charm AT lists.siebelschool.illinois.edu
Subject: Charm++ parallel programming system
List archive
- From: Phil Miller <mille121 AT illinois.edu>
- To: "Matthew B. Roark" <Roarkma AT wabash.edu>
- Cc: "charm AT cs.uiuc.edu" <charm AT cs.uiuc.edu>
- Subject: Re: [charm] [ppl] NAMD and Charm++ with OpenMPI 1.2.6
- Date: Tue, 25 Jan 2011 15:21:29 -0600
- List-archive: <http://lists.cs.uiuc.edu/pipermail/charm>
- List-id: CHARM parallel programming system <charm.cs.uiuc.edu>
It seems odd that charmxi is linked against libmpi_cxx.so.0. Could you
send us the output of ldd
/export/home/charmm/NAMD_2.7_Source/charm-6.2.2/mpi-linux-x86_64-openmpi-mpicxx/bin/charmxi
Phil
On Tue, Jan 25, 2011 at 14:49, Matthew B. Roark
<Roarkma AT wabash.edu>
wrote:
> I am running Rocks 5.1 and want to install NAMD. I have downloaded the
> source files for v2.7 (which uses Charm-6.2.2). I want to build
> several versions to test efficiency and scalability with both a gigabit
> ethernet connection and infiniband.
> I am able to install (and make a megatest) with the following build
> commands:
>
> CHARM_FLAGS="--no-build-shared --with-production"
> ./build charm++ multicore-linux64 gcc -j4 ${CHARM_FLAGS}
> ./build charm++ net-linux-x86_64 gcc -j4 ${CHARM_FLAGS}
> ./build charm++ net-linux-x86_64 gcc ibverbs -j4 ${CHARM_FLAGS}
>
> I am not able to build Charm-6.2.2 with OpenMPI v1.2.6 that came with the
> OFED package for Rocks 5.1. I am using a script to automate the setup,
> and here are the relevant parts:
> MPI_INCLUDE="/usr/mpi/gcc/openmpi-1.2.6/include"
> MPI_LIB="/usr/mpi/gcc/openmpi-1.2.6/lib64"
>
> CHARMSRC="${NAMDSRC}/charm-6.2.2"
> cp -r ${CHARMSRC}/src/arch/mpi-linux-x86_64
> ${CHARMSRC}/src/arch/mpi-linux-x86_64-openmpi
> sed -e 's/MPICXX_DEF=mpgcc/MPICXX_DEF=mpicxx/' -i
> ${CHARMSRC}/src/arch/mpi-linux-x86_64-openmpi/conv-mach.sh
>
> env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64-openmpi mpicxx -j4
> ${CHARM_FLAGS} --incdir ${MPI_INCLUDE} --libdir ${MPI_LIB} -O
>
> I save the output of the build command in a log file and it reads:
>
> Selected Compiler: mpicxx
> Selected Options:
> Copying src/scripts/Makefile to mpi-linux-x86_64-openmpi-mpicxx/tmp
> Soft-linking over bin
> Soft-linking over lib
> Soft-linking over lib_so
> Soft-linking over include
> Soft-linking over tmp
> Generating mpi-linux-x86_64-openmpi-mpicxx/tmp/conv-mach-pre.sh
> Performing '/usr/bin/gmake -j 4 basics OPTS=-optimize -O QUIET=' in
> mpi-linux-x86_64-openmpi-mpicxx/tmp
> /usr/bin/gmake charmxi
> gmake[1]: Entering directory
> `/export/home/charmm/NAMD_2.7_Source/charm-6.2.2/mpi-linux-x86_64-openmpi-mpicxx/tmp'
> gmake[1]: Nothing to be done for `charmxi'.
> gmake[1]: Leaving directory
> `/export/home/charmm/NAMD_2.7_Source/charm-6.2.2/mpi-linux-x86_64-openmpi-mpicxx/tmp'
> /usr/bin/gmake headerlinks
> gmake[1]: Entering directory
> `/export/home/charmm/NAMD_2.7_Source/charm-6.2.2/mpi-linux-x86_64-openmpi-mpicxx/tmp'
> ../bin/charmc -intrinsic -optimize -O -nobs ckcallback.ci
> Passing -O to charmc no longer uses charm's platform-specific
> optimization defaults. Use -optimize for that instead.
> The -O flag is being passed to the underlying compiler.
> ../bin/charmxi: error while loading shared libraries: libmpi_cxx.so.0:
> cannot open shared object file: No such file or directory
> Fatal Error by charmc in directory
> /export/home/charmm/NAMD_2.7_Source/charm-6.2.2/mpi-linux-x86_64-openmpi-mpicxx/tmp
> Command ../bin/charmxi -intrinsic ckcallback.ci returned error code 127
> charmc exiting...
