[MITgcm-support] basics

[Gus Correa]

Hi Mario

If you compiled the model with MPI, and your SIZE.h file is setup to
run the model in parallel (i.e. more than one processor),
then you cannot launch it simply with:

./mitgcmuv > output.txt

Instead, you need to launch it with mpirun (or mpiexec),
something like this:

mpirun -np 16 ./mitgcmuv > output.txt

where I made up 16 as the number of processors, but you need to use
the appropriate number that matches the number of processors
that you set up in SIZE.h.

**

In addition, you may also have an environment problem,
maybe a mixup of different MPI implementations.

Make sure the MPI used for compilation and linking
(check your build option file in tools/build_options/)
is the same used to launch the mitgcmuv executable
(through mpiexec or mpirun).

It may help also if you check the output of:

'which mpif77' (or 'which mpif90', or 'which mpifortran')

and

'which mpirun' (or 'which mpiexec')

Very often people have a variety of MPI flavors installed (MPICH, 
OpenMPI, even duplicate ancient versions) and their PATH and 
LD_LIBRARY_PATH environment variables are set up inconsistently,
which can lead to the mixup.
The runtime environment must match the compilation/linking environment.

I hope this helps,
Gus Correa

On 06/18/2015 01:27 PM, Edwards, Erick (LCDR) wrote:
> Mario,
>
> I have some batch files and other information to help out.  Let’s meet
> this morning in my office.
>
> Erick
>
> *From:*MARIO DURAN CAMEJO [mailto:mdcamejo at ing.uc3m.es]
> *Sent:* Thursday, June 18, 2015 7:19 AM
> *To:* MITgcm-support at mitgcm.org
> *Subject:* [MITgcm-support] basics
>
> Hello,
>
> I'm just beginning with MITgcm and I have a very simple question.
>
> I have built my executable in the build directory and made a copy to
> input, but when I enter ./mitgcmuv > output.txt I get an error like this:
>
> [unset]: aborting job:
>
> Fatal error in MPI_Init:
>
> Other MPI error, error stack:
>
> MPIR_Init_thread (436)..........:
>
> MPID_Init (371).....................: channel initialization failed
>
> MPIDI_CH3_Init (335)............:
>
> MPIDI_CH3I_SMP_Init (1723):  LiMIC2 device does not exist: No such file
> or directory
>
> Does someone know what is going on?
>
> Thank you very much!
>
> Mario
>
> --
>
> MARIO DURAN CAMEJO
> Universidad Carlos III de Madrid
>
>
>
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