Dear Jason,
Thank you for your comments and help!
I followed your comments and corrected the small discrepancies.
The passphrase method still did not work, so I turned to the public key, and
it seemed worked.
Thanks!
Yan
On Tue, Jul 27, 2010 at 10:57 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 Tue Jul 27 2010 - 12:30:06 PDT
