[torqueusers] How to catch PBS environment variables in executing time

Hong, Xin xinhong at indiana.edu
Tue Jul 8 03:57:00 MDT 2008


Hello Groups,

We are converting a shell script that generates Loadleveler submit scripts to PBS. I found all the environment variables during the executing time are missed, although I still can successfully submit and run the job. For example, $PBS_O_JOBID only can be caught within a PBS submission script itself, or can be print out during executing time, but cannot be caught in the script that generates the PBS script.

Here is the script and a example output.

xinhong at BigRed:/N/soft/linux-rhel4-x86_64/local-utils/bin> more serialjob4
#! /bin/bash
......omit part that catch parameters from command line......
source quoteargs
                                        # get program options from command line
quoteSOMEcmd "$WANTED" "$@"

## 2006-10-06: Temporary fix -- using account_no = NONE for now -AG
## 2006-11-08: Added account_no and wallclock parameters -AG
cat <<EOJ | qsub -
#!/bin/bash -l
#PBS -l nodes=1:ppn=1,walltime=00:03:00
#PBS -o $JOBNAME.out.$PBS_JOBID
#PBS -e $JOBNAME.err.$PBS_JOBID
#PBS -N $JOBNAME
#PBS -V

printenv
echo PWD
pwd
echo $PBS_O_WORKDIR
echo "PBS_JOBID!!!!!!!!!$PBS_JOBID@@@@@ $SCRIPTNAME"
echo $PBS_O_WORKDIR
echo $PBS_JOBNAME
echo $PBS_JOBID
echo $PBS_O_HOME
echo $PBS_O_LOGNAME
echo $PBS_O_MAIL
echo `pwd`
$QARGS

