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

Neil Patel nigellius at gmail.com
Tue Feb 13 19:54:45 EST 2018


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:
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>   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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