Ricardo O. S. Soares wrote:
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)
Not necessary anymore.
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.
From the message below it seems you are mixing two. Use the mpirun that
belongs to the library you compiled with.
Cheers,
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.
[email protected],[email protected]
------------------------------------------------------------------------
Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10
<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/>
- Celebridades
<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/>
- Música
<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/>
- Esportes
<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[email protected] [email protected] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
