[gmx-users] mpirun.gromacs errors

[David van der Spoel]

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.
> 
> 
> ross_usp at yahoo.com.br,rsoares at fcfrp.usp.br
> 
>  
> 
> 
> 
> 
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-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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