My apologies
I should have written something instead of someting
--- Mer 10/2/10, Riccardo Corradini <riccardocorrad...@yahoo.it> ha scritto:
Da: Riccardo Corradini <riccardocorrad...@yahoo.it>
Oggetto: Re: [OctDev] R: undefined symbol: _ZN3MPI3Win4FreeEv executing
MPI_Init of openmpi_ext
A: "Eduardo Díaz Díaz" <eduardo.d...@cttc.es>
Cc: octave-dev@lists.sourceforge.net
Data: Mercoledì 10 febbraio 2010, 17:43
I think there is someting wrong with the whole set of mpi libs
Infact mine is different
mkoctfile -s -I/home/corradin/openmpi-1.3.3/include -lpthread
-L/home/corradin/openmpi-1.3.3/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl
-lnsl -lutil -lm -ldl
Because this is my output of
mpiCC --showme
g++ -I/home/corradin/openmpi-1.3.3/include -pthread
-L/home/corradin/openmpi-1.3.3/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl
-Wl,--export-dynamic -lnsl -lutil -lm -ldl
What do you have when you type mpiCC --showme?
My guess is -lmpi_cxx missing
In the configure help
is also written
--enable-orterun-prefix-by-default
Bests
Riccardo
--- Mer 10/2/10, Eduardo Díaz Díaz <eduardo.d...@cttc.es> ha scritto:
Da: Eduardo Díaz Díaz <eduardo.d...@cttc.es>
Oggetto: Re: R: [OctDev] undefined symbol: _ZN3MPI3Win4FreeEv executing
MPI_Init of openmpi_ext
A: "Riccardo Corradini" <riccardocorrad...@yahoo.it>
Cc: octave-dev@lists.sourceforge.net
Data: Mercoledì 10 febbraio 2010, 17:00
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
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