Starting to answer myself, I did this test with a custom compiled version of
apbs:
~/Programmes/apbs-1.1.0-source% ./configure --enable-fast
--with-openmpi=/usr
make all
cd examples/actin-dimer
/usr/bin/mpirun -c 8 ../../bin/apbs apbs-mol-parallel.in
WORKED!
Than I realise that "--with-openmpi=" flag is missing in apbs-mpi-openmpi,
although it's using mpicc and mpif77, but it seems not to be enough,
specially because mpi is not compatible with python as I read from the
"configure" script. And looking better at the configure script, this
mpif77/python combination only pass because '--with-openmpi' is not declared
and to test to avoid this incompatibility is not checked. So, I am sorry
Bill Scott, but "apbs-mpi" is not OK yet.
HOWEVER, if I put "./configure --enable-fast --with-openmpi=/sw" I got this
error:
[snip]
checking for --with-openmpi option... /sw
checking for /sw/include/mpi.h... yes
checking for /sw/lib/libmpi.a... no
checking for /sw/lib/libmpi.so... no
checking for /sw/lib/libmpi.dylib... no
configure: error: Error...Could not find OpenMPI libraries in /sw/lib
Well, libmpi.dylib is in /sw/lib/openmpi and frankly after reading
./configure --help all combinations I tried and I didn't get it to work with
Fink openmpi libs.
Any help here would be very appreciated.
Cheers,
Alan
On Thu, Aug 13, 2009 at 17:22, Alan <[email protected]> wrote:
> Hi There,
> So I installed apbs-mpi-openmpi and it seems to work fine but when trying
> this link to run in multi-core machine:
>
> http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_run_a_calculation_that%27s_too_big_for_my_computer%3F
>
> I got this message and nothing done.
>
> [snip]
> Reading PQR-format atom data from complex.pqr.
> 11754 atoms
> Centered at (2.518e+00, -2.465e+00, 1.674e+01)
> Net charge -2.40e+01 e
> NOsh_setupCalcMGPARA: Oops! You're trying to perform an 'mg-para'
> (parallel) calculation
> NOsh_setupCalcMGPARA: with a version of APBS that wasn't compiled with
> MPI!
> NOsh_setupCalcMGPARA: Perhaps you meant to use the 'async' flag?
> NOsh_setupCalcMGPARA: Bailing out!
> [snip]
>
> Checking my apbs and libmpi is there:
>
> > ldd `which apbs`
> /sw/bin/apbs:
> /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
> (compatibility version 1.0.0, current version 242.0.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 111.1.4)
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> (compatibility version 1.0.0, current version 218.0.0)
> /sw/lib/openmpi/libmpi_f77.0.dylib (compatibility version 1.0.0, current
> version 1.0.0)
> /sw/lib/openmpi/libmpi.0.dylib (compatibility version 1.0.0, current
> version 1.0.0)
> /sw/lib/openmpi/libopen-rte.0.dylib (compatibility version 1.0.0, current
> version 1.0.0)
> /sw/lib/openmpi/libopen-pal.0.dylib (compatibility version 1.0.0, current
> version 1.0.0)
> /usr/lib/libutil.dylib (compatibility version 1.0.0, current version
> 1.0.0)
> /sw/lib/gcc4.4/lib/libgfortran.3.dylib (compatibility version 4.0.0,
> current version 4.0.0)
> /sw/lib/gcc4.4/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> version 1.0.0)
>
> om-mpirun -c 2 apbs ... doesn't work either.
>
> Any ideas?
>
> Cheers,
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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