[Users] MPI trouble on 64-bit Mac OS X 10.6.7 (fink version)
Scott Hawley
scott.hawley at belmont.edu
Fri May 20 12:08:57 CDT 2011
Got it to build and run! See below for config "options"
Yes, it is complicated on the Mac because Apple ships its own messed up version of MPI which you have to be careful not to use, and Apple uses the gnu v4.2.1 compiler but in order to get a fortran 90 compiler you need the straight-GNU compiler which for me is v4.4
This, then, is my "options.mac" file, which produces a complete build of my thorn and runs properly with MPI. Consider using it for a "known architectures" file. The /sw directory is where fink puts things. One needs to get gfortran and openmpi from fink. Some of the libraries I'm using will not be necessary for all people, but I'll let you take them out. This works for me! ...Oh, that is to say, with all the "CarpetIO..." thorns not activated. Haven't gotten those working yet.
% cat options.mac
CC = /sw/bin/mpicc
CXX = /sw/bin/mpic++
F77 = /sw/bin/mpif77
F90 = gfortran
CFLAGS = -m64 -std=c99
CXXFLAGS = -m64
FFLAGS = -m64
F90FLAGS = -m64
LIBS = texmex bbhutil sv mfhdf df jpeg z gfortran
LDFLAGS = -L/sw/lib -L/sw/lib/gcc4.4/lib/ -L/Users/shawley/lib -L/Users/shawley/texmex/lib
MPI = OPENMPI
OPENMPI_DIR = /sw
TEXMEX_DIR = /Users/shawley/texmex
On May 20, 2011, at 11:43 AM, Erik Schnetter wrote:
> Scott
>
> This usually means that the libraries used to build the executable and
> the mpirun command don't belong together. In other words, either the
> libraries used for building, or the shared libraries used at run time
> (if you use shared libraries), or the mpirun executable are not what
> you think they are.
>
> make texmex SILENT=no shows you (at the end) which libraries are used
> during the build.
>
> ldd exe/cactus_texmex (or otool -L exe/cactus_texmex) shows which
> shared libraries will be used. Certain environment variables influence
> this; make sure you use the same settings that you use when you call
> mpirun.
>
> "which mpirun" shows which mpirun will be used.
>
> -erik
>
> On Fri, May 20, 2011 at 12:36 PM, Scott Hawley <scott.hawley at belmont.edu> wrote:
>> My code works totally ok with MPI on my linux machine, but as I'm porting to my Mac, I find that MPI isn't working right. I'm using the OpenMPI version from fink) A simple "hello world" MPI program works fine (proof at the bottom of this message), but Cactus does not.
>>
>> That is to say, e.g. an 8-processor run ("/sw/bin om-mpirun -np 8 ....") results in 8 processes, but each processes thinks it's processor 0, and that there are no other processors.
>>
>> Any ideas why this might happen?
>> Thanks,
>> Scott
>>
>>
>> I'm using Cactus version 4.0.b17 (Compile date: May 20 2011 (11:13:49)).
>>
>> Cactus run:
>>> mpirun -np 8 ~/Cactus/exe/cactus_texmex sep20a0.5fmrbbh97_cactus.par
>> --------------------------------------------------------------------------------
>>
>> 10
>> 1 0101 ************************
>> 01 1010 10 The Cactus Code V4.0
>> 1010 1101 011 www.cactuscode.org
>> 1001 100101 ************************
>> 00010101
>> 100011 (c) Copyright The Authors
>> 0100 GNU Licensed. No Warranty
>> 0101
>>
>> --------------------------------------------------------------------------------
>>
>> Cactus version: 4.0.b17
>> Compile date: May 20 2011 (11:13:49)
>> --------------------------------------------------------------------------------
>>
>> 10
>> 1 0101 ************************
>> 01 1010 10 The Cactus Code V4.0
>> 1010 1101 011 www.cactuscode.org
>> 1001 100101 ************************
>> 00010101
>> 100011 (c) Copyright The Authors
>> 0100 GNU Licensed. No Warranty
>> 0101
>>
>> --------------------------------------------------------------------------------
>>
>> Cactus version: 4.0.b17
>> Compile date: May 20 2011 (11:13:49)
>> --------------------------------------------------------------------------------
>>
>> 10
>> 1 0101 ************************
>> 01 1010 10 The Cactus Code V4.0
>> 1010 1101 011 www.cactuscode.org
>> 1001 100101 ************************
>> 00010101
>> 100011 (c) Copyright The Authors
>> 0100 GNU Licensed. No Warranty
>> 0101
>>
>> --------------------------------------------------------------------------------
>>
>> Cactus version: 4.0.b17
>> Compile date: May 20 2011 (11:13:49)
>> --------------------------------------------------------------------------------
>>
>> 10
>> 1 0101 ************************
>> 01 1010 10 The Cactus Code V4.0
>> 1010 1101 011 www.cactuscode.org
>> 1001 100101 ************************
>> 00010101
>> 100011 (c) Copyright The Authors
>> 0100 GNU Licensed. No Warranty
>> 0101
>>
>> --------------------------------------------------------------------------------
>>
>> Cactus version: 4.0.b17
>> Compile date: May 20 2011 (11:13:49)
>> --------------------------------------------------------------------------------
>>
>> 10
>> 1 0101 ************************
>> 01 1010 10 The Cactus Code V4.0
>> 1010 1101 011 www.cactuscode.org
>> 1001 100101 ************************
>> 00010101
>> 100011 (c) Copyright The Authors
>> 0100 GNU Licensed. No Warranty
