[MITgcm-support] Running a test in parallel

[Luis Cebamanos]

Hi Jody,

This sounds sensible, where can I find nx times ny value? My SIZE.h
under the global_ocean.90x40x15 directory looks like this:

      PARAMETER (
     &           sNx =  10,
     &           sNy =  10,
     &           OLx =   3,
     &           OLy =   3,
     &           nSx =   9,
     &           nSy =   4,
     &           nPx =   2,
     &           nPy =   2,
     &           Nx  = sNx*nSx*nPx,
     &           Ny  = sNy*nSy*nPy,
     &           Nr  =  15)


Cheers,
Luis

On 03/02/2017 20:40, Klymak Jody wrote:
> Sorry my fault.  If you can't read a record on a file it usually means that it is the wrong size.  Does nx times ny in the file equal what's in Size.h?   
>
> Cheers.   Jody
>
> Sent from my iPhone
>
>> On Feb 3, 2017, at 11:09, Luis Cebamanos <l.cebamanos at epcc.ed.ac.uk> wrote:
>>
>> Hi Jody,
>>
>> I am sorry for the confusion. It is still on the same system, just
>> different partitions. The computing nodes can only see some partitions
>> of the system.
>> I guess my question is, why is MITgcm failing to read  bathymetry.bin
>> although the file is created?
>>
>> Thanks,
>> Luis
>>> On 03/02/2017 18:58, Jody Klymak wrote:
>>> Hi Luis,
>>>
>>> You must recompile `mitgcmuv` on the new computer.  Executable programs aren’t usually portable between architectures.  Hopefully there is a helpful file in `tools/build_options` to help w/ your genmake2 step.
>>>
>>> Cheers,   Jody
>>>
>>>
>>>> On 3 Feb 2017, at  10:53 AM, Luis Cebamanos <l.cebamanos at epcc.ed.ac.uk> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> I am totally new to MITgcm, so apologies if I say any  nonsense. I m
>>>> trying to run a test in parallel,so I started with
>>>> global_ocean.90x40x15. I changed the SIZE.h to run on 4 mpi processes
>>>> and built it successfully. Now, I am working on a Cray system, meaning
>>>> that it has to be run on a different location. So I copied over to the
>>>> right place /work/MITgcm/ the following directories from
>>>> global_ocean.90x40x15:
>>>>
>>>> global_ocean.90x40x15/input
>>>> global_ocean.90x40x15/build/mitgcmuv
>>>> tutorial_global_oce_latlon/input
>>>>
>>>> I then created the directory /work/MITgcm/run and run the following:
>>>> ln -s ../input/* .
>>>> ../input/prepare_run
>>>> ln -s ../mitgcmuv .
>>>>
>>>> My script calls MITgcm:
>>>>
>>>> aprun -n 4 -N 4 -d 1 ./mitgcmuv
>>>>
>>>> It appears to start running properly but soon fails with the following
>>>> errors:
>>>>
>>>> lib-4016 : UNRECOVERABLE library error
>>>> A READ operation tried to read a nonexistent record (721).
>>>>
>>>> Encountered during a direct access unformatted READ from unit 9
>>>> Fortran unit 9 is connected to a direct unformatted unblocked file:
>>>> "bathymetry.bin"
>>>>
>>>> lib-4016 : UNRECOVERABLE library error
>>>> A READ operation tried to read a nonexistent record (730).
>>>>
>>>> lib-4016 : UNRECOVERABLE library error
>>>> A READ operation tried to read a nonexistent record (370).
>>>>
>>>>
>>>> Could someone please help me to run a simple test case ?
>>>>
>>>> Regards,
>>>> Luis
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> The University of Edinburgh is a charitable body, registered in
>>>> Scotland, with registration number SC005336.
>>>> _______________________________________________
>>>> MITgcm-support mailing list
>>>> MITgcm-support at mitgcm.org
>>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>> --
>>> Jody Klymak    
>>> http://web.uvic.ca/~jklymak/
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> MITgcm-support mailing list
>>> MITgcm-support at mitgcm.org
>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
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