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Subject: Re: [OMPI users] ompi + bash + GE + modules
From: Reuti (reuti_at_[hidden])
Date: 2012-01-11 13:51:23


Hi,

Am 11.01.2012 um 19:12 schrieb Mark Suhovecky:

> Edmund-
>
> Yeah, I've tried that. No difference. Our template .bash_profile sources
> the user's .bashrc, so non-interactive bash shells in our setup are sourcing .bashrc.

SGE 6.2u5 can't handle multi line environment variables or functions, it was fixed in 6.2u6 which isn't free. Do you use -V while submitting the job? Just ignore the error or look into Son of Gridengine which fixed it too.

If you can avoid -V, then it could be defined in any of the .profile or alike if you use -l as suggested. You could even define a started_method in SGE to define it for all users by default and avoid to use -V:

#!/bin/sh
module() { ...command...here... }
export -f module
exec "${@}"

-- Reuti

> The modules environment is defined, and works- only jonbs that run across multiple machines see this error.
>
> Mark Suhovecky
> HPC System Administrator
> Center for Research Computing
> University of Notre Dame
> suhovecky_at_[hidden]
> ________________________________________
> From: users-bounces_at_[hidden] [users-bounces_at_[hidden]] On Behalf Of Edmund Sumbar [esumbar_at_[hidden]]
> Sent: Wednesday, January 11, 2012 12:52 PM
> To: Open MPI Users
> Subject: Re: [OMPI users] ompi + bash + GE + modules
>
> Hi Mark,
>
> Have you tried adding -l to the #! line?
>
> #!/bin/bash -l
>
> On Wed, Jan 11, 2012 at 10:42 AM, Mark Suhovecky <suhovecky_at_[hidden]<mailto:suhovecky_at_[hidden]>> wrote:
> #!/bin/bash
> #$ <some GE directives>
>
> module load ompi
>
> mpiexec
>
> when the mpiexec is run, we'll see the following errors
>
>
> bash: module: line 1: syntax error: unexpected end of file
> bash: error importing function definition for `module'
>
>
>
> --
> Edmund Sumbar
> Research Computing Support
> University of Alberta
> +1 780 492 9360
>
>
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