think you just solved Bertrams problem!! Replying
in that<br>
> thread.<br>
<br>
Well glad I could help...<br>
<br>
<br>
<br>
> This looks all good. Could you post the output of<br>
><br>
> condor_q -l 44.140<br>
><br>
> so we can see what it is trying to run. From the cluster ID it
seems<br>
> that this is an actual TBBS analisys, not the FEEDS test, right?
Getting<br>
> some more details might shed some light.<br>
<br>
OK -><br>
<br>
<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">stefan
at gehirne</a>:~$ condor_q -l 45.399<br>
<br>
-- Submitter: gehirne.fritz.box : <127.0.0.1:46801> :
gehirne.fritz.box<br>
BufferSize = 524288<br>
NiceUser = false<br>
CoreSize = 0<br>
CumulativeSlotTime = 0<br>
OnExitHold = false<br>
GlobalJobId = "gehirne.fritz.box#45.399#1337110950"<br>
RequestCpus = 1<br>
Err = "tbss_logs/tbss_2_reg.e45.400"<br>
BufferBlockSize = 32768<br>
ImageSize = 125<br>
CurrentTime = time()<br>
WantCheckpoint = false<br>
CommittedTime = 0<br>
TargetType = "Machine"<br>
WhenToTransferOutput = "ON_EXIT"<br>
ServerTime = 1337110979<br>
Cmd = "/bin/sh"<br>
JobUniverse = 5<br>
ExitBySignal = false<br>
TransferIn = false<br>
Iwd = "/home/stefan/studies/tbss_-n/FA"<br>
NumRestarts = 0<br>
CommittedSuspensionTime = 0<br>
Owner = "stefan"<br>
NumSystemHolds = 0<br>
CumulativeSuspensionTime = 0<br>
Environment = <br>
"PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/fsl/4.1
<br>
XDG_SESSION_COOKIE=98f228034f053963585a8d1100000008-1337108340.39690-977355352
<br>
LD_LIBRARY_PATH=/usr/lib/fsl/4.1 FSLTCLSH=/usr/bin/tclsh
LANG=en_US.utf8 <br>
COLORTERM=gnome-terminal FSLREMOTECALL= WINDOWPATH=7 <br>
GNOME_KEYRING_CONTROL=/tmp/keyring-TA1iOj <br>
XAUTHORITY=/var/run/gdm3/auth-for-stefan-Zhyelq/database <br>
FSLOUTPUTTYPE=NIFTI_GZ SSH_AUTH_SOCK=/tmp/keyring-TA1iOj/ssh <br>
FSLMULTIFILEQUIT=TRUE <br>
XDG_DATA_DIRS=/usr/share/gnome:/usr/share/gdm/:/usr/local/share/:/usr/share/
<br>
FSLBROWSER=/etc/alternatives/x-www-browser <br>
<a class="moz-txt-link-abbreviated" href="mailto:SESSION_MANAGER=local/gehirne:@/tmp/.ICE-unix/2025,unix/gehirne:/tmp/.ICE-unix/2025">SESSION_MANAGER=local/gehirne:@/tmp/.ICE-unix/2025,unix/gehirne:/tmp/.ICE-unix/2025</a>
<br>
GDM_LANG=en_US.utf8 FSLDIR=/usr/share/fsl/4.1 <br>
ORBIT_SOCKETDIR=/tmp/orbit-stefan FSLPARALLEL=condor SGE_TASK_LAST=400 <br>
SHELL=/bin/bash GNOME_DESKTOP_SESSION_ID=this-is-deprecated <br>
PWD=/home/stefan/studies/tbss_-n/FA _=/usr/lib/fsl/4.1/tbss_2_reg <br>
USERNAME=stefan SGE_TASK_STEPSIZE= WINDOWID=16777219 <br>
FSLWISH=/usr/bin/wish USER=stefan <br>
GTK_RC_FILES=/etc/gtk/gtkrc:/home/stefan/.gtkrc-1.2-gnome2 <br>
DESKTOP_SESSION=default FSLMACHINELIST= FSLLOCKDIR= SHLVL=1 <br>
POSSUMDIR=/usr/share/fsl/4.1 POSIXLY_CORRECT=1 GDMSESSION=default <br>
SGE_TASK_ID=400 HOME=/home/stefan <br>
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-Ovra5yhakV,guid=41b5e4185d4605edca2138e900000021
<br>
