I think it's fixed at least with openmpi since apbs-mpi is working as
expected AFAIK.
Cheers,
Alan
On Mon, Aug 17, 2009 at 03:57, William G. Scott
<[email protected]>wrote:
> 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<<
>>>>
>>>
>
--
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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