[Neurodebian-users] condor and fsl: again

Wed May 16 06:03:06 UTC 2012

Sorry for the html-gibberish in the previous mail - here's another 
attempt...

 > Ahhhhhhhhhh! I think you just solved Bertrams problem!! Replying in that
 > thread.

Well glad I could help...

 > This looks all good. Could you post the output of
 >
 > condor_q -l 44.140
 >
 > so we can see what it is trying to run. From the cluster ID it seems
 > that this is an actual TBBS analisys, not the FEEDS test, right? Getting
 > some more details might shed some light.

OK ->

stefan at gehirne:~$ condor_q -l 45.399

-- Submitter: gehirne.fritz.box : <127.0.0.1:46801> : gehirne.fritz.box
BufferSize = 524288
NiceUser = false
CoreSize = 0
CumulativeSlotTime = 0
OnExitHold = false
GlobalJobId = "gehirne.fritz.box#45.399#1337110950"
RequestCpus = 1
Err = "tbss_logs/tbss_2_reg.e45.400"
BufferBlockSize = 32768
ImageSize = 125
CurrentTime = time()
WantCheckpoint = false
CommittedTime = 0
TargetType = "Machine"
WhenToTransferOutput = "ON_EXIT"
ServerTime = 1337110979
Cmd = "/bin/sh"
JobUniverse = 5
ExitBySignal = false
TransferIn = false
Iwd = "/home/stefan/studies/tbss_-n/FA"
NumRestarts = 0
CommittedSuspensionTime = 0
Owner = "stefan"
NumSystemHolds = 0
CumulativeSuspensionTime = 0
Environment = 
"PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/fsl/4.1 
XDG_SESSION_COOKIE=98f228034f053963585a8d1100000008-1337108340.39690-977355352 
LD_LIBRARY_PATH=/usr/lib/fsl/4.1 FSLTCLSH=/usr/bin/tclsh LANG=en_US.utf8 
COLORTERM=gnome-terminal FSLREMOTECALL= WINDOWPATH=7 
GNOME_KEYRING_CONTROL=/tmp/keyring-TA1iOj 
XAUTHORITY=/var/run/gdm3/auth-for-stefan-Zhyelq/database 
FSLOUTPUTTYPE=NIFTI_GZ SSH_AUTH_SOCK=/tmp/keyring-TA1iOj/ssh 
FSLMULTIFILEQUIT=TRUE 
XDG_DATA_DIRS=/usr/share/gnome:/usr/share/gdm/:/usr/local/share/:/usr/share/ 
FSLBROWSER=/etc/alternatives/x-www-browser 
SESSION_MANAGER=local/gehirne:@/tmp/.ICE-unix/2025,unix/gehirne:/tmp/.ICE-unix/2025 
GDM_LANG=en_US.utf8 FSLDIR=/usr/share/fsl/4.1 
ORBIT_SOCKETDIR=/tmp/orbit-stefan FSLPARALLEL=condor SGE_TASK_LAST=400 
SHELL=/bin/bash GNOME_DESKTOP_SESSION_ID=this-is-deprecated 
PWD=/home/stefan/studies/tbss_-n/FA _=/usr/lib/fsl/4.1/tbss_2_reg 
USERNAME=stefan SGE_TASK_STEPSIZE= WINDOWID=16777219 
FSLWISH=/usr/bin/wish USER=stefan 
GTK_RC_FILES=/etc/gtk/gtkrc:/home/stefan/.gtkrc-1.2-gnome2 
DESKTOP_SESSION=default FSLMACHINELIST= FSLLOCKDIR= SHLVL=1 
POSSUMDIR=/usr/share/fsl/4.1 POSIXLY_CORRECT=1 GDMSESSION=default 
SGE_TASK_ID=400 HOME=/home/stefan 
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-Ovra5yhakV,guid=41b5e4185d4605edca2138e900000021 
TERM=xterm OLDPWD=/home/stefan/studies/tbss_-n SSH_AGENT_PID=2062 
GDM_KEYBOARD_LAYOUT=de' 'nodeadkeys LOGNAME=stefan SGE_TASK_FIRST=1 
DISPLAY=:0.0"
RequestDisk = DiskUsage
Requirements = ( TARGET.Arch == "X86_64" ) && ( TARGET.OpSys == "LINUX" 
) && ( TARGET.Disk >= RequestDisk ) && ( TARGET.Memory >= RequestMemory 
) && ( TARGET.HasFileTransfer )
MinHosts = 1
JobNotification = 0
NumCkpts = 0
LastSuspensionTime = 0
NumJobStarts = 0
WantRemoteSyscalls = false
JobLeaseDuration = 1200
ImageSize_RAW = 102
JobPrio = 0
RootDir = "/"
CurrentHosts = 0
StreamOut = false
WantRemoteIO = true
DiskUsage_RAW = 102
OnExitRemove = true
DiskUsage = 125
In = "/dev/null"
PeriodicRemove = false
RemoteUserCpu = 0.0
LocalUserCpu = 0.0
ExecutableSize = 125
RemoteSysCpu = 0.0
LocalSysCpu = 0.0
ClusterId = 45
CompletionDate = 0
RemoteWallClockTime = 0.0
Rank = 0.0
LeaveJobInQueue = false
MyType = "Job"
CondorVersion = "$CondorVersion: 7.8.0 May 09 2012 
Debian-7.8.0~dfsg.1-1~nd60+1 $"
NumCkpts_RAW = 0
StreamErr = false
ProcId = 399
PeriodicHold = false
User = "stefan at gehirne.fritz.box"
LastJobStatus = 0
Out = "tbss_logs/tbss_2_reg.o45.400"
JobStatus = 1
ExecutableSize_RAW = 102
PeriodicRelease = false
AutoClusterAttrs = 
"JobUniverse,LastCheckpointPlatform,NumCkpts,RemoteGroup,SubmitterGroup,DiskUsage,ImageSize,RequestDisk,RequestMemory,Requirements,NiceUser,ConcurrencyLimits"
Args = "/home/stefan/studies/tbss_-n/FA/tbss_2_reg_qsub.HRdir6mUJNkG1"
RequestMemory = ifthenelse(MemoryUsage =!= undefined,MemoryUsage,( 
ImageSize + 1023 ) / 1024)
MaxHosts = 1
TotalSuspensions = 0
CommittedSlotTime = 0
NotifyUser = "stefan at localhost"
CondorPlatform = "$CondorPlatform: X86_64-Debian_6.0 $"
AutoClusterId = 1
ShouldTransferFiles = "YES"
ExitStatus = 0
QDate = 1337110949
EnteredCurrentStatus = 1337110950

Interestingly: If I run tbss_2_reg -n a second time in the same terminal 
(on a fresh copy of the original data) I get following  error without 
anything happening.

stefan at gehirne:~/studies/tbss_-n$ tbss_2_reg -n
wc: .commands: No such file or directory

I wonder what the word count command is doing here?

Cheers

Stefan