[MITgcm-support] MITgcm-support Digest, Vol 176, Issue 4

Martin Losch Martin.Losch at awi.de
Wed Feb 14 13:36:07 EST 2018 

Neil,

before you use MPI, try without. Does the test pass without MPI?

The model is tested every day with and without MPI on many different machines. If you encounter problems with MPI then I would first make sure that simple MPI programs run successfully.
For testreport, on top of the -mpi flag you need to pass the command to testreport that you need to run an mpi program, e.g. with -command "mpirun -n 2 mpirun” or whatever your command is, and how many processes you can allow (I’d use two for a simple test).

M.

> On 14. Feb 2018, at 01:54, Neil Patel <nigellius at gmail.com> wrote:
> 
> Thanks. I think my issues might be I trying to run it with MPI. I’ve gotten mitgcm to run on the machine I’m using with MPI with a different setup; there must be an setup detail I’m missing. I tried testreport as you suggested but turned on the -mpi flag and specified a build options file. Here’s the result::
> 
> genmake ... successful
> clean build-dir: make Clean ... successful
> make depend ... successful
> make ... successful
> clean run-dir ... successful
> linkdata from dirs: input
> ldir=input: bathymetry.bin data data.~1.10.~ data.cal data.diagnostics data.exf data.gmredi data.pkg data.profiles eedata eedata.mth flatgrid_test flatgrid_test~ lev_s.bin lev_sss.bin lev_sst.bin lev_t.bin mitgcm_cubet1.o4429963 mitgcm_cubet1.o4434266 ncep_emp.bin ncep_qnet.bin POLY3.COEFFS prepare_run prof_exemple.nc RhoRef.data RhoRef.meta trenberth_taux.bin trenberth_tauy.bin ; link files: from dir: ../../tutorial_global_oce_latlon/input
> runmodel in global_with_exf/run ... failed (run: 36  end: 0 )
> => output from running in global_with_exf/run :
>> mitgcmuv           000000000062E112  read_rec_xy_rs_          1782  read_rec.f
>> mitgcmuv           000000000085BCFB  ini_depths_.R            3108  ini_depths.f
>> mitgcmuv           0000000000891CFD  initialise_fixed_        1849  initialise_fixed.f
>> mitgcmuv           00000000008CF6A3  the_model_main_          2387  the_model_main.f
>> mitgcmuv           00000000007D12E7  MAIN__                   4623  main.f
>> mitgcmuv           0000000000404C4E  Unknown               Unknown  Unknown
>> libc-2.19.so       00007FFFEAA35B25  __libc_start_main     Unknown  Unknown
>> mitgcmuv           0000000000404B59  Unknown               Unknown  Unknown
>> MPT ERROR: MPI_COMM_WORLD rank 1 has terminated without calling MPI_Finalize()
>> 	aborting job
> 
> clean run-dir ... successful
> linkdata from dirs: input.yearly input
> ldir=input.yearly: data data.bbl data.cal data.diagnostics data.exf data.pkg eedata.mth prepare_run ; link files: bathymetry.bin from dir: ../../tutorial_global_oce_latlon/input
> link files: lev_sss.bin_1991 lev_sss.bin_1992 lev_sst.bin_1991 lev_sst.bin_1992 ncep_emp.bin_1991 ncep_emp.bin_1992 ncep_qnet.bin_1991 ncep_qnet.bin_1992 trenberth_taux.bin_1991 trenberth_taux.bin_1992 trenberth_tauy.bin_1991 trenberth_tauy.bin_1992 from dir: ../../tutorial_global_oce_latlon/input
> ldir=input: data.~1.10.~ data.gmredi data.profiles eedata flatgrid_test flatgrid_test~ lev_s.bin lev_sss.bin lev_sst.bin lev_t.bin mitgcm_cubet1.o4429963 mitgcm_cubet1.o4434266 ncep_emp.bin ncep_qnet.bin POLY3.COEFFS prof_exemple.nc RhoRef.data RhoRef.meta trenberth_taux.bin trenberth_tauy.bin ; link files: from dir: ../../tutorial_global_oce_latlon/input
> runmodel in global_with_exf/tr_run.yearly ... failed (run: 0  end: 0 )
> => output from running in global_with_exf/tr_run.yearly :
>> link mitgcmuv from dir ../build
>> ABNORMAL END: S/R EXF_CHECK
>> ABNORMAL END: S/R EXF_CHECK
>> MPT ERROR: MPI_COMM_WORLD rank 1 has terminated without calling MPI_Finalize()
