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

Thu, 11 Feb 2010 01:08:25 -0800

Hello Riccardo,

I recompiled again the openmpi1.3.3 with the configure option -lmpi_cxx and openmpi_ext and in my mpiCC apper the option, but not in the mkoctfile

mpiCC --showme
c...@hpcmaster:~$ mpiCC --showme
g++ -I/home/csi/openmpi-1.3.3/include -pthread -L/home/csi/openmpi-1.3.3/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

mkoctfile
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

Then, I suppose that the problem was with my "make openmpi_ext". Effectively I did "make install all" and make command look for the Makefile file first. First error. I needed to do "make -f Makefile.OPENMPI1.3.3". Evidently, I need to modify it with my particular $HOME options (not /home/corradini). Then, I propose this one (works for me):

# <<<<<<< .mine
MY_INC=`ompi_info -a | grep Incdir | cut -d: -f2 | sed -e 's/^[ \t]*//'`
MY_LIBS=`ompi_info --path libdir | cut -d: -f2 | sed -e 's/^[ \t]*//'`

MPIINC = -I$(MY_INC)
MPILIBS = -lpthread -L$(MY_LIBS) -lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl -lnsl -lutil -lm -ldl
# =======
# MPIINC = -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi
# MPILIBS = -lpthread -L/usr/lib/openmpi/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
# >>>>>>> .r6543

all: MPI_Init.oct \
     MPI_Initialized.oct \
     MPI_Comm_rank.oct \
     MPI_Comm_size.oct \
     MPI_Finalize.oct \
     MPI_Finalized.oct \
     MPI_Send.oct \
     MPI_Recv.oct \
     MPI_Iprobe.oct \
     MPI_Probe.oct \
     MPI_Barrier.oct \
     MPI_Comm_Load.oct \
     MPI_Comm_Test.oct \


%.oct: %.cc
    mkoctfile -s $(MPIINC)  $(MPILIBS)   $<
clean:
    -rm *.o  *.oct *~

Riccardo, thanks a lot for your effort with openmpi_ext and your help.

PS: Michael Creel, thanks too. 




-- 
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:
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




------------------------------------------------------------------------------
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
 


------------------------------------------------------------------------------
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

Reply via email to