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.
---
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_...@yahoo.com.br,rsoa...@fcfrp.usp.br
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