Dear Steven, dear users, thanks for providing this tool and so much useful information. This mailing list and of course the wiki always helped to find quick solutions, but now I stumbled on a problem, I'm not able to solve. I've been using meep in serial mode for some time. Running on an Ubuntu machine I conveniently installed meep from the repositories. Now I got access to this multicore rhel system and since a couple of days I'm trying to make meep-mpi work. Here is what I did:
Mainly I followed the instructions from this link: http://www.doe.carleton.ca/~kmedri/research/centosmeepinstall.html I obtained the binaries from Epel and from here: http://www.elders.princeton.edu/data/PU_IAS/5/en/os/x86_64/Workstation/ HDF5 was compiled from source: CC=/path/to/openmpi/bin/mpicc ./configure --prefix=/path/to/hdf5 --enable-parallel make make install Same for meep: ./configure --with-mpi --with-hdf5=/path/to/hdf5/ But make check already spits out errors: PASS: bench PASS: bragg_transmission FAIL: convergence_cyl_waveguide PASS: cylindrical PASS: flux PASS: harmonics PASS: integrate FAIL: known_results PASS: one_dimensional PASS: physical FAIL: symmetry FAIL: three_d PASS: two_dimensional PASS: 2D_convergence PASS: h5test PASS: pml Nevertheless I installed meep and I'm able to calculate some of the examples, but not all of them: mpirun -np 12 meep-mpi bend-flux.ctl librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list -------------------------------------------------------------------------- [[8627,1],1]: A high-performance Open MPI point-to-point messaging module was unable to find any relevant network interfaces: Module: OpenFabrics (openib) Host: host Another transport will be used instead, although this may result in lower performance. -------------------------------------------------------------------------- librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list librdmacm: couldn't read ABI version. librdmacm: assuming: 4 CMA: unable to get RDMA device list Using MPI version 2.1, 12 processes ----------- Initializing structure... Working in 2D dimensions. Computational cell is 16 x 32 x 0 with resolution 10 block, center = (-2,-11.5,0) size (12,1,1e+20) axes (1,0,0), (0,1,0), (0,0,1) dielectric constant epsilon diagonal = (12,12,12) block, center = (3.5,2,0) size (1,28,1e+20) axes (1,0,0), (0,1,0), (0,0,1) dielectric constant epsilon diagonal = (12,12,12) time for set_epsilon = 0.00918102 s ----------- meep: meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft meep: incorrect dataset size (0 vs. 8800) in load_dft_hdf5 ./bend-flux-refl-flux.h5:ey_dft -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. I get the same results with a serial HDF5 from a rpm package. All tests are failing with a manually compiled openmpi --without-openib. Any hints? Thanks for the time... -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de _______________________________________________ meep-discuss mailing list [email protected] http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
