Thanks Bill. I include my input command with this message.
Hi there,
I tried to run amber with openmpi on a unix system. I used below input with
command: qsub
*****************************************************************************************************************
#!/bin/csh -f
#$ -cwd
#$ -N sim.MD
#$ -S /bin/tcsh
#$ -l h_rt=120:00:00
#$ -e SGE.err
#$ -o SGE.out
#$ -pe mpich 4
set INTELF=/nas/y1gao/soft/intel-11.1.072
set INTELC=/nas/y1gao/soft/intel-c-11.1.072
set MPI_HOME=/home/y1gao/soft/openmpi-1.4.2
set GROHOME=/home/y1gao/soft/gromacs-4.0.5
set GSL=/home/y1gao/soft/gsl-1.9
set AMBERHOME=/nas/y1gao/soft/amber10
set AMBERTOOL=/nas/y1gao/soft/amber11/AmberTool
set SANDEREXEC=$AMBERHOME/bin/sander
set LEAPEXEC=$AMBERTOOL/bin/tleap
setenv PATH
$INTELF/bin:$INTELC/bin:$GROHOME/bin:$MPI_HOME/bin:$AMBERHOME/exe:$AMBERTOOL/exe:$PATH
setenv LD_LIBRARY_PATH
$INTELF/lib/ia32:$INTELC/lib/ia32:$INTELF/idb/lib/ia32:$INTELC/idb/lib/ia32:$MPI_HOME/lib:$GSL/lib:$AMBERTOOL/lib:$LD_LIBRARY_PATH
## Checking setenvm, mpi and sander
echo
"######################################################################################################"
which mpirun
ldd /home/y1gao/soft/openmpi-1.4.2/bin/mpirun
which sander.MPI
ldd /nas/y1gao/soft/amber10/bin/sander.MPI
echo
"######################################################################################################"
mpirun -np 4 sander.MPI -O -i test.in -o test.out -c test.rst -p test.prmtop
-r test.rst
***************************************************************************************************************************************
I got below errors when I did a trial:
*******************************************SGE.err**************************************************************************
Permission denied, please try again.
Permission denied, please try again.
Permission denied (publickey,gssapi-with-mic,password).
--------------------------------------------------------------------------
A daemon (pid 17525) died unexpectedly with status 129 while attempting
to launch so we are aborting.
There may be more information reported by the environment (see above).
This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
mpirun: clean termination accomplished
*****************************************************SGE.out***********************************************************
-catch_rsh
/opt/gridengine/default/spool/compute-0-19/active_jobs/426880.1/pe_hostfile
compute-0-19
compute-0-19
compute-0-18
compute-0-18
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
######################################################################################################
/home/y1gao/soft/openmpi-1.4.2/bin/mpirun
libopen-rte.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libopen-rte.so.0
(0x40001000)
libopen-pal.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libopen-pal.so.0
(0x40078000)
libnuma.so.1 => /usr/lib/libnuma.so.1 (0x0077c000)
libdl.so.2 => /lib/libdl.so.2 (0x400d7000)
libnsl.so.1 => /lib/libnsl.so.1 (0x0080e000)
libutil.so.1 => /lib/libutil.so.1 (0x007c3000)
libm.so.6 => /lib/tls/libm.so.6 (0x00782000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x007b9000)
libpthread.so.0 => /lib/tls/libpthread.so.0 (0x0089a000)
libc.so.6 => /lib/tls/libc.so.6 (0x0064f000)
libimf.so => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libimf.so
(0x400dc000)
libsvml.so => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libsvml.so
(0x40341000)
libintlc.so.5 => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libintlc.so.5
(0x4046c000)
/lib/ld-linux.so.2 (0x00631000)
/nas/y1gao/soft/amber10/exe/sander.MPI
libsvml.so => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libsvml.so
(0x40001000)
libmpi_f90.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libmpi_f90.so.0
(0x4012b000)
libmpi_f77.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libmpi_f77.so.0
(0x4012e000)
libmpi.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libmpi.so.0
(0x40154000)
libopen-rte.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libopen-rte.so.0
(0x40305000)
libopen-pal.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libopen-pal.so.0
(0x4037d000)
libnuma.so.1 => /usr/lib/libnuma.so.1 (0x0077c000)
libdl.so.2 => /lib/libdl.so.2 (0x403dc000)
libnsl.so.1 => /lib/libnsl.so.1 (0x0080e000)
libutil.so.1 => /lib/libutil.so.1 (0x007c3000)
libm.so.6 => /lib/tls/libm.so.6 (0x00782000)
libpthread.so.0 => /lib/tls/libpthread.so.0 (0x0089a000)
libc.so.6 => /lib/tls/libc.so.6 (0x0064f000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x007b9000)
libifport.so.5 => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libifport.so.5
(0x403e1000)
libifcoremt.so.5 =>
/nas/y1gao/soft/intel-11.1.072/lib/ia32/libifcoremt.so.5 (0x40401000)
libimf.so => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libimf.so
(0x40511000)
libintlc.so.5 => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libintlc.so.5
(0x40776000)
/lib/ld-linux.so.2 (0x00631000)
######################################################################################################
*****************************************************************************************************************
I then google "*Permission denied (publickey,gssapi-with-mic,password)*",
and setup/cp the passphrase. So I can automatically log onto a node without
inputting the password/passphrase manually.
Then I tried again with mpi, and got the same output. I am kind of stuck
here, could anyone help me. Thanks!
Regards,
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Mon Jul 26 2010 - 19:00:05 PDT
