[MITgcm-support] MITgcm-support Digest, Vol 126, Issue 31
李志远
oceanlizy at 163.com
Wed Dec 18 10:47:34 EST 2013
Hi, thank you ,Mirek !
I did it as you told ,and it succeeded . I use the tutorial_barotropic_gyre as a test ,and it generated the 'mitgcmuv' file . there seems no problem with the compile ,next step I will compile my own study model with mpi in the way you told me ,I hope it will go successfully .
best regards!
At 2013-12-18 01:00:02,mitgcm-support-request at mitgcm.org wrote:
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>Today's Topics:
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> 1. Re: Parameters to parallelise a coupled run ? (Jean-Michel Campin)
> 2. problems with compile with MPI (???)
> 3. Re: problems with compile with MPI (MIT)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 16 Dec 2013 12:47:46 -0500
>From: Jean-Michel Campin <jmc at ocean.mit.edu>
>To: mitgcm-support at mitgcm.org
>Subject: Re: [MITgcm-support] Parameters to parallelise a coupled run
> ?
>Message-ID: <20131216174746.GA8588 at ocean.mit.edu>
>Content-Type: text/plain; charset=us-ascii
>
>Hi Alexandre,
>
>There was a problem in the coupler mapping interface (specially
>regarding the run-off mapp that the coupler uses) that has been
>found recently and fixed (Nov 27, 2013 and Dec 02, 2013).
>I would recommand to update your code (checkpoint64r contains
>these fixes).
>
>However, this would have very little or no impact on the
>how fast the model will run on 1+48+48 procs.
>
>One (obvious) thing is that the default option in "run_cpl_test"
>is to compile with "-devel" (very slow).
>Otherwise, you my want to try smaller number of procs (e.g.,
>1+12+12 and 1+24+24) to check when this scaling/speed degrades.
>
>Cheers,
>Jean-Michel
>
>On Thu, Dec 12, 2013 at 10:53:35AM +0100, Alexandre Pohl wrote:
>> Hi all,
>>
>> I asked you a few weeks ago about a way to merge netcdf output files. I am still learning to use the MITgcm, to hopefully be able to apply it soon to paleoclimate modelling (the Ordovician glaciation).
>>
>> But I am now having problems to parallelise the code. I use the cubed-sphere exch2 grid. I started from the "cpl_aim+ocn" verification case. It runs well with 6 faces, 6 tiles and 3 processes (1 for the ocean, 1 for the atmosphere and 1 for the coupler).
>>
>> To parallelise the code, I then divided each face of the cube into 8 tiles using the SIZE.h file :
>>
>> & sNx = 16,
>> & sNy = 8,
>> & OLx = 2,
>> & OLy = 2,
>> & nSx = 1,
>> & nSy = 1,
>> & nPx = 48,
>> & nPy = 1,
>> & Nx = sNx*nSx*nPx, > which gives 768 points in X
>> & Ny = sNy*nSy*nPy, > which gives 8 points in Y
>> & Nr = 15) [Nr=5 for the atmosphere]
>>
>> It used the "adjustment.cs-32x32x1" verification files to write my own, except that I gave 1 process to each tile ("nSx=1" above), which finally makes 6*8=48 processes ("nPx=48") instead of a single process.
>>
>> I added " usingMPI=.TRUE.," to my eedata files and set "nTx=1".
>>
>> I am now wondering how processes I have to use for the ocean and for the atmosphere. I use the "run_cpl_test" script to prepare, compile and execute the model. I tried "Npr=97; NpOc=48;" which means 48 processes for the ocean, 48 for the atmosphere and 1 single processor for the coupler, but the model unfortunately does not run faster with these 97 processes than with only 3.
>>
>> Could you tell me if my parameters are wrong?
>> Have I forgotten something?
>>
>> I would be very interested if somebody could describe a set of parameters that allow to parallelise the model efficiently.
