Hello,
I'm not sure how this would affect your results (if at all), but AMBERTOOL
should be set to /nas/y1gao/soft/amber11/AmberTools/ (unless of course you
changed it, but I think you should avoid that).
On Mon, Jul 26, 2010 at 9:45 PM, Yan Gao <yan.gao.2001.gmail.com> wrote:
> 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
>
These environment variables should be set just fine if you source
/nas/y1gao/soft/intel-11.1.072/bin/ifortvars.csh and the corresponding
iccvars.csh. Also, you should not have to load $MPI_HOME/lib into your
LD_LIBRARY_PATH. Same with $AMBERTOOL/lib (that's not needed in
LD_LIBRARY_PATH).
>
> ## Checking setenvm, mpi and sander
> echo
>
> "######################################################################################################"
> which mpirun
> ldd /home/y1gao/soft/openmpi-1.4.2/bin/mpirun
>
Why not use $MPI_HOME/bin/mpirun, just to be consistent...
> which sander.MPI
> ldd /nas/y1gao/soft/amber10/bin/sander.MPI
>
same with $AMBERHOME/bin.
> echo
>
> "######################################################################################################"
>
> mpirun -np 4 sander.MPI -O -i test.in -o test.out -c test.rst -p
> test.prmtop
> -r test.rst
>
You should specify mpirun and sander.MPI the same way you did above, with
$MPI_HOME and $AMBERHOME, I think. Consistency helps make sure you're
checking everything properly.
>
>
>
> ***************************************************************************************************************************************
>
>
>
> 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).
>
This is not an amber issue, this has to do with the fact that you don't have
permissions with your ssh key on the nodes you're trying to run on. If you
have a system admin you can talk to about this, they would probably help
more.
Good luck!
Jason
> --------------------------------------------------------------------------
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jul 27 2010 - 11:00:05 PDT
