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,