I notice that "ompi_info -c" prints out the CXX flags and so forth that were
used to compile Open MPI. I guess we can use that to make a Makefile that is
generic. Do you see -lmpi_cxx in the output of that command?
Cheers, M.
On Thu, Feb 11, 2010 at 11:21 AM, Eduardo Díaz Díaz <[email protected]>wrote:
> Hello Michael,
>
> I was using the newest version but look what is happening:
>
> First, the Makefile replace the -lpthread with -pthread:
> c...@hpcmaster:~/openmpi_ext/src$ mpicc --showme:compile
> -I/home/csi/openmpi-1.3.3/include -pthread
> c...@hpcmaster:~/openmpi_ext/src$ mpicc --showme:compile | sed -e
> "s/-pthread/-lpthread/g"
> -I/home/csi/openmpi-1.3.3/include -lpthread
>
> After this, more or less with the libdir:
> c...@hpcmaster:~/openmpi_ext/src$ mpicc -showme:link
> -pthread -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal
> -libverbs -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
> c...@hpcmaster:~/openmpi_ext/src$ mpicc -showme:link | sed -e "s/-pthread/
> /g"
> -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl
> -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>
> and then, the result is:
> mkoctfile -s -I/home/csi/openmpi-1.3.3/include
> -L/home/csi/openmpi-1.3.3/lib -lmpi -lopen-rte -lopen-pal -libverbs -ldl
> -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>
> That doesn't contains the *-lmpi_cxx* configure option that I need to run
> the openmpi_ext (the problem I had). Nevertheless using the
> Makefile.OPENMPI1.3.3 (modified) works fine because:
> 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
>
> MY_INC will be /home/csi/openmpi-1.3.3/include and MY_LIBS will be
> /home/csi/openmpi-1.3.3/lib (in my specific case), so the mkoctfile result
> is:
> mkoctfile -s -I/home/csi/openmpi-1.3.3/include -lpthread
> -L/home/csi/openmpi-1.3.3/lib *-lmpi_cxx* -lmpi -lopen-rte -lopen-pal -ldl
> -lnsl -lutil -lm -ldl
>
> That has included the -lmpi_cxx.
> The problem I see is that the mpicc -showme:compile doesn't include (for
> me?) the -lmpi_cxx. What do you think is happening?. Is it normal that my
> mpicc -showme:compile doesn't include it?
>
> Thanks,
>
> --
> 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 [email protected]http://www.cttc.es
>
>
>
> Michael Creel escribió:
>
> Hi all,
> Eduardo, I think you were operating with an old version of the Makefile. As
> of a week or so ago, the Makefile attempts to read the needed information
> automatically. Could you please do a checkout of the whole package, and try
> making it just doing "make all"?
> Michael
>
> On Thu, Feb 11, 2010 at 9:59 AM, Eduardo Díaz Díaz
> <[email protected]>wrote:
>
>> 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) $<
>> clean:
>> -rm *.o *.oct *~
>>
>> Riccardo, thanks a lot for your effort with openmpi_ext and your help.
>>
>> PS: Michael Creel, thanks too.
>>
>>
>>
>>
>> --
>> Eduardo Díaz Díaz
>> Centre Tecnològic de Telecomunicacions de Catalunya
>> Telecommunications Technological Center of Catalonia
>> Parc Mediterrani de la Tecnologia
>> Av. Carl Friedrich Gauss 7 (formerly, Av. Canal Olímpic SN)
>> 08860 Castelldefels (Barcelona)
>> Tel.: +34 93 645 29 26
>> Fax. +34 93 645 29 [email protected]http://www.cttc.es
>>
>>
>>
>>
>> Riccardo Corradini escribió:
>>
>> I think there is someting wrong with the whole set of mpi libs
>> Infact mine is different
>> mkoctfile -s -I/home/corradin/openmpi-1.3.3/include -lpthread
>> -L/home/corradin/openmpi-1.3.3/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal
>> -ldl -lnsl -lutil -lm -ldl
>> Because this is my output of
>> mpiCC --showme
>> g++ -I/home/corradin/openmpi-1.3.3/include -pthread
>> -L/home/corradin/openmpi-1.3.3/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal
>> -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>> What do you have when you type mpiCC --showme?
>> My guess is -lmpi_cxx missing
>> In the configure help
>> is also written
>> --enable-orterun-prefix-by-default
>> Bests
>> Riccardo
>>
>>
>> --- *Mer 10/2/10, Eduardo Díaz Díaz
>> <[email protected]><[email protected]>
>> * ha scritto:
>>
>>
>> Da: Eduardo Díaz Díaz <[email protected]> <[email protected]>
>> Oggetto: Re: R: [OctDev] undefined symbol: _ZN3MPI3Win4FreeEv executing
>> MPI_Init of openmpi_ext
>> A: "Riccardo Corradini"
>> <[email protected]><[email protected]>
>> Cc: [email protected]
>> Data: Mercoledì 10 febbraio 2010, 17:00
>>
>> Thanks Riccardo,
>>
>> I recompiled openmpi-1.3.3 again with this:
>> ./configure --enable-mpirun-prefix-by-default
>> --prefix=$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/:$LD_LIBRARY_PATH
>> unset ompi_info OMPIBIN OMPILIB OMPISCD
>>
>> --
>> Eduardo Díaz Díaz
>> Centre Tecnològic de Telecomunicacions de Catalunya
>> Telecommunications Technological Center of Catalonia
>> Parc Mediterrani de la Tecnologia
>> Av.. Carl Friedrich Gauss 7 (formerly, Av. Canal Olímpic SN)
>> 08860 Castelldefels (Barcelona)
>> Tel.: +34 93 645 29 26
>> Fax. +34 93 645 29 [email protected]http://www.cttc.es
>>
>>
>>
>>
>> Riccardo Corradini escribió:
>>
>> Hi *Eduardo*,
>> have a look at
>>
>> http://octave.svn.sourceforge.net/viewvc/octave/trunk/octave-forge/extra/openmpi_ext/doc/README?revision=6476&view=markup
>> If you dot include all the mpi libs required you will have this type of
>> problem
>> Also if the problem persists try to recompile openmpi1.3.3 from source
>> with the following options
>> ./configure --enable-mpirun-prefix-by-default --enable-heterogeneous
>> --prefix=$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 <[email protected]>* ha scritto:
>>
>>
>> Da: Eduardo Díaz Díaz <[email protected]>
>> Oggetto: [OctDev] undefined symbol: _ZN3MPI3Win4FreeEv executing MPI_Init
>> of openmpi_ext
>> A: [email protected]
>> 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 <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 <[email protected]> (but first, please read
>> http://www.octave..org/bugs.html <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
>> [email protected]
>> http://www.cttc.es
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>> [email protected]
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>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
>> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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>>
>
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