megatest test failure/MPI problem

From: Meij, Henk (
Date: Wed Oct 15 2008 - 10:14:48 CDT

cluster: redhat linux AS4 x86_64 with 2.6.9-34 kernel
namd: 2.6 source, trying to compile linux-amd64-MPI with gcc
mpi: 2 flavors (topspin infiniband libs came with cluster), openmpi (1.2 compiled with gigE and Infiniband libs).

i'm trying to pass the megatest and detail my steps below. when i get to invoke pgm i run into a problem that i do not encounter when invoking other problems. seems basic but i can not find a way out. (invoking mpirun directly as i'm running LSF 6.2).


tar zxvf /share/apps/src/fftw-linux-amd64.tar.gz
vi fftw/linux-amd64/arch/Linux-amd64.fftw # fix path
tar zxvf /share/apps/src/tcl-linux-amd64.tar.gz
vi tcl/linux-amd64/arch/Linux-amd64.fftw # fix path
tar zxvf /share/apps/src/NAMD_2.6_Source.tar.gz
cd NAMD_2.6_Source/
not edits in arch/Linux-amd64-MPI.arch
cd charm-5.9/
vi src/arch/mpi-linux-amd64/ # point to Topspin's or Openmpi's mpirun
/usr/local/topspin/mpi/mpich/bin/mpiCC -show 2>/dev/null | cut -d' ' -f1 # returns g++
/share/apps/openmpi-1.2/bin/mpiCC -show 2>/dev/null | cut -d' ' -f1 # returns g++
# no changes in src/arch/common/
./build charm++ mpi-linux-amd64
# charm++ built successfully.
cd mpi-linux-amd64/tests/charm++/megatest/
make # no errors

# first attempt, missing libs using Topspin
[root_at_swallowtail NAMD]# echo $LD_LIBRARY_PATH
[root_at_swallowtail megatest]# ldd pgm => /usr/local/topspin/mpi/mpich/lib64/ (0x0000002a95557000) => /lib64/ (0x0000003684000000) => not found => /opt/lam/gnu/lib/ (0x0000002a97797000) => not found => not found => /lib64/tls/ (0x0000003689000000) => /usr/lib64/ (0x0000002a9790f000) => /lib64/ (0x0000003686d00000) => /lib64/ (0x0000003688600000) => /lib64/tls/ (0x00000034d3600000) => /usr/lib64/ (0x00000034d3800000) => /lib64/ (0x0000003687b00000) => /lib64/tls/ (0x0000003684400000) => /lib64/tls/ (0x0000003683b00000) => /usr/lib64/ (0x00000039aa100000) => /usr/local/topspin/mpi/mpich/lib64/ (0x0000002a97a17000) => /usr/local/topspin/mpi/mpich/lib64/ (0x0000002a97b37000)
        /lib64/ (0x0000003683900000)

# second attempt with OpenMPI
[root_at_swallowtail megatest]# echo $LD_LIBRARY_PATH
[root_at_swallowtail megatest]# ldd ./pgm => /usr/local/topspin/mpi/mpich/lib64/ (0x0000002a95576000) => /lib64/ (0x0000003684000000) => /share/apps/openmpi-1.2/lib/ (0x0000002a97797000) => /share/apps/openmpi-1.2/lib/ (0x0000002a978ba000) => /share/apps/openmpi-1.2/lib/ (0x0000002a97a4e000) => /share/apps/openmpi-1.2/lib/ (0x0000002a97ba7000) => /lib64/tls/ (0x0000003689000000) => /usr/lib64/ (0x0000002a97d03000) => /lib64/ (0x0000003686d00000) => /lib64/ (0x0000003688600000) => /lib64/tls/ (0x00000034d3600000) => /usr/lib64/ (0x00000034d3800000) => /lib64/ (0x0000003687b00000) => /lib64/tls/ (0x0000003684400000) => /lib64/tls/ (0x0000003683b00000) => /usr/lib64/ (0x00000039aa100000) => /usr/local/topspin/mpi/mpich/lib64/ (0x0000002a97e0b000) => /usr/local/topspin/mpi/mpich/lib64/ (0x0000002a97f2b000)
        /lib64/ (0x0000003683900000)

# run pgm on infiniband enabled node, create a file with 4 lines of node name 'compute-1-1'
# using OpenMPI

[root_at_swallowtail megatest]# /share/apps/openmpi-1.2/bin/mpirun_ssh -np 4
Can't read MPIRUN_HOST
Can't read MPIRUN_HOST
Can't read MPIRUN_HOST
Can't read MPIRUN_HOST
[root_at_swallowtail megatest]# cat

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