Re: [OctDev] R: undefined symbol: _ZN3MPI3Win4FreeEv executing MPI_Init of openmpi_ext

[Eduardo Díaz Díaz]

Thanks Riccardo, I recompiled openmpi-1.3.3 again with this: ./configure --enable-mpirun-prefix-by-default --prefix=$HOME/openmpi-1.3.3/ --enable-static nevertheless there are something wrong with warnings: (..) configure: WARNING: Unrecognized options: --enable-mpirun-prefix-by-default, --enable-ltdl-convenience (..) But finally compiles and then I make install all. After that, I re-compile openmpi_ext: c...@hpcmaster:~/openmpi_ext/src$ make mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Init.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Initialized.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Comm_rank.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Comm_size.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Finalize.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Finalized.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Send.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Recv.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Iprobe.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Probe.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Barrier.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Comm_Load.cc mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread   -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl MPI_Comm_Test.cc But the problem with MPI_Init persists. Any ideas? PS: I modified the .bashrc too following the documentation: ompi_info=/home/csi/openmpi-1.3.3/bin/ompi_info OMPIBIN=`$ompi_info  -path      bindir  -parsable  | cut -d: -f3` OMPILIB=`$ompi_info  -path      libdir  -parsable  | cut -d: -f3` OMPISCD=`$ompi_info  -path  sysconfdir  -parsable  | cut -d: -f3` export  PATH=$OMPIBIN:$PATH export  LD_LIBRARY_PATH=:$OMPILIB:/usr/lib/octave-3.2.2/:$LD_LIBRARY_PATH unset ompi_info  OMPIBIN OMPILIB OMPISCD -- Eduardo Díaz Díaz Centre Tecnològic de Telecomunicacions de Catalunya Telecommunications Technological Center of Catalonia Parc Mediterrani de la Tecnologia Av. Carl Friedrich Gauss 7 (formerly, Av. Canal Olímpic SN) 08860 Castelldefels (Barcelona) Tel.: +34 93 645 29 26 Fax. +34 93 645 29 01 eduardo.d...@cttc.es http://www.cttc.es Riccardo Corradini escribió: Hi Eduardo, have a look at http://octave.svn.sourceforge.net/viewvc/octave/trunk/octave-forge/extra/openmpi_ext/doc/README?revision=6476&view=markup If you dot include all the mpi libs required you will have this type of problem Also if the problem persists try to recompile openmpi1.3.3 from source with the following options ./configure --enable-mpirun-prefix-by-default --enable-heterogeneous --prefix=$HOME/openmpi-1.3.3/ --enable-static You are not using an heterogeneous  cluster (ie. 32 bit and 64 bit cpus) you do not need --enable-heterogeneous Please let me know if this helps Bests regards Riccardo Corradini --- Mer 10/2/10, Eduardo Díaz Díaz <eduardo.d...@cttc.es> ha scritto: Da: Eduardo Díaz Díaz <eduardo.d...@cttc.es> Oggetto: [OctDev] undefined symbol: _ZN3MPI3Win4FreeEv executing MPI_Init of openmpi_ext A: octave-dev@lists.sourceforge.net Data: Mercoledì 10 febbraio 2010, 12:16 Hello, I have problems to run successfully the openmpi_ext set instructions for parallel computing. Following the instructions I made: octave3.2 installed openmpi 1.3.3 installed openmpi_ext compiled I run octave on the folder where I have the *.oct files of openmpi_ext: c...@hpcmaster:~/ompi_ext$ octave GNU Octave, version 3.2.2 Copyright (C) 2009 John W. Eaton and others. This is free software; see the source code for copying conditions. There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  For details, type `warranty'. Octave was configured for "i486-pc-linux-gnu". Additional information about Octave is available at http://www.octave..org. Please contribute if you find this software useful. For more information, visit http://www.octave.org/help-wanted.html Report bugs to <b...@octave.org> (but first, please read http://www.octave.org/bugs.html to learn how to write a helpful report). For information about changes from previous versions, type `news'. octave:1> MPI_Init error: /home/csi/ompi_ext/MPI_Init.oct: undefined symbol: _ZN3MPI3Win4FreeEv octave:1> == EXTRA INFO ABOUT THE VERSIONS INSTALLED == mkoctfile 3.2.2: c...@hpcmaster:~/openmpi_ext/openmpi_ext/src$ which mkoctfile /usr/bin/mkoctfile c...@hpcmaster:~/ompi_ext$ ls -alth /usr/bin | grep mkoctfile lrwxrwxrwx  1 root   root      27 2010-02-09 16:53 mkoctfile -> /etc/alternatives/mkoctfile lrwxrwxrwx  1 root   root      15 2010-02-09 16:53 mkoctfile3.2 -> mkoctfile-3.2.2 -rwxr-xr-x  1 root   root     13K 2009-09-19 00:29 mkoctfile-3.2.2 c...@hpcmaster:~/ompi_ext$ ls -alth /etc/alternatives/ | grep mkoctfile lrwxrwxrwx   1 root root   24 2010-02-09 16:53 mkoctfile -> /usr/bin/mkoctfile-3.2.2 lrwxrwxrwx   1 root root   40 2010-02-09 16:53 mkoctfile.1.gz -> /usr/share/man/man1/mkoctfile-3.2.2.1.gz Octave 3.2.2 c...@hpcmaster:~/ompi_ext$ octave GNU Octave, version 3.2.2 Open MPI 1.3.3 c...@hpcmaster:~/ompi_ext$ ompi_info | head -n2                 Package: Open MPI c...@hpcmaster Distribution                Open MPI: 1.3.3 Ubuntu 9.10: c...@hpcmaster:~/ompi_ext$ lsb_release -a | grep Description No LSB modules are available. Description:    Ubuntu 9.10 -- Eduardo Díaz Díaz Centre Tecnològic de Telecomunicacions de Catalunya Telecommunications Technological Center of Catalonia Parc Mediterrani de la Tecnologia Av. Carl Friedrich Gauss 7 (formerly, Av. Canal Olímpic SN) 08860 Castelldefels (Barcelona) Tel.: +34 93 645 29 26 Fax. +34 93 645 29 01 eduardo.d...@cttc.es http://www.cttc.es ------------------------------------------------------------------------------ SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev _______________________________________________ Octave-dev mailing list Octave-dev@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/octave-dev

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