Hi, All We've installed MEEP on our SunFire V890 based cluster. The software (MEEP) ain't working properly and that's the main reason of posting to this mailing list. Perhaps we could get some guidance on this forum on how to resolve the issue.
-bash-3.00$ uname -a SunOS indus1 5.10 Generic_118833-36 sun4u sparc SUNW,Sun-Fire-V890 Contents of the email ===================== a) Three tests that show MEEP failing b) Installation procedure c) Environment Information d) Contents of logs.tar.gz - you can download it from http://hpc.niit.edu.pk/~aamir/res/logs.tar.gz a) Three tests that show MEEP failing ===================================== Basically, three "tests" that suggest some problem with installation. These include, MEEP's "make check", $MEEP_HOME/examples/ring.ctl simulation, and $MEEP_HOME/examples/ring.ctl. 1. MEEP's "make check" fails. [ .. the output is attached .. ] 2. Running $MEEP_HOME/examples/ring.ctl simulation fails: _________________________________________________ bash-3.00$ mpirun -np 1 ~/install/meep/bin/meep-mpi ring.ctl Using MPI version 2.0, 1 processes ----------- Initializing structure... Working in 2D dimensions. cylinder, center = (0,0,0) radius 2, height 1e+20, axis (0, 0, 1) dielectric constant epsilon = 11.56 cylinder, center = (0,0,0) radius 1, height 1e+20, axis (0, 0, 1) dielectric constant epsilon = 1 Halving computational cell along direction y time for set_epsilon = 0.177334 s ----------- creating output file "./ring-eps-000000.00.h5"... Meep progress: 0.05/300.0 = 0.0% done in 6.6s, 39728.3s to go harminv0:, frequency, imag. freq., Q, |amp|, amplitude, error harminv: failure on line 853 of harminv.c: argument out of range in harminv_get_amplitude Some deprecated features have been used. Set the environment variable GUILE_WARN_DEPRECATED to "detailed" and rerun the program to get more information. Set it to "no" to suppress this message. _________________________________________________ 3. Running $MEEP_HOME/examples/ring.ctl simulation fails: _________________________________________________ bash-3.00$ mpirun -np 1 ~/install/meep/bin/meep-mpi bend-flux.ctl Using MPI version 2.0, 1 processes ----------- Initializing structure... Working in 2D dimensions. block, center = (-2,-11.5,0) size (12,1,1e+20) axes (1,0,0), (0,1,0), (0,0,1) dielectric constant epsilon = 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 = 12 time for set_epsilon = 0.443259 s ----------- ADIOI_NFS_OPEN (line 55): **filenoexist ./bend-flux-refl-flux.h5ADIOI_NFS_OPEN (line 55): **filenoexist ./bend-flux-refl-flux.h5MPI_FILE_CLOSE (line 51): **iobadfh HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 MPI-process 0. Back trace follows. #000: H5F.c line 2048 in H5Fopen(): unable to open file major(04): File interface minor(17): Unable to open file #001: H5F.c line 1725 in H5F_open(): unable to open file major(04): File interface minor(17): Unable to open file #002: H5FD.c line 1044 in H5FD_open(): open failed major(22): Virtual File Layer minor(29): Unable to initialize object #003: H5FDmpio.c line 798 in H5FD_mpio_open(): MPI_File_open failed major(03): Internal HDF5 error minor(78): Some MPI function failed #004: H5FDmpio.c line 798 in H5FD_mpio_open(): MPI_ERR_NO_SUCH_FILE: no such file or directory major(03): Internal HDF5 error minor(79): MPI Error String meep: error on line 243 of h5file.cpp: error opening HDF5 input file [indus1:11331] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1 Some deprecated features have been used. Set the environment variable GUILE_WARN_DEPRECATED to "detailed" and rerun the program to get more information. Set it to "no" to suppress this message. _________________________________________________ b) Installation procedure ========================= It turns out that Sun Studio installation contains BLAS and LAPACK. These are contained in /opt/SUNWspro directory. Install Harminv --------------- These instructions are valid for indus1 (the head node of our SunFire V890 cluster). Install harminv with the following commands: ./configure --with-blas=/opt/SUNWspro/lib/libsunperf.so --with-lapack=/opt/SUNWspro/lib/libsunperf.so --prefix=/home/aamir/install/harminv make ; make install Install Guile ------------- Guile is install through pkg-get install. The version of guile is 1.6.7. It is installed in /opt/csw/bin and /opt/csw/lib Install libctl -------------- Install libctl with the following commands: ./configure --prefix=/home/aamir/install/libctl make ; make install Install hdf5 ------------ Install hdf5 with the following commands: ./configure --prefix=/home/aamir/install/hdf5 --enable-parallel make ; make install Install MPI ----------- Sun HPC Cluster Toolkit 7.0 now contains a customized version od Open MPI. The version 6.0 had Sun MPI. This toolkit is installed in /opt/SUNWhpc/HPC7.0 and I'm using the MPI library inside this toolkit. Install Meep ------------ Install meep with the following commands: ./configure --prefix=/home/aamir/install/meep --with-mpi --with-libctl=/home/aamir/install/libctl/share/libctl --with-blas=/opt/SUNWspro/lib/libsunperf.so --with-lapack=/opt/SUNWspro/lib/libsunperf.so make ; make install c) Environment Information ========================== -bash-3.00$ echo $LD_LIBRARY_PATH /home/aamir/install/meep/lib:/home/aamir/install/hdf5/lib:/opt/SUNWhpc/HPC7.0/lib:/home/aamir/install/harminv/lib:/opt/csw/lib:/home/aamir/install/libctl/lib -bash-3.00$ echo $PATH /home/aamir/install/harminv/bin:/opt/SUNWspro/bin:/opt/csw/gcc3/bin:/usr/bin:/opt/csw/bin:/opt/SUNWspro/bin:/usr/sfw/bin:/usr/cluster/bin:/usr/ccs/bin:/usr/sbin:/opt/SUNWexplo/bin:/opt/SUNWrtvc/bin:/opt/SUNWsneep/bin:/bin:/usr/openwin/bin:/usr/ucb:/usr/sfw/bin:/opt/csw/bin:/usr/bin:/opt/SUNWhpc/HPC7.0/bin:/home/aamir/install/hdf5/bin:/home/aamir/install/libctl/bin:/home/aamir/install/meep/bin -bash-3.00$ echo $CPPFLAGS -I/home/aamir/install/harminv/include -I/opt/csw/include -I/home/aamir/install/libctl/include -I/opt/SUNWhpc/HPC7.0/include -I/home/aamir/install/hdf5/include -I/home/aamir/install/meep/include -bash-3.00$ echo $LDFLAGS -L/home/aamir/install/harminv/lib -L/opt/csw/lib -L/home/aamir/install/libctl/lib -L/opt/SUNWhpc/HPC7.0/lib -L/home/aamir/install/hdf5/lib -L/home/aamir/install/meep/lib -bash-3.00$ echo $PKG_CONFIG_PATH :/home/aamir/install/harminv/lib/pkgconfig d) Contents of logs.tar.gz (http://hpc.niit.edu.pk/~aamir/res/logs.tar.gz) ====================================== (http://hpc.niit.edu.pk/~aamir/res/logs.tar.gz) Output of bend-flux example --> bendflux_example.log Output of MEEP's make --> make.log Output of ring example --> ring_example.log Output of MEEP's ./configure --> config.log Output of MEEP's make all --> make_all.log Output of HDF5 make check --> hdf5_makecheck.log Output of MEEP's make check --> make_check.log --Aamir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
