I've been able to get it working on a cluster computer running 64 bit linux. I'm by no means an expert, and after trying compiler suits by pgi, intel and gnu, I only have been able to get it running with the gnu compiler set. I'm quite sure anyone with more experience could have gotten it to work with the other two compilers as well, but gcc was the only compiler that compiled everything without errors. Then I've had difficulties getting the MPI part to work (with gcc): any other implementation than OpenMPI failed while writing data in parallel mode. As the cluster seemingly only had libraries for MVAPICH2, I have compiler HDF5 support myself. In the end, this is what worked for me:
Compiler suite: GNU HDF5: 1.8.5-patch1 OpenMPI: 1.4.3 (compiled and provided by cluster admin) guile: 1.8.8 libctl: 3.1 h5utils: 1.12.1 harminv: 1.3.1 MEEP: 1.1.1 (but patched to add dft export and fix a memory leak) With this configuration, I have been running MEEP on 50 CPUs in parallel. HTH Robert Moerland On Sat, Dec 3, 2011 at 4:42 AM, Maicon Faria <[email protected]> wrote: > This works for me: ./configure LDFLAGS=-L/opt/hdf5/lib > CPPFLAGS=-I/opt/hdf5/include --prefix=/opt/meep-ompi --with-mpi --with-hdf5 > Don't know if this is the problem, but you can try this kind of syntax. > If you are able to run meep-mpi correctly without parallel hdf5 errors, > report to the list please. I have tried do that without results for ages... > > Regards > > Maicon Faria > Reseacher Unicamp/FEEC/DMO > Brazil > > > >> Date: Thu, 1 Dec 2011 16:19:12 -0800 >> From: K Jonathan Harker <[email protected]> >> To: [email protected] >> Subject: [Meep-discuss] Trouble building Meep 1.1.1 against parallel >> HDF5 1.8.8 >> Message-ID: >> >> <cadbpaqnyzif_aevsaoascec8d9ldbexvfspcnzdxcusrpl3...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> I have been trying to install a parallel version of meep on an mpi cluster >> for a while now. Eventually I discovered that I was using the serial >> version of HDF5 and so I built a parallel version of HDF5 1.8.8 with the >> following configuration: >> >> CC=mpicc LDFLAGS="-L/share/apps/lib $LDFLAGS" >> CPPFLAGS="-I/share/apps/include $CPPFLAGS" ./configure >> --prefix=/share/apps >> --enable-parallel --enable-fortran >> >> As you can see, I built this package into the /share/apps directory. I >> was >> able to successfully build H5utils 1.12.1 against this with the following >> configuration: >> >> F77=mpif77 CC=mpicc LDFLAGS="-L/share/apps/lib $LDFLAGS" >> CPPFLAGS="-I/share/apps/include $CPPFLAGS" ./configure --without-octave >> --prefix=/share/apps >> >> But then when I try to build Meep 1.1.1 against this HDF5 with the >> configuration: >> >> F77=mpif77 CC=mpicc LDFLAGS="-L/share/apps/lib $LDFLAGS" >> CPPFLAGS="-I/share/apps/include -DH5_USE_16_API=1 $CPPFLAGS" ./configure >> --with-libctl=$RPM_BUILD_DIR/libctl-3.1 --with-mpi=/opt/openmpi/lib >> --prefix=/share/apps >> >> I see the following output from ./configure: >> >> checking for H5Pcreate in -lhdf5... yes >> checking hdf5.h usability... no >> checking hdf5.h presence... no >> checking for hdf5.h... no >> configure: WARNING: Couldn't find the HDF5 library!! Switching to >> --without-hdf5. >> >> I have checked the /share/apps/include directory, and it does indeed >> contain the hdf5.h header file -- with world-readable permissions. For >> the >> life of me I can't figure out why configure can't see the header file. >> Any >> thoughts? >> >> -- >> Jonathan Harker >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> <http://ab-initio.mit.edu/pipermail/meep-discuss/attachments/20111201/6b72bc2d/attachment-0001.html> >> >> > > > > _______________________________________________ > meep-discuss mailing list > [email protected] > http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss _______________________________________________ meep-discuss mailing list [email protected] http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
