JISCMail - FSL Archives

On 7 September 2015 at 13:18, mohamad reza khodaei <[log in to unmask]> wrote:

Thanks for your response

I tried ''qstat -j jobID | grep error'' command

[m.khodaei@cluster ~]$ qstat -j 104 | grep error
error reason 1: 09/06/2015 13:56:39 [523:12664]: execvp(/usr/local/fsl/bin/bedpostx_preproc.sh, "/usr/local/fsl/bin/bedpostx_preproc.sh" "/home/m.kh odaei/bio/dti" "0") failed: No such file or directory

I had installed FSL in /usr/local/ directory, is it possible that the problem to be the location of FSL?

Best regards
On Mon, Sep 7, 2015 at 2:30 PM, paul mccarthy <[log in to unmask]> wrote:
Hi Khodaei,

Again, this looks like an SGE configuration issue, so I can't really help. But you should be able to get more information as to why the job is not running if you turn on scheduler job information logging, via the 'schedd_job_info' setting: http://gridscheduler.sourceforge.net/htmlman/htmlman5/sched_conf.html

Cheers,

Paul
On 5 September 2015 at 23:01, mohamad reza khodaei <[log in to unmask]> wrote:
Thanks for your response

Unfortunately our local system administrator is a freshman and he is not familiar with SGE so i have to configure it my self.

I tried 'qstat -j 104' :

[m.khodaei@cluster bio]$ qstat -u m.khodaei
job-ID prior name user state submit/start at queue slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
104 0.55500 bpx_prepro m.khodaei qw 09/05/2015 08:59:08 1
105 0.00000 bedpostx m.khodaei hqw 09/05/2015 08:59:10 1 1-145:1
106 0.00000 bpx_postpr m.khodaei hqw 09/05/2015 08:59:10 1

[m.khodaei@cluster bio]$ qstat -j 104
==============================================================
job_number: 104
exec_file: job_scripts/104
submission_time: Sat Sep 5 08:59:08 2015
owner: m.khodaei
uid: 523
group: m.khodaei
gid: 525
sge_o_home: /home/m.khodaei
sge_o_log_name: m.khodaei
sge_o_path: /opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/bio/wgs/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/maven/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/condor/bin:/opt/condor/sbin:/opt/gridengine/bin/linux-x64:/usr/local/fsl/bin:/usr/local/fsl:/home/m.khodaei/bin
sge_o_shell: /bin/bash
sge_o_workdir: /home/m.khodaei/bio
sge_o_host: cluster
account: sge
cwd: /home/m.khodaei/bio
stderr_path_list: NONE:NONE:/home/m.khodaei/bio/dti.bedpostX/logs
mail_options: as
mail_list: [log in to unmask]
notify: FALSE
job_name: bpx_preproc
stdout_path_list: NONE:NONE:/home/m.khodaei/bio/dti.bedpostX/logs
jobshare: 0
restart: y
env_list: PDSHROOT=/opt/pdsh,BIOROLL=/opt/bio,HOSTNAME=********,TERM=xterm,SHELL=/bin/bash,ECLIPSE_HOME=/opt/eclipse,HISTSIZE=1000,CONDOR_IDS=407.407,HMMER_DB=/home/m.khodaei/bio/hmmer/db,SSH_CLIENT=********* 2222,FSLMULTIFILEQUIT=TRUE,SGE_CELL=default,SGE_ARCH=linux-x64,MPICH_PROCESS_GROUP=no,QTDIR=/usr/lib64/qt-3.3,QTINC=/usr/lib64/qt-3.3/include,ROCKSROOT=/opt/rocks/share/devel,SSH_TTY=/dev/pts/1,ANT_HOME=/opt/rocks,LC_ALL=C,USER=m.khodaei,LD_LIBRARY_PATH=/opt/gridengine/lib/linux-x64:/opt/openmpi/lib,LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.tbz=01;31:*.tbz2=01;31:*.bz=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:,FSLGECUDAQ=cuda.q,ROCKS_ROOT=/opt/rocks,POSIXLY_CORRECT=y,MAVEN_HOME=/opt/maven,MAIL=/var/spool/mail/m.khodaei,PATH=/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/bio/wgs/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/maven/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/condor/bin:/opt/condor/sbin:/opt/gridengine/bin/linux-x64:/usr/local/fsl/bin:/usr/local/fsl:/home/m.khodaei/bin,CONDOR_CONFIG=/opt/condor/etc/condor_config,PWD=/home/m.khodaei/bio,_LMFILES_=/usr/share/Modules/modulefiles/rocks-openmpi,JAVA_HOME=/usr/java/latest,SGE_EXECD_PORT=537,LANG=en_US.iso885915,FSLTCLSH=/usr/local/fsl/bin/fsltclsh,SGE_QMASTER_PORT=536,MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles,FSLMACHINELIST=NONE,SGE_ROOT=/opt/gridengine,CONDOR_ROOT=/opt/condor,LOADEDMODULES=rocks-openmpi,BLASTDB=/home/m.khodaei/bio/ncbi/db,FSLREMOTECALL=NONE,FSLWISH=/usr/local/fsl/bin/fslwish,SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass,HISTCONTROL=ignoredups,SHLVL=2,HOME=/home/m.khodaei,ROLLSROOT=/opt/rocks/share/devel/src/roll,MPIHOME=/opt/openmpi,LOGNAME=m.khodaei,FSLDIR=/usr/local/fsl,QTLIB=/usr/lib64/qt-3.3/lib,CVS_RSH=ssh,SSH_CONNECTION=172.16.46.3 59591 172.16.46.9 2222,MODULESHOME=/usr/share/Modules,LESSOPEN=|/usr/bin/lesspipe.sh %s,FSLSUBALREADYRUN=true,BLASTMAT=/opt/bio/ncbi/data,FSLLOCKDIR=NONE,FSLOUTPUTTYPE=NIFTI_GZ,OMPI_MCA_btl=tcp,self,G_BROKEN_FILENAMES=1
job_args: /home/m.khodaei/bio/dti,0
script_file: /usr/local/fsl/bin/bedpostx_preproc.sh
jid_successor_list: 105
scheduling info: (Collecting of scheduler job information is turned off)

================================================================

Any idea?

Best regards
On Sat, Sep 5, 2015 at 3:18 PM, mohamad reza khodaei <[log in to unmask]> wrote:
Thanks for your response

Unfortunately our local system administrator is a freshman and he is not familiar with SGE so i have to configure it my self.

I tried 'qstat -j 89' and i attached the outputs.

Any idea?

Best regards
On Thu, Sep 3, 2015 at 2:08 PM, paul mccarthy <[log in to unmask]> wrote:
Hi Khodaei,

This looks like a SGE configuration issue - you may want to talk to your local system administrator.

In the meantime, could you run 'qstat -j 89', to see the state of bpx_preproc?

Cheers,

Paul

--
Mohammad Reza Khodaei M.Sc. student of Biomedical Engineering, School of medicine, Shahid Beheshti university, Tehran, Iran
--
Mohammad Reza Khodaei M.Sc. student of Biomedical Engineering, School of medicine, Shahid Beheshti university, Tehran, Iran
--
Mohammad Reza Khodaei
M.Sc. student of Biomedical Engineering,
School of medicine, 
Shahid Beheshti university,
Tehran, Iran