> gmake[1]: *** [CkCallback.decl.h] Error 1
> gmake[1]: Leaving directory
> `/export/home/charmm/NAMD_2.7_Source/charm-6.2.2/mpi-linux-x86_64-openmpi-mpicxx/tmp'
> gmake: *** [headers] Error 2
> -------------------------------------------------
> Charm++ NOT BUILT. Either cd into mpi-linux-x86_64-openmpi-mpicxx/tmp and
> try
> to resolve the problems yourself, visit
> http://charm.cs.uiuc.edu/
> for more information. Otherwise, email the developers at
> charm AT cs.uiuc.edu
>
>
> I do not understand why it is not able to find this shared library. It
> does exist in the specified library directory:
> [charmm@rocks2
> NAMD_2.7_Source]$ ls -l /usr/mpi/gcc/openmpi-1.2.6/lib64/
> total 11752
> -rwxr-xr-x 1 root root 1034 Jun 5 2008 libmca_common_sm.la
> lrwxrwxrwx 1 root root 25 Apr 29 2009 libmca_common_sm.so ->
> libmca_common_sm.so.0.0.0
> lrwxrwxrwx 1 root root 25 Apr 29 2009 libmca_common_sm.so.0 ->
> libmca_common_sm.so.0.0.0
> -rwxr-xr-x 1 root root 27894 Jun 5 2008 libmca_common_sm.so.0.0.0
> -rwxr-xr-x 1 root root 994 Jun 5 2008 libmpi_cxx.la
> lrwxrwxrwx 1 root root 19 Apr 29 2009 libmpi_cxx.so ->
> libmpi_cxx.so.0.0.0
> lrwxrwxrwx 1 root root 19 Apr 29 2009 libmpi_cxx.so.0 ->
> libmpi_cxx.so.0.0.0
> -rwxr-xr-x 1 root root 1446431 Jun 5 2008 libmpi_cxx.so.0.0.0
> -rwxr-xr-x 1 root root 998 Jun 5 2008 libmpi_f77.la
> lrwxrwxrwx 1 root root 19 Apr 29 2009 libmpi_f77.so ->
> libmpi_f77.so.0.0.0
> lrwxrwxrwx 1 root root 19 Apr 29 2009 libmpi_f77.so.0 ->
> libmpi_f77.so.0.0.0
> -rwxr-xr-x 1 root root 1756773 Jun 5 2008 libmpi_f77.so.0.0.0
> -rwxr-xr-x 1 root root 989 Jun 5 2008 libmpi_f90.la
> lrwxrwxrwx 1 root root 19 Apr 29 2009 libmpi_f90.so ->
> libmpi_f90.so.0.0.0
> lrwxrwxrwx 1 root root 19 Apr 29 2009 libmpi_f90.so.0 ->
> libmpi_f90.so.0.0.0
> -rwxr-xr-x 1 root root 35008 Jun 5 2008 libmpi_f90.so.0.0.0
> -rwxr-xr-x 1 root root 1075 Jun 5 2008 libmpi.la
> lrwxrwxrwx 1 root root 15 Apr 29 2009 libmpi.so -> libmpi.so.0.0.0
> lrwxrwxrwx 1 root root 15 Apr 29 2009 libmpi.so.0 -> libmpi.so.0.0.0
> -rwxr-xr-x 1 root root 5298971 Jun 5 2008 libmpi.so.0.0.0
> -rwxr-xr-x 1 root root 1009 Jun 5 2008 libopen-pal.la
> lrwxrwxrwx 1 root root 20 Apr 29 2009 libopen-pal.so ->
> libopen-pal.so.0.0.0
> lrwxrwxrwx 1 root root 20 Apr 29 2009 libopen-pal.so.0 ->
> libopen-pal.so.0.0.0
> -rwxr-xr-x 1 root root 1002148 Jun 5 2008 libopen-pal.so.0.0.0
> -rwxr-xr-x 1 root root 1057 Jun 5 2008 libopen-rte.la
> lrwxrwxrwx 1 root root 20 Apr 29 2009 libopen-rte.so ->
> libopen-rte.so.0.0.0
> lrwxrwxrwx 1 root root 20 Apr 29 2009 libopen-rte.so.0 ->
> libopen-rte.so.0.0.0
> -rwxr-xr-x 1 root root 2176406 Jun 5 2008 libopen-rte.so.0.0.0
> -rwxr-xr-x 1 root root 210202 Jun 5 2008 mpi.mod
> drwxr-xr-x 2 root root 4096 Apr 29 2009 openmpi
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- [charm] NAMD and Charm++ with OpenMPI 1.2.6, Matthew B. Roark, 01/25/2011
- Re: [charm] [ppl] NAMD and Charm++ with OpenMPI 1.2.6, Phil Miller, 01/25/2011
- Re: [charm] [ppl] NAMD and Charm++ with OpenMPI 1.2.6, Jim Phillips, 01/25/2011
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