>> 	aborting job
> 
> 
>> On Feb 12, 2018, at 12:00 PM, mitgcm-support-request at mitgcm.org wrote:
>> 
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>> Today's Topics:
>> 
>>  1. running the global_with_exf tutorial (Neil Patel)
>>  2. Re: running the global_with_exf tutorial (Martin Losch)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Mon, 12 Feb 2018 11:42:22 -0500
>> From: Neil Patel <nigellius at gmail.com>
>> To: mitgcm-support at mitgcm.org
>> Subject: [MITgcm-support] running the global_with_exf tutorial
>> Message-ID: <4DFB1FCE-9482-47CA-A812-FF3E5D3F7913 at gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> I got an error when trying to run the global_with_exf tutorial. Running it in the input directory, with the mitgcm executable in the build directory I got the error below. I copied bathymetry.bin from the global_ocean.90x40x15 directory to the input directory, left the input data file alone. Anyone try this example? Is there something else I need to add?
>> 
>> forrtl: severe (36): attempt to access non-existent record, unit 9, file /glade/u/home/neilp/MITgcm/verification/global_with_exf/input/bathymetry.bin
>> 
>> it?s odd because the file does exist. If I type
>> 
>> neilp at cheyenne5:~> ls -l /glade/u/home/neilp/MITgcm/verification/global_with_exf/input/bathymetry.bin
>> -rw-r--r-- 1 neilp ncar 14400 Feb 10 21:02 /glade/u/home/neilp/MITgcm/verification/global_with_exf/input/bathymetry.bin
>> 
>> so clearly there
>> 
>> 
>> 
>> Thanks, 
>> 
>> Neil Patel
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>> ------------------------------
>> 
>> Message: 2
>> Date: Mon, 12 Feb 2018 17:54:00 +0100
>> From: Martin Losch <Martin.Losch at awi.de>
>> To: MITgcm Support <mitgcm-support at mitgcm.org>
>> Subject: Re: [MITgcm-support] running the global_with_exf tutorial
>> Message-ID: <33C511D5-4CD4-4379-A9E2-F982E00A91AD at awi.de>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Hi Neil,
>> 
>> I can?t reproduce your problem. I tried this:
>> 
>> cd verification
>> ./testreport -t global_with_exf
>> 
>> Can you try this, too? (after removing everything from the run directory)
>> 
>> Usually the error means that the model tries to read past the end of the file, but your file size appears to be OK.
>> 
>> Both global_with_exf and global_ocean.90x40x15 get their input data from tutorial_global_oce_latlon/input
>> 
>> Martin
>> 
>> 
>>> On 12. Feb 2018, at 17:42, Neil Patel <nigellius at gmail.com> wrote:
>>> 
>>> I got an error when trying to run the global_with_exf tutorial. Running it in the input directory, with the mitgcm executable in the build directory I got the error below. I copied bathymetry.bin from the global_ocean.90x40x15 directory to the input directory, left the input data file alone. Anyone try this example? Is there something else I need to add?
>>> 
>>> forrtl: severe (36): attempt to access non-existent record, unit 9, file /glade/u/home/neilp/MITgcm/verification/global_with_exf/input/bathymetry.bin
>>> 
>>> it?s odd because the file does exist. If I type
>>> 
>>> neilp at cheyenne5:~> ls -l /glade/u/home/neilp/MITgcm/verification/global_with_exf/input/bathymetry.bin
>>> -rw-r--r-- 1 neilp ncar 14400 Feb 10 21:02 /glade/u/home/neilp/MITgcm/verification/global_with_exf/input/bathymetry.bin
>>> 
>>> so clearly there
>>> 
>>> 
>>> 
>>> Thanks, 
>>> 
>>> Neil Patel
>>> _______________________________________________
>>> MITgcm-support mailing list
>>> MITgcm-support at mitgcm.org
>>> http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support
>> 
>> 
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>> End of MITgcm-support Digest, Vol 176, Issue 4
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