>>
>> Thank you for your help,
>> Alexandre
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>
>------------------------------
>
>Message: 2
>Date: Tue, 17 Dec 2013 21:48:36 +0800 (CST)
>From: ??? <oceanlizy at 163.com>
>To: MITgcm <mitgcm-support at mitgcm.org>
>Subject: [MITgcm-support] problems with compile with MPI
>Message-ID: <103a0553.f734.14300d0bbb2.Coremail.oceanlizy at 163.com>
>Content-Type: text/plain; charset="gbk"
>
>From: lizhiyuan <oceanlizy at 163.com>
>To: mitgcm-support at mitgcm.orgSubject: problems with compile with MPIDear,all;
> I want to use mpi run my model , but I don't know how to compile it wiht mpi . my computer system is linux_amd64 with gfortran and openmpi. The openmpi is installed at '/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/ ' and have five subdirectories : bin , etc ,include ,lib ,share .
> I find my mpif90 is located at '/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/bin/mpif90 '
>should I just modify the files 'linux_amd64_pgf90+mpi_xd1'in the /tools/build_options as follows:
>
>
>FC='mpif90'
>CC='mpicc'
>LINK='mpif90'
>
>
>MPI='true'
>INCLUDEDIRS='/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/include'
>DEFINES='-DWORDLENGTH=4'
>CPP='/usr/bin/cpp -P -traditional'
>EXTENDED_SRC_FLAG='-Mextend'
>
>
>INCLUDES='-I/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/include'
>LIBS='-L/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/lib'
>
>
>and then,cd build,type " ../../../tools/genmake2 -mods=../code -of=../../../tools/build_options/linux_amd64_pgf90+mpi_xd1=/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90"?
>I am some confused , someone met the same questions, can any one help me ?
>I am looking forward to your quick reply .
>thanks so much !
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>------------------------------
>
>Message: 3
>Date: Tue, 17 Dec 2013 10:01:24 -0500
>From: MIT <jahn at MIT.EDU>
>To: mitgcm-support at mitgcm.org
>Subject: Re: [MITgcm-support] problems with compile with MPI
>Message-ID: <52B06744.4030609 at mit.edu>
>Content-Type: text/plain; charset=UTF-8
>
>Dear Lizhi,
>
>the modification you made look reasonable. Why don't you give it a try
>and report back how it went? The last part of your genmake2 command
>looks funny, though. It should just be
>
>../../../tools/genmake2 -mods=../code
>-of=../../../tools/build_options/linux_amd64_pgf90+mpi_xd1
>
>And make sure your SIZE.h (in code) has nPx or nPy > 1. If you don't
>know how to modify SIZE.h, have a look at one of the verification
>experiments, like verification/tutorial_barotropic_gyre. SIZE.h_mpi is
>the version for mpi with 2 processors.
>
>Cheers,
>Oliver
>
>
>On 2013-12-17 08:48, ??? wrote:
>> From: lizhiyuan <oceanlizy at 163.com <mailto:oceanlizy at 163.com>>
>> To: mitgcm-support at mitgcm.org <mailto:mitgcm-support at mitgcm.org>
>>
>> Subject: <mailto:mitgcm-support at mitgcm.org> problems with compile with MPI
>>
>> Dear,all;
>> I want to use mpi run my model , but I don't know how to compile
>> it wiht mpi . my computer system is linux_amd64 with gfortran and
>> openmpi. The openmpi is installed at
>> '/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/ ' and have five
>> subdirectories : bin , etc ,include ,lib ,share .
>> I find my mpif90 is located at
>> '/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/bin/mpif90 '
>> should I just modify the files 'linux_amd64_pgf90+mpi_xd1'in the
>> /tools/build_options as follows:
>>
>> FC='mpif90'
>> CC='mpicc'
>> LINK='mpif90'
>>
>> MPI='true'
>> INCLUDEDIRS='/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/include'
>> DEFINES='-DWORDLENGTH=4'
>> CPP='/usr/bin/cpp -P -traditional'
>> EXTENDED_SRC_FLAG='-Mextend'
>>
>> INCLUDES='-I/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/include'
>> LIBS='-L/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90/lib'
>>
>> and then,cd build,type " ../../../tools/genmake2 -mods=../code
>> -of=../../../tools/build_options/linux_amd64_pgf90+mpi_xd1=/dcfs2/program/mpi/openmpi/1.4.3/pgcc_pgf90"?
>> I am some confused , someone met the same questions, can any one help me ?
>> I am looking forward to your quick reply .
>> thanks so much !
>>
>>
>>
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>
>
>
>
>
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>End of MITgcm-support Digest, Vol 126, Issue 31
>***********************************************
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