Re: [Fink-users] testing apbs-mpi
Alan, I have uploaded a first pass of new apbs-mpi packaging which builds apbs properly against openmpi. It probably still needs work to make compatible with the lammpi variant. The packaging is on fink tracking at... https://sourceforge.net/tracker/index.php?func=detail&aid=2838001&group_id=17203&atid=414256 Jack -- 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 Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] openmpi with xgrid
Yep, I did some tests and found out that to have xgrid support I need to have --disable-static. So I did in openmpi.info and it compiled and installed OK. But when I went to test... /sw/bin/om-mpirun -c 2 mpiapp [amadeus.local:38063] [[2798,0],0] ORTE_ERROR_LOG: Unknown error: 1 in file src/plm_xgrid_module.m at line 119 [amadeus.local:38063] [[2798,0],0] ORTE_ERROR_LOG: Unknown error: 1 in file src/plm_xgrid_module.m at line 153 I will bother openmpi mailing list now :-) AFAIK, you need 'sudo xgridctl c start' running if using openmpi with xgrid. I understand that many doesn't want or need this functionality but having a 'openmpi-xgrid' option in fink would be plus (at least for me). Cheers, Alan On Thu, Aug 13, 2009 at 14:18, Jack Howarth wrote: > The failure to build the Xgrid support appears to be related to > its incompatibility with the -enable-static configure option... > > http://www.open-mpi.org/community/lists/users/2007/08/3900.php > > I would complain to upstream. > > > -- > 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 > Fink-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/fink-users > -- 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 Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] problems with rsync upgrades
Felix Frolow wrote: > Recently, doing update o software using FINK I get: > > [adsl-mbfrolow:~] mbfrolow% sudo fink selfupdate > rsync -az -q rsync://msn.wi.us.finkmirrors.net/finkinfo//TIMESTAMP / > sw/fink/TIMESTAMP.tmp > @ERROR: chroot failed [] > Choosing another site > rsync -az -q rsync://sjc.ca.us.finkmirrors.net/finkinfo//TIMESTAMP / > sw/fink/TIMESTAMP.tmp > is picked, but still http://msn.wi.us.finkmirrors.net Not found > is announced several times > How dangerous it is? Is this my site problem (changes in firewall) or > http://msn.wi.us > is down? It seems that currently the mirror rsync://msn.wi.us.finkmirrors.net/finkinfo/ is broken. Another one that is broken is rsync://trd.no.eu.finkmirrors.net/finkinfo/, it gives "Connection refused". All other mirrors seem to work normally at the moment. I am CCing to the msn email address, too, so they can fix it. -- Martin -- 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 Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] testing apbs-mpi
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 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 Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
