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I have an executable file mpiexec, whose full path is ~/petsc-3.2-p6/petsc-arch/bin/mpiexec. Since I want to execute this command in different directories (without having to retype the entire path), I setup an alias in my home .bashrc file:

alias petsc="~/petsc-3.2-p6/petsc-arch/bin/mpiexec"  

which allows me to execute this mpiexec file at the command prompt easily by typing:

petsc myexecutable

I tried to write a shell script file, named script, using my new alias petsc as a command. After giving my shell script the appropriate permissions (using chmod), I tried to run the script. However, it gave me the following error:

./script: line 1: petsc: command not found

I know that I could just write the full path to the mpiexec file, but it is cumbersome to write the full path everytime that I want to write a new script. Is there a way that I can use my alias petsc inside the script file? Is there a way I can edit my .bashrc or .bash_profile to make this happen?

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How about adding the alias to .bash_aliases ? Also how about aliasing the absolute path instead of relative path like alias petsc='/home/user/petsc-3.2-p6/petsc-arch/bin/mpiexec' –  nitstorm Jan 26 '12 at 18:17
@nitstorm: Neither solution seems to work... I still get the same error as before –  Paul Jan 26 '12 at 18:21

4 Answers 4

up vote 17 down vote accepted
  1. In your shell script use the full path rather then an alias.

  2. In your shell script, set a variable, different syntax

    $petsc myexecutable
  3. Use a function in your script. Probably better if petsc is complex

    function petsc () {
        command 1
        command 2
    petsc myexecutable
  4. Source your aliases

    shopt -s expand_aliases
    source /home/your_user/.bashrc

You probably do not want to source your .bashrc, so, IMO, one of the first 3 would be better.

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Point 4 don't work, unless you use shopt -s expand_aliases in the same script. –  enzotib Jan 26 '12 at 18:29
Your suggestion 2) works, but I want to be able to use the same command in multiple shell scripts without having to write the first line petsc="...". Is there a way to do this? –  Paul Jan 26 '12 at 18:31
Sounds as if you should put the command in a more standard location, such as /usr/local/bin –  bodhi.zazen Jan 26 '12 at 18:35
@enzotib - thank you, I added that to my answer. –  bodhi.zazen Jan 26 '12 at 18:36
In the point 2 you do not set an alias but a variable. –  pabouk Nov 1 '14 at 9:58

Alias are deprecated in favor of shell functions. From bash manual page:

For almost every purpose, aliases are superseded by shell functions.

To create a function, and export it to subshells, put the following in your ~/.bashrc:

petsc() {
    ~/petsc-3.2-p6/petsc-arch/bin/mpiexec "$@"
export -f petsc

Then you can freely call your command from your scripts.

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That almost works... the only problem is that I need to be able to pass different flags to the executable "mpiexec"... For instance, I need to be able to execute something like "petsc -n 40 myexecutable" with the alias "petsc" –  Paul Jan 26 '12 at 18:46
@Paul: I added "$@" just to handle arguments. –  enzotib Jan 26 '12 at 19:47

Shell functions and aliases are limited to the shell and do not work in executed shell scripts. Alternatives for your case:

  • (if you do not bother to use mpiexec instead of petsc) Add $HOME/petsc-3.2-p6/petsc-arch/bin to your PATH variable. This can be done by editing ~/.profile and appending:


    Re-login to apply these changes

  • Create the directory ~/bin and

    • make a wrapper script named petsc containing:

      exec ~/petsc-3.2-p6/petsc-arch/bin/mpiexec "$@"
    • if the program allows for it, you can skip the shellscript and make a symlink using the command:

      ln -s ~/petsc-3.2-p6/petsc-arch/bin/mpiexec ~/bin/petsc
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(EDIT: removed functions since I misread calling of mpiexec.)

If the only thing you need is less typing, why don't you just put the folder in $PATH? Or make a symlink to mpiexec from some folder in $PATH? Or (my favourite) put the alias in a script that you source in the calling script?

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The reason why I can't put it into my $PATH is because I have another 'mpiexec' file in another directory that is alredy in my $PATH. If I add the path to this new 'mpiexec', it will probably try to execute both of them... wouldn't it? –  Paul Jan 26 '12 at 19:34
Cannot understand why not simply use "$@". –  enzotib Jan 26 '12 at 19:49
Paul, it'll try to execute the one that's first in the PATH, not both. –  unhammer Jan 27 '12 at 9:41
enzotib, ah I misread the way mpiexec was called, I thought it needed all args as one. Will edit my answer :) –  unhammer Jan 27 '12 at 9:44

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