First, make sure that you actually CAN log in w/o a passphrase:
ssh localhost
If so, everything is fine, if not, you should make sure that the permissions are correct on your ~/.ssh and home directories, and that permissions are correct on your ~/.ssh/authorized_keys file and perhaps every other file under ~/.ssh
Another gotcha is that if you set a passphrase, then you must use ssh-agent in order to facilitate logging in w/o a password (see the manual pages for ssh-agent for examples).
Otherwise, if everything is fine then try the following:
You may need to specify the full path to your openmpi executable (e.g. /path/to/mpirun) and also to sander.MPI (e.g. /path/to/amber/sander.MPI) in order for things to work correctly.
Good luck
On Jul 26, 2010, at 8:26 PM, Yan Gao wrote:
> Hi there,
>
> I tried to run amber with openmpi on a unix system.
> I got below errors when I did a trial:
>
>
> *********************************************************************************************************************
> 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
>
> *****************************************************this is in a separate
> output file************************************************************
> -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 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 - 19:00:04 PDT
