Hi Alan: Sorry, I was away in the most inaccessible part of Utah I could find. I think Jack Howarth fixed it in my absence, but if not, please let me know. Sorry for this continuing nightmare.
Bill On Aug 14, 2009, at 12:35 AM, Alan wrote: > 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<< ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Fink-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/fink-users
