Built in shell command not working

Users/Site Administrators
1

Hi

I’m new to pbs and coming from SGE.
I’m trying to use the source command when I submit jobs and I get error message:
pbs_mom, exec of source failed with error: No such file or directory
I understand it related some how to that its built in shell commands and don’t have real path on the system, there is any option to use the source command?

2

Please share your script.
source command or . should work when used in a script.

3

something like that not working:

  1. qsub -q servers_q -V – source /home/chagai/test.sh
  2. qsub -q servers_q -V – echo 1

~> cat STDIN.e244
pbs_mom, exec of source failed with error: No such file or directory
~> cat STDIN.e245
pbs_mom, exec of echo failed with error: No such file or directory

4

~> qrsh -q servers.q echo 1 SUNGRID
1
~> qsub -I -q servers_q -V – echo 1 PBS
qsub: waiting for job 280.pbs-ce7 to start
qsub: job 280.pbs-ce7 ready

qsub: job 280.pbs-ce7 completed

why the output not goes to the screen like in qrsh?

5

Please try this:

qsub -q servers_q -V -- /bin/hostname

echo "hello" | qsub -V -q servers_q

Please check the standard out and error files created

qsub -q server_q -V -I  
Once you get a remote console of the compute node 
echo "hello"
exit to come out of the interactive job

Please check the man page for qsub

6

~> qsub -q servers_q -V – /bin/hostname – working fine
298.pbs-ce7
~> cat STDIN.o298
n001-srv-ce7
2.
~> echo “hello” | qsub -V -q servers_q
~> cat STDIN.e299
Usage: grep [OPTION]… PATTERN [FILE]…
Try ‘grep --help’ for more information.
/var/spool/pbs/mom_priv/jobs/299.pbs-ce7.SC: line 1: hello: command not found
~> cat STDIN.o299
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
3. its working

The problem only with built in shell commands, it can be related to installation?

7

Please try this

make sure /home/chagai/test.sh has executable permissions and is available across all the compute nodes in the same location. ( chmod +x /home/chagai/test.sh)

qsug -q servers_q -V -- /home/chagai/test.sh

qsub -V -q servers_q -- /bin/echo "hello"

8

First of all big thx for all support!!
qsub -V -q servers_q – /bin/echo “hello” → with executable permissions its working
qsub -V -q servers_q – /bin/echo “hello” → working too

what about source command something like this (before we loading some tool in interactive job, we need to source some file):
qsub -V -q servers_q – “source /home/chagain/tool.sh;tool” → not working
in SGE that’s what i used:
qrsh -q servers.q -V -cwd “source /home/chagain/tool.sh;tool”

9

You can try this

qsub -V   -q servers_q   <press return>
source /home/chagain/tool.sh
tool
<cttr>+d
10

it possible to work in one line? and not with multiple actions

11

Hi thx for all help I found a solution