[MITgcm-support] MITgcm-support Digest, Vol 126, Issue 31
李志远
oceanlizy at 163.com
Tue Dec 17 20:49:05 EST 2013
thanks for your quick reply, Oliver ;
I tried as you told , I cd hs94.1x64x5/build ,then type " ../../../tools/genmake2 -mods=../code -of=../ ../../tools/build_options/linux_amd64_pgf90+mpi_xd1"
then,it occured "
getting OPTFILE information:
using OPTFILE="../../../tools/build_options/linux_amd64_pgf90+mpi_xd1"
getting AD_OPTFILE information:
using AD_OPTFILE="../../../tools/adjoint_options/adjoint_default"
check makedepend (local: 0, system: 0, 0)
Turning on MPI cpp macros
=== Checking system libraries ===
Do we have the system() command using mpif90... no
Do we have the fdate() command using mpif90... no
Do we have the etime() command using mpif90... no
Can we call simple C routines (here, "cloc()") using mpif90... no
Can we unlimit the stack size using mpif90... no
Can we register a signal handler using mpif90... no
Can we use stat() through C calls... no
Can we create NetCDF-enabled binaries... no
Can we create LAPACK-enabled binaries... no
Can we call FLUSH intrinsic subroutine... no
=== Setting defaults ===
Adding MODS directories: ../code
Making source files in eesupp from templates
Making source files in pkg/exch2 from templates
Making source files in pkg/regrid from templates
=== Determining package settings ===
getting package dependency info from ../../../pkg/pkg_depend
getting package groups info from ../../../pkg/pkg_groups
checking list of packages to compile:
using PKG_LIST="../code/packages.conf"
before group expansion packages are: gfd shap_filt diagnostics mypackage mnc
replacing "gfd" with: mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor
after group expansion packages are: mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor shap_filt diagnostics mypackage mnc
applying DISABLE settings
applying ENABLE settings
packages are: debug diagnostics generic_advdiff mdsio mnc mom_common mom_fluxform mom_vecinv monitor mypackage rw shap_filt
*********************************************************************
WARNING: the "mnc" package was enabled but tests failed to compile
NetCDF applications. Please check that:
1) NetCDF is correctly installed for this compiler and
2) the LIBS variable (within the "optfile") specifies the correct
NetCDF library to link against.
Due to this failure, the "mnc" package is now DISABLED.
*********************************************************************
applying package dependency rules
packages are: debug diagnostics generic_advdiff mdsio mom_common mom_fluxform mom_vecinv monitor mypackage rw shap_filt
Adding STANDARDDIRS='eesupp model'
Searching for *OPTIONS.h files in order to warn about the presence
of "#define "-type statements that are no longer allowed:
found CPP_EEOPTIONS="../../../eesupp/inc/CPP_EEOPTIONS.h"
found CPP_OPTIONS="../../../model/inc/CPP_OPTIONS.h"
Creating the list of files for the adjoint compiler.
=== Creating the Makefile ===
setting INCLUDES
Determining the list of source and include files
Writing makefile: Makefile
Add the source list for AD code generation
Making list of "exceptions" that need ".p" files
Making list of NOOPTFILES
Add rules for links
Adding makedepend marker
=== Done ===
I don't know where does it go wrong , I can compile and run successfully without mpi before .
thank you very much !
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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