meme 4.10.0_1 parallel error

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Jason H

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Sep 6, 2014, 2:22:43 PM9/6/14
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I installed meme 4.10.0_1 at Linux Enterprise 5 cluster.
The installation goes with no complain of errors or warnings.   When run with mpi, I got errors.

Here is installation process:
export LD_LIBRARY_PATH=/usr/local/mpich2/1.4.1p1/gcc_4.5.3/lib:/usr/local/gcc/4.5.3/lib:/usr/local/gcc/4.5.3/lib64:${LD_LIBRARY_PATH}
./configure --prefix=/usr/local/meme/4.10.0 --with-url="http://meme.nbcr.net/meme"  --enable-build-libxslt --enable-build-libxml2 --with-mpicc=MPICC --with-mpidir=/usr/local/mpich2/1.4.1p1/gcc_4.5.3 CXX=/usr/local/gcc/4.5.3/bin/g++ 
make CFLAGS="-Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -O3" 
make install 

Here is tail of config output:
        ========================
        Configuration parameters
        ========================

  Install path:               /usr/local/meme/4.10.0
  Install UID:               
  Version:                    4.10.0
  C compiler:                 gcc
  C compiler flags:           -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__  
  Linker:                     /usr/bin/ld -m elf_x86_64
  Special Libs:               -lz -lm
  MPICC                       /usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpicc
  MPIRUN                      /usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun
  MPI_CMD                     /usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np
  MPIINC                      -DMPI -I/usr/local/mpich2/1.4.1p1/gcc_4.5.3/include
  MPILIBDIR                   /usr/local/mpich2/1.4.1p1/gcc_4.5.3/lib
  MPIFLAGS                    -DPARALLEL
  MEME URL:                   http://meme.nbcr.net/meme
  PREVIOUS VERSION URL:      
  SERVER CONTACT:            
  DEVELOPER CONTACT:          me...@sdsc.edu
  GO-SERVER URL:              http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO_TERM_ID
  PERL:                       /usr/local/perl/5.14.1/bin/perl
  PYTHON:                     /usr/bin/python
  CONVERT:                    /usr/bin/convert
  GHOSTSCRIPT:                /usr/bin/gs
  BUILD LIBXML2:              yes
  LIBXML2 compiler flags:     -I${top_srcdir}/src/libxml2/include
  LIBXML2 libs:               ${top_builddir}/src/libxml2/libxml2.la
  BUILD LIBXSLT:              yes
  LIBXSLT compiler flags:     -I${top_srcdir}/src/
  LIBXSLT libs:               ${top_builddir}/src/libxslt/libxslt.la
  MEME DB:                    ${prefix}/db
  MEME LOGS:                  ${prefix}/LOGS
  MEME TEMP FILES:           
  OPAL URL:                   no
  OPAL DEPLOY DIRECTORY:  

Here is test command:
export LD_LIBRARY_PATH=/usr/local/mpich2/1.4.1p1/gcc_4.5.3/lib:${LD_LIBRARY_PATH}
export PATH=/usr/local/meme/4.10.0/bin:${PATH}
/usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np $NSLOTS /usr/local/meme/4.10.0/bin/meme -o test-output -dna -mod zoops -minsites 50 -minw 4 -maxw 10 -maxsize 1000000000 -p 4 test.fasta


Here is the error:
[proxy:0:0...@compute-15-4.local] HYDU_create_process (./utils/launch/launch.c:36): dup2 error (Bad file descriptor)
[proxy:0:0...@compute-15-4.local] launch_procs (./pm/pmiserv/pmip_cb.c:751): create process returned error
[proxy:0:0...@compute-15-4.local] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:935): launch_procs returned error
[proxy:0:0...@compute-15-4.local] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0...@compute-15-4.local] main (./pm/pmiserv/pmip.c:226): demux engine error waiting for event
[mpi...@compute-8-17.local] HYDU_parse_hostfile (./utils/args/args.c:303): unable to open host file: /var/spool/uge/the_zcluster/compute-15-4/active_jobs/5622179.1/pe_hostf
ile
[mpi...@compute-8-17.local] HYDT_bscd_sge_query_node_list (./tools/bootstrap/external/sge_query_node_list.c:62): error parsing hostfile
[mpi...@compute-8-17.local] HYDT_bsci_query_node_list (./tools/bootstrap/src/bsci_query_node_list.c:19): RMK returned error while querying node list
[mpi...@compute-8-17.local] main (./ui/mpich/mpiexec.c:283): unable to query the RMK for a node list
[mpi...@compute-8-17.local] HYDU_parse_hostfile (./utils/args/args.c:303): unable to open host file: /var/spool/uge/the_zcluster/compute-15-4/active_jobs/5622179.1/pe_hostf
ile
[mpi...@compute-8-17.local] HYDT_bscd_sge_query_node_list (./tools/bootstrap/external/sge_query_node_list.c:62): error parsing hostfile
[mpi...@compute-8-17.local] HYDT_bsci_query_node_list (./tools/bootstrap/src/bsci_query_node_list.c:19): RMK returned error while querying node list
[mpi...@compute-8-17.local] main (./ui/mpich/mpiexec.c:283): unable to query the RMK for a node list
[mpi...@compute-8-17.local] HYDU_parse_hostfile (./utils/args/args.c:303): unable to open host file: /var/spool/uge/the_zcluster/compute-15-4/active_jobs/5622179.1/pe_hostf
ile
[mpi...@compute-8-17.local] HYDT_bscd_sge_query_node_list (./tools/bootstrap/external/sge_query_node_list.c:62): error parsing hostfile
[mpi...@compute-8-17.local] HYDT_bsci_query_node_list (./tools/bootstrap/src/bsci_query_node_list.c:19): RMK returned error while querying node list
[mpi...@compute-8-17.local] main (./ui/mpich/mpiexec.c:283): unable to query the RMK for a node list


If I run the same command with version 4.9.1, there is no such error. So there is no problem of mpich2 or environment setting.

Could anyone share any experience how to further debug/fix this issue?

Thanks in advance,

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