[CIG-SEISMO] Issue Configuring SPECFEM3D on Stampede2 Supercomputer

[Dimitri Komatitsch]

Hi all,

Yes, '-assume nobuffered_io' should solve the issue (depending on the 
version of the compiler it needs to be there or not).
Otherwise, configuring with gfortran is another option that should fix 
it, but then the executable may be slower.

Best regards,
Dimitri.

On 05/18/2018 03:52 AM, Malladi, Rama Kishan V wrote:
> Hi Ian,
> 
> Not sure if your issue is related to an earlier post. Can you try using 
> this compiler flag? : '-assume nobuffered_io'
> 
> Thanks
> 
> -Rama
> 
> *From:*CIG-SEISMO [mailto:cig-seismo-bounces at geodynamics.org] *On Behalf 
> Of *Ian Stone
> *Sent:* Thursday, May 17, 2018 11:19 PM
> *To:* cig-seismo at geodynamics.org
> *Subject:* [CIG-SEISMO] Issue Configuring SPECFEM3D on Stampede2 
> Supercomputer
> 
> Hello,
> 
> My name is Ian Stone, and I am a PhD student at the University of 
> Washington. I am trying to install Specfem3D Cartesian on the TACC 
> Stampede2 supercomputer so I can simulate earthquake scenarios.
> 
> I have run into an issue where MPI processes do not seem to execute 
> correctly, where either xgenerate_databases is not producing proper 
> database files, or xspecfem3D is not reading them correctly. This is the 
> error message I receive when I attempt to run the MountStHelens example 
> on 4 cores; it is created when xspecfem3D starts reading the database files:
> 
> -----------
> 
> forrtl: severe (24): end-of-file during read, unit 27, file 
> /<path>/specfem3d/EXAMPLES/Mount_StHelens/OUTPUT_FILES/DATABASES_MPI/proc000001_external_mesh.bin
> 
> ImagePCRoutineLineSource
> 
> xspecfem3D 0000000001022F89Unknown UnknownUnknown
> 
> xspecfem3D 00000000010489C4Unknown UnknownUnknown
> 
> xspecfem3D 0000000000C7CE00read_mesh_databas68read_mesh_databases.F90
> 
> xspecfem3D 0000000000DD6B43MAIN__353specfem3D.F90
> 
> xspecfem3D 000000000040423EUnknown UnknownUnknown
> 
> libc.so.600002ABACC0FFC05Unknown UnknownUnknown
> 
> xspecfem3D 0000000000404142Unknown UnknownUnknown
> 
> forrtl: severe (24): end-of-file during read, unit 27, file 
> /<path>/specfem3d/EXAMPLES/Mount_StHelens/OUTPUT_FILES/DATABASES_MPI/proc000002_external_mesh.bin
> 
> ImagePCRoutineLineSource
> 
> xspecfem3D 0000000001022F89Unknown UnknownUnknown
> 
> xspecfem3D 00000000010489C4Unknown UnknownUnknown
> 
> xspecfem3D 0000000000C7CE00read_mesh_databas68read_mesh_databases.F90
> 
> xspecfem3D 0000000000DD6B43MAIN__353specfem3D.F90
> 
> xspecfem3D 000000000040423EUnknown UnknownUnknown
> 
> libc.so.600002BA144606C05Unknown UnknownUnknown
> 
> xspecfem3D 0000000000404142Unknown UnknownUnknown
> 
> forrtl: severe (24): end-of-file during read, unit 27, file 
> /<path>/specfem3d/EXAMPLES/Mount_StHelens/OUTPUT_FILES/DATABASES_MPI/proc000003_external_mesh.bin
> 
> ImagePCRoutineLineSource
> 
> xspecfem3D 0000000001022F89Unknown UnknownUnknown
> 
> xspecfem3D 00000000010489C4Unknown UnknownUnknown
> 
> xspecfem3D 0000000000C7CE00read_mesh_databas68read_mesh_databases.F90
> 
> xspecfem3D 0000000000DD6B43MAIN__353specfem3D.F90
> 
> xspecfem3D 000000000040423EUnknown UnknownUnknown
> 
> libc.so.600002B83ACB71C05Unknown UnknownUnknown
> 
> xspecfem3D 0000000000404142Unknown UnknownUnknown
> 
> -----------
> 
> I can run this simulation on a single core without invoking MPI, so I 
> know specfem is working. It is just when I attempt to run using MPI that 
> things go awry. The nodes & cores values match between my Par_file and 
> sbatch script, so I figure that means something is wrong with the way I 
> configured specfem initially.
> 
> To configure, I load intel version 16.0.3 and impi version 17.0.3, and 
> use the command:
> 
> ./configure CC=icc FC=ifort MPIFC=mpif90 
> MPI_INC="/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include" 
> --with-mpi
> 
> Does this look ok? Or do any of you have experience installing specfem 
> either on Stampede or Stampede2? I should add that running after using 
> the "--enable-debug" flag does not produce any outstanding messages.
> 
> Thank you,
> 
> Ian Stone
> 
> 
> 
> _______________________________________________
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> 

-- 
Dimitri Komatitsch, CNRS Research Director (DR CNRS)
Laboratory of Mechanics and Acoustics, Marseille, France
http://komatitsch.free.fr