bash script command not found - command correctly implemented

Question

I wrote a bash script and i got these message:

/home/myname/documents/myscripts/run_tearingmode.sh: line 44: mpirun2: command not found:

Here the relevant part of the script

if [[ "$run_jobs" == "y" ]]
 then
 printf "The jobs run one after the other. Have fun with the analysis. \n "
 for ((i=1;i<=$number_subfolders;i++))
  do
  sub_folder=${main_folder}_$i
  cd
  cd gkw/run/${main_folder}/$sub_folder #change into certain subfold
  pwd
  mpirun2 -np 8 ./gkw_btppx-gnu-DP_3481.x  #run on all 8 frames #line 44 Here is the problem 
  cd
 done
fi

My problem is, that when i type in the line as just a command in the certain folder, the programm runs correctly. This shows to me that i implemented it correctly. With pwd i also know that i am in the right folder. I didn't found out where i made the mistake. Do i need a certain bracket or equivalent things in a script for running a program? I also deleted the blank in front of the command, but nothing changed. What is wrong/missing?

EDIT: The problem was, that you can't run an alias from bashrc in such a script. So i added:

mpirun2='/Path/to/mpirun'

to my script and changed the command in the script to:

"$mpirun2" -np 8 ./gkw_btppx-gnu-DP_3481.x  #run on all 8 frames

This works. Thanks a lot. (I unfortunately can't write this answer myself as a starter :) )

Check the value of the PATH environment variable when your script is run (i.e. echo $PATH). Specifying the full path to mpirun2 should help. — Stefan Näwe
– Stefan Näwe, Commented Oct 10, 2013 at 13:39

LMC · Accepted Answer · 2013-10-10 13:36:17Z

1

If mpirun2 is not on the user's PATH ('which -a' will return nothing). You must invoke it using full path to it:

/full/path/to/mpirun2 -np 8 ./gkw_btppx-gnu-DP_3481.x

answered Oct 10, 2013 at 13:36

LMC

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Comments

zzeroo · Accepted Answer · 2013-10-10 17:33:14Z

1

I think if you add a shebang on top of your script

#/usr/bin/env bash

and the full path to your executable (this command shows it which mpirun2) this should work.

edited Oct 10, 2013 at 17:33

answered Oct 10, 2013 at 13:19

zzeroo

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2 Comments

user2867054 Over a year ago

I do have #!/bin/bash at the beginning of my script. Until i want to start the programm, my script runs well. I also have named the mpirun2 as an alias in the bashcr alias mpirun2='/home/myname/mpich2/bin/mpirun' .What is the acutal path of that folder?

chepner Over a year ago

Your alias is not available in your script. Instead of an alias, add this to your .profile or .bash_profile (not .bashrc): PATH="/home/myname/mpich2/bin/mpirun:$PATH".

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