EOJ


xinhong at Quarry: ~/test> more sj4.out.
LPATH=
MANPATH=/N/soft/linux-rhel4-x86_64/intel/cce/10.0.025/man:/N/soft/linux-rhel4-x86_64/intel/fce/10.0.025/man:/N/soft/linux-rhe
l4-x86_64/openmpi-1.2.3/man:/N/u/xinhong/Quarry/man:/usr/local/man:/usr/share/man:/usr/X11R6/man:/usr/kerberos/man:/N/soft/li
nux-rhel4-x86_64/softenv-1.6.2/man:/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/man:/N/soft/linux-rhel4-x86_64/intel/fce/10.
1.013/man:/N/soft/linux-rhel4-x86_64/intel/idbe/10.1.013/man:/N/soft/linux-rhel4-x86_64/local-utils/man:/N/soft/linux-rhel4-x
86_64/nano-1.2.5/man:/N/soft/linux-rhel4-x86_64/moab-5.1.0/man
HOSTNAME=b029
SHELL=/bin/bash
TERM=xterm
MATLABPATH=
HISTSIZE=1000
SSH_CLIENT=::ffff:156.56.195.18 2030 22
PBS_JOBNAME=sj4
PERL5LIB=/N/soft/linux-rhel4-x86_64/perl5/5.8.5/lib:/N/soft/linux-rhel4-x86_64/perl5/5.8.5/lib/x86_64-linux-thread-multi:/usr
/lib/perl5/5.8.3/ppc-linux-thread-multi:/usr/lib/perl5/5.8.3:/usr/lib/perl5/site_perl/.8.3/ppc-linux-thread-multi:/usr/lib/pe
rl5/site_perl/5.8.3:/usr/lib/perl5/site_perl:/usr/lib/perl5/vendor_perl/5.8.3/ppc-linux-thread-multi:/usr/lib/perl5/vendor_pe
rl/5.8.3:/usr/lib/perl5/vendor_perl
FPATH=
PBS_ENVIRONMENT=PBS_BATCH
PBS_O_WORKDIR=/N/u/xinhong/Quarry/test
SSH_TTY=/dev/pts/2
GTHDATADIR=/N/gpfsbr/xinhong/build/gth-1.0.4-Linux_x86-64-32bit/gthdata
USER=xinhong
PBS_TASKNUM=1
LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cm
d=01;32:*.exe=01;32:*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;3
1:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio=01;31:*.jpg=01;
35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png=01;35:*.tif=01;35:
LD_LIBRARY_PATH=/N/soft/linux-rhel4-x86_64/intel/cce/10.0.025/lib:/N/soft/linux-rhel4-x86_64/intel/fce/10.0.025/lib:/N/soft/l
inux-rhel4-x86_64/openmpi-1.2.3/lib:/N/soft/linux-rhel4-x86_64/openmpi-1.2.3/lib/openmpi:/N/soft/linux-rhel4-x86_64/intel/cce
/10.1.013/lib:/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/lib:/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64/lib
PBS_O_HOME=/N/u/xinhong/Quarry
CPATH=/N/soft/linux-rhel4-x86_64/openmpi-1.2.3/include
PBS_MOMPORT=15003
PBS_O_QUEUE=batch
PATH=/N/u/xinhong/Quarry/bin/x86_64:/N/gpfsbr/xinhong/build/gth-1.0.4-Linux_x86_64-32bit/bin:/N/soft/linux-rhel4-x86_64/intel
/cce/10.0.025/bin:/N/soft/linux-rhel4-x86_64/intel/fce/10.0.025/bin:/N/soft/linux-rhel4-x86_64/openmpi-1.2.3/bin:/N/u/xinhong
/Quarry/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/kerberos/bin:/N/soft/linux-rhel4-x86_64/softenv-1.6.2/bin:/N/sof
t/linux-rhel4-x86_64/intel/cce/10.1.013/bin:/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin:/N/soft/linux-rhel4-x86_64/inte
l/idbe/10.1.013/bin:/N/soft/linux-rhel4-x86_64/local-utils/bin:/N/soft/linux-rhel4-x86_64/nano-1.2.5/bin:/N/soft/linux-rhel4-
x86_64/moab-5.1.0/bin:/N/soft/linux-rhel4-x86_64/moab-5.1.0/sbin:/N/soft/linux-rhel4-x86_64/mpiblast-1.5.0-pio-openmpi/bin:/N
/u/xinhong/Quarry/bin
PBS_O_LOGNAME=xinhong
MAIL=/var/spool/mail/xinhong
PBS_JOBCOOKIE=2F6587B62B7A2B886D632B2EB4668F72
XARCH=x86_64
SOFTENV_ALIASES=/N/soft/linux-rhel4-x86_64/softenv-1.6.2/etc/softenv-aliases.sh
LD_RUN_PATH=
PWD=/N/hd01/xinhong/Quarry
INPUTRC=/etc/inputrc
PBS_NODENUM=0
WHATAMI=linux-rhel4-x86_64
PBS_O_SHELL=/bin/bash
PBS_SERVER=b001
LM_LICENSE_FILE=
PBS_JOBID=443570.qm2
KRB5CCNAME=FILE:/tmp/krb5cc_52816_7Wp8dF
ENVIRONMENT=BATCH
SOFTENV_LOAD=/N/soft/linux-rhel4-x86_64/softenv-1.6.2/etc/softenv-load.sh
TEXINPUTS=
HOME=/N/u/xinhong/Quarry
SHLVL=4
PBS_DEFAULT=m2
PBS_O_HOST=b001
IDL_PATH=
PBS_VNODENUM=0
LOGNAME=xinhong
MACHTYPE=x86_64
PYTHONPATH=
MPIBLAST_RUN=/N/soft/linux-rhel4-x86_64/openmpi-1.2.3/bin/mpiexec
SSH_CONNECTION=::ffff:156.56.195.18 2030 ::ffff:149.165.230.1 22
PBS_QUEUE=serial
PBS_O_MAIL=/var/spool/mail/xinhong
LESSOPEN=|/usr/bin/lesspipe.sh %s
ARCH=linux-rhel4-x86_64
INFOPATH=/N/soft/linux-rhel4-x86_64/local-utils/info
SIDL_DLL_PATH=
G_BROKEN_FILENAMES=1
BSSMDIR=/N/gpfsbr/xinhong/build/gth-1.0.4-Linux_x86-64-32bit/bssm
PBS_NODEFILE=/var/spool/torque/aux//443570.qm2
PBS_O_PATH=/N/u/xinhong/Quarry/bin/x86_64:/N/gpfsbr/xinhong/build/gth-1.0.4-Linux_x86_64-32bit/bin:/N/soft/linux-rhel4-x86_64
/intel/cce/10.0.025/bin:/N/soft/linux-rhel4-x86_64/intel/fce/10.0.025/bin:/N/soft/linux-rhel4-x86_64/openmpi-1.2.3/bin:/N/u/x
inhong/Quarry/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/kerberos/bin:/N/soft/linux-rhel4-x86_64/softenv-1.6.2/bin:
/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin:/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin:/N/soft/linux-rhel4-x86_6
4/intel/idbe/10.1.013/bin:/N/soft/linux-rhel4-x86_64/local-utils/bin:/N/soft/linux-rhel4-x86_64/nano-1.2.5/bin:/N/soft/linux-
rhel4-x86_64/moab-5.1.0/bin:/N/soft/linux-rhel4-x86_64/moab-5.1.0/sbin:/N/soft/linux-rhel4-x86_64/mpiblast-1.5.0-pio-openmpi/
bin:/N/u/xinhong/Quarry/bin
_=/usr/bin/printenv
PWD
/N/hd01/xinhong/Quarry

PBS_JOBID!!!!!!!!!@@@@@ serialjob4






/N/u/xinhong/Quarry/test
hello world!
bye

Any suggestion are highly appreciated.

Xin




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