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<<
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