TERM=xterm OLDPWD=/home/stefan/studies/tbss_-n SSH_AGENT_PID=2062 <br>
GDM_KEYBOARD_LAYOUT=de' 'nodeadkeys LOGNAME=stefan SGE_TASK_FIRST=1 <br>
DISPLAY=:0.0"<br>
RequestDisk = DiskUsage<br>
Requirements = ( TARGET.Arch == "X86_64" ) && ( TARGET.OpSys ==
"LINUX" <br>
) && ( TARGET.Disk >= RequestDisk ) && (
TARGET.Memory >= RequestMemory <br>
) && ( TARGET.HasFileTransfer )<br>
MinHosts = 1<br>
JobNotification = 0<br>
NumCkpts = 0<br>
LastSuspensionTime = 0<br>
NumJobStarts = 0<br>
WantRemoteSyscalls = false<br>
JobLeaseDuration = 1200<br>
ImageSize_RAW = 102<br>
JobPrio = 0<br>
RootDir = "/"<br>
CurrentHosts = 0<br>
StreamOut = false<br>
WantRemoteIO = true<br>
DiskUsage_RAW = 102<br>
OnExitRemove = true<br>
DiskUsage = 125<br>
In = "/dev/null"<br>
PeriodicRemove = false<br>
RemoteUserCpu = 0.0<br>
LocalUserCpu = 0.0<br>
ExecutableSize = 125<br>
RemoteSysCpu = 0.0<br>
LocalSysCpu = 0.0<br>
ClusterId = 45<br>
CompletionDate = 0<br>
RemoteWallClockTime = 0.0<br>
Rank = 0.0<br>
LeaveJobInQueue = false<br>
MyType = "Job"<br>
CondorVersion = "$CondorVersion: 7.8.0 May 09 2012 <br>
Debian-7.8.0~dfsg.1-1~nd60+1 $"<br>
NumCkpts_RAW = 0<br>
StreamErr = false<br>
ProcId = 399<br>
PeriodicHold = false<br>
User = "<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">stefan
at gehirne.fritz.box</a>"<br>
LastJobStatus = 0<br>
Out = "tbss_logs/tbss_2_reg.o45.400"<br>
JobStatus = 1<br>
ExecutableSize_RAW = 102<br>
PeriodicRelease = false<br>
AutoClusterAttrs = <br>
"JobUniverse,LastCheckpointPlatform,NumCkpts,RemoteGroup,SubmitterGroup,DiskUsage,ImageSize,RequestDisk,RequestMemory,Requirements,NiceUser,ConcurrencyLimits"<br>
Args = "/home/stefan/studies/tbss_-n/FA/tbss_2_reg_qsub.HRdir6mUJNkG1"<br>
RequestMemory = ifthenelse(MemoryUsage =!= undefined,MemoryUsage,( <br>
ImageSize + 1023 ) / 1024)<br>
MaxHosts = 1<br>
TotalSuspensions = 0<br>
CommittedSlotTime = 0<br>
NotifyUser = "<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">stefan
at localhost</a>"<br>
CondorPlatform = "$CondorPlatform: X86_64-Debian_6.0 $"<br>
AutoClusterId = 1<br>
ShouldTransferFiles = "YES"<br>
ExitStatus = 0<br>
QDate = 1337110949<br>
EnteredCurrentStatus = 1337110950<br>
<br>
<br>
<br>
Interestingly: If I run tbss_2_reg -n a second time in the same
terminal <br>
(on a fresh copy of the original data) I get following error without <br>
anything happening.<br>
<br>
<a
href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users">stefan
at gehirne</a>:~/studies/tbss_-n$ tbss_2_reg -n<br>
wc: .commands: No such file or directory<br>
<br>
I wonder what the word count command is doing here?<br>
<br>
<br>
<br>
Cheers<br>
<br>
Stefan<br>
<br>
<br>
<br>
-> MESSAGE 3.<br>
Hi all.<br>
Reinstalled Debian plus tried the process on the neurodebian virtual <br>
machine; no luck, both routes do not lead to success. Any help out
there?<br>
Cheers<br>
Stefan<br>
<br>
<br class="Apple-interchange-newline">
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