[gmx-users] Help! --- Permission denied (publickey, gssapi-with-mic, password).

[Yan Gao]

Hi There,

Please help me with this permission issue! Thanks. (Below are the input and
output, followed by the information of my compiling procedure)

#!/bin/csh -f
#$ -cwd
#$ -N gro.t.4
#$ -S /bin/tcsh
#$ -l h_rt=120:00:00
#$ -e SGE.err
#$ -o SGE.out
#$ -pe mpich 4
mpirun -np 4 mdrun_mpi -s topol.tpr -o output_test.trr -e topol.tpr -x
output_test.trr

-catch_rsh
/opt/gridengine/default/spool/compute-2-9/active_jobs/424509.1/pe_hostfile
compute-2-9
compute-2-9
compute-2-21
compute-2-21
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 (0x004cf000)
    libdl.so.2 => /lib/libdl.so.2 (0x400d7000)
    libnsl.so.1 => /lib/libnsl.so.1 (0x0054c000)
    libutil.so.1 => /lib/libutil.so.1 (0x00516000)
    libm.so.6 => /lib/tls/libm.so.6 (0x004d5000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0050c000)
    libpthread.so.0 => /lib/tls/libpthread.so.0 (0x005ed000)
    libc.so.6 => /lib/tls/libc.so.6 (0x003a2000)
    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 (0x00384000)
/home/y1gao/soft/gromacs-4.0.5/bin/mdrun_mpi
    libnsl.so.1 => /lib/libnsl.so.1 (0x0054c000)
    libm.so.6 => /lib/tls/libm.so.6 (0x004d5000)
    libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x004fa000)
    libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x00611000)
    libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x40008000)
    libmpi.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libmpi.so.0
(0x400e7000)
    libopen-rte.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libopen-rte.so.0
(0x40299000)
    libopen-pal.so.0 => /home/y1gao/soft/openmpi-1.4.2/lib/libopen-pal.so.0
(0x40310000)
    libnuma.so.1 => /usr/lib/libnuma.so.1 (0x004cf000)
    libdl.so.2 => /lib/libdl.so.2 (0x40368000)
    libutil.so.1 => /lib/libutil.so.1 (0x00516000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0050c000)
    libpthread.so.0 => /lib/tls/libpthread.so.0 (0x005ed000)
    libc.so.6 => /lib/tls/libc.so.6 (0x003a2000)
    /lib/ld-linux.so.2 (0x00384000)
    libimf.so => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libimf.so
(0x4036d000)
    libsvml.so => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libsvml.so
(0x405d2000)
    libintlc.so.5 => /nas/y1gao/soft/intel-11.1.072/lib/ia32/libintlc.so.5
(0x406fc000)
######################################################################################################
---------------------------------------------------------------------------------------
Warning: Permanently added 'compute-2-21.local' (RSA) to the list of known
hosts.
Permission denied, please try again.
Permission denied, please try again.
Permission denied (publickey,gssapi-with-mic,password).
--------------------------------------------------------------------------
A daemon (pid 11510) 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
------------------------------------------------------------------------------------


I got this error when I started the parallel runs of the gromacs on the
cluster via MPI.
My compiling procedure was: intel_fortran_11.1.072 --> intel_c++_11.1.072
--> openmpi 1.4.2--> fftw3.2.2 --> gromacs4.0.5
(LAM/MPI was already installed but does not work properly.)


-- 
Yan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100611/27529fea/attachment.html>