Submit job but command not found

#1

Hi,

I submit Abaqus job but I have error message :

/var/spool/pbs/mom_priv/jobs/89.centos7-1.SC: ligne7: abq6145 : command not found

Below my job file :

#PBS -l ncpus=2
#PBS -q qabaqus
#PBS -N abaq6145

cd /home/nekcorp/Work/Abaqus/LinearBuckling
abq6145 job=Linear_Buckling input=/home/nekcorp/Work/Abaqus/LinearBuckling/Linear_Buckling.inp interactive

When I launch this command into my terminal without use qsub command all it is ok and abq6145 is correct command.

I have launch this job last week and everything was good.

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#2

Please try to use absolute paths in the PBS Scripts and also makes sure you reference the #!/bin/bash at the top. This is related to the PATH variable and shell interpreter. Run dos2unix on the script before submitting the job.

Use the absolute path to the abq6145 executable in the script and submit the job.

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#3

Thank you for awnser.

I have added #!/bin/bash at the begining of my job file and the absolute path all it is OK, but I would like understand why without absolute path the command it not correct ?

I have into my .bashrc the absolute path of Abaqus command and all alias works into my terminal.

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#4

The environment variables on the compute node with respect to the user are not loaded.
You have to manually set using -v or using -V ( not recommended if the user environment has too much text)

Check man qsub and search for -V (capital V ) and -v (lower case v)

-V Declares that all environment variables and shell functions in the user’s login environment where qsub is run are to be exported to the job. The job’s Variable_List attribute is appended with all of these environment variables and their values.

-v variable_list
Lists environment variables and shell functions to be exported to the job. This is the list of environment variables which is added to those already automatically exported. These variables exist in the user’s login environment from which qsub is run. The job’s Variable_List attribute is appended with the variables in user_list and their values.

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#5

Excuse me but what do you mean about

Check man qsub and search for -V (capital V ) and -v (lower case v)

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#6

I have mentioned them above
-V Declares that all environment variables and shell functions in the user’s login environment where qsub is run are to be exported to the job. The job’s Variable_List attribute is appended with all of these environment variables and their values.

-v variable_list
Lists environment variables and shell functions to be exported to the job. This is the list of environment variables which is added to those already automatically exported. These variables exist in the user’s login environment from which qsub is run. The job’s Variable_List attribute is appended with the variables in user_list and their values.

Also, you can run man qsub and find details about these qsub arguments

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