>> 0101
>>
>> --------------------------------------------------------------------------------
>>
>> Cactus version: 4.0.b17
>> Compile date: May 20 2011 (11:13:49)
>> --------------------------------------------------------------------------------
>>
>> 10
>> 1 0101 ************************
>> 01 1010 10 The Cactus Code V4.0
>> 1010 1101 011 www.cactuscode.org
>> 1001 100101 ************************
>> 00010101
>> 100011 (c) Copyright The Authors
>> 0100 GNU Licensed. No Warranty
>> 0101
>>
>> --------------------------------------------------------------------------------
>>
>> Cactus version: 4.0.b17
>> Compile date: May 20 2011 (11:13:49)
>> --------------------------------------------------------------------------------
>>
>> 10
>> 1 0101 ************************
>> 01 1010 10 The Cactus Code V4.0
>> 1010 1101 011 www.cactuscode.org
>> 1001 100101 ************************
>> 00010101
>> 100011 (c) Copyright The Authors
>> 0100 GNU Licensed. No Warranty
>> 0101
>>
>> --------------------------------------------------------------------------------
>>
>> Cactus version: 4.0.b17
>> Compile date: May 20 2011 (11:13:49)
>> --------------------------------------------------------------------------------
>>
>> 10
>> 1 0101 ************************
>> 01 1010 10 The Cactus Code V4.0
>> 1010 1101 011 www.cactuscode.org
>> 1001 100101 ************************
>> 00010101
>> 100011 (c) Copyright The Authors
>> 0100 GNU Licensed. No Warranty
>> 0101
>>
>> --------------------------------------------------------------------------------
>>
>> Cactus version: 4.0.b17
>> Compile date: May 20 2011 (11:13:49)
>> Run date: May 20 2011 (11:24:38-0500)
>> Run host: provision.local (pid=6067)
>> Working directory: /Users/shawley/runs/cactus
>> Executable: /Users/shawley/Cactus/exe/cactus_texmex
>> Parameter file: sep20a0.5fmrbbh97_cactus.par
>> --------------------------------------------------------------------------------
>> Run date: May 20 2011 (11:24:38-0500)
>> Run host: provision.local (pid=6071)
>> Working directory: /Users/shawley/runs/cactus
>> Executable: /Users/shawley/Cactus/exe/cactus_texmex
>> Parameter file: sep20a0.5fmrbbh97_cactus.par
>> --------------------------------------------------------------------------------
>>
>>
>> Activating thorn Cactus...Success -> active implementation Cactus
>> Run date: May 20 2011 (11:24:38-0500)
>> Run host: provision.local (pid=6070)
>> Activating thorn Cactus...Success -> active implementation Cactus
>> Run date: May 20 2011 (11:24:38-0500)
>> Run host: provision.local (pid=6074)
>> Working directory: /Users/shawley/runs/cactus
>> Executable: /Users/shawley/Cactus/exe/cactus_texmex
>> Parameter file: sep20a0.5fmrbbh97_cactus.par
>> --------------------------------------------------------------------------------
>>
>> Activating thorn Cactus...Success -> active implementation Cactus
>> Run date: May 20 2011 (11:24:38-0500)
>> Run host: provision.local (pid=6073)
>> Working directory: /Users/shawley/runs/cactus
>> Executable: /Users/shawley/Cactus/exe/cactus_texmex
>> Parameter file: sep20a0.5fmrbbh97_cactus.par
>> --------------------------------------------------------------------------------
>> Working directory: /Users/shawley/runs/cactus
>> Executable: /Users/shawley/Cactus/exe/cactus_texmex
>> Parameter file: sep20a0.5fmrbbh97_cactus.par
>> --------------------------------------------------------------------------------
>>
>> Activating thorn Cactus...Success -> active implementation Cactus
>>
>> Activating thorn Cactus...Success -> active implementation Cactus
>> Run date: May 20 2011 (11:24:38-0500)
>> Run host: provision.local (pid=6068)
>> Run date: May 20 2011 (11:24:38-0500)
>> Run host: provision.local (pid=6069)
>> Run date: May 20 2011 (11:24:38-0500)
>> Run host: provision.local (pid=6072)
>> Working directory: /Users/shawley/runs/cactus
>> Executable: /Users/shawley/Cactus/exe/cactus_texmex
>> Parameter file: sep20a0.5fmrbbh97_cactus.par
>>
>> ....and so on.....
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Yet a imple program works:
>> The simple example which works fine is...
>>> cat hello.c
>> #include <stdio.h>
>> #include "mpi.h"
>>
>> int main(argc, argv)
>> int argc;
>> char **argv;
>> {
>> int rank, size;
>> MPI_Init(&argc,&argv);
>> MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>> MPI_Comm_size(MPI_COMM_WORLD, &size);
>> printf("Hello world! I am %d of %d\n",rank,size);
>> MPI_Finalize();
>> return 0;
>> }
>>> mpicc -o hello hello.c
>>> which mpirun
>> /sw/bin/mpirun
>>> ls -l /sw/bin/mpirun
>> lrwxr-xr-x 1 root shawley 9 May 20 10:55 /sw/bin/mpirun@ -> om-mpirun
>>> mpirun -np 8 ./hello
>> Hello world! I am 0 of 8
>> Hello world! I am 6 of 8
>> Hello world! I am 3 of 8
>> Hello world! I am 1 of 8
>> Hello world! I am 2 of 8
>> Hello world! I am 4 of 8
>> Hello world! I am 5 of 8
>> Hello world! I am 7 of 8
>>
>>
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>>
>>
>
>
>
> --
> Erik Schnetter <schnetter at cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/
>
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