Charm++ parallel programming system

[Phil Miller <mille121 AT illinois.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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