[gmx-users] mpirun.gromacs errors

Ricardo O. S. Soares ross_usp at yahoo.com.br
Wed Aug 5 22:50:59 CEST 2009

Dear users,

I use LAM/MPI with no problems for quite a while. However as I am now trying to use the Openmpi along with gromacs 4.0.5, I get some errors. 

First I have some questions:

1. I probably should start the openmpi before using the mpirun, right?
2. If so, how do I start it? (the mpdboot is abscent)
3. I have both mpirun and mpirun.openmpi in my computer, which one should I use? Note that there's no other mpi program other than openmpi installed in this cpu.

The 1st command line I used:

                    mpirun.openmpi -np 8 /usr/local/bin/mdrun -s pr.tpr -v 

The 1st error:

orted: symbol lookup error: orted: undefined symbol: orte_daemon
[user:shell] [0,0,0] ORTE_ERROR_LOG: Timeout in file base/pls_base_orted_cmds.c at line 275
[user:shell] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line 1166
[user:shell] [0,0,0] ORTE_ERROR_LOG: Timeout in file errmgr_hnp.c at line 90
[user:shell] ERROR: A daemon on node FB-Xeon01 failed to start as expected.
[user:shell] ERROR: There may be more information available from
[user:shell] ERROR: the remote shell (see above).
[user:shell] ERROR: The daemon exited unexpectedly with status 127.
[user:shell] [0,0,0] ORTE_ERROR_LOG: Timeout in file base/pls_base_orted_cmds.c at line 188
[user:shell] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line 1198
mpirun.openmpi was unable to cleanly terminate the daemons for this job. Returned value Timeout instead of ORTE_SUCCESS.

The 2nd command:

                   mpirun -np 8 /usr/local/bin/mdrun -s pr.tpr -v

The 2nd error:

                    mpirun: symbol lookup error: mpirun: undefined symbol: orted_cmd_line

The command   "mdrun -s pr.tpr -v"      if fine, though it uses only one node...

Thanks a lot for any clarification!


 Ricardo O. S. Soares , MsC.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.
Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo,  Brazil.
Phone: +55 16 36024840.

ross_usp at yahoo.com.br,rsoares at fcfrp.usp.br

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