<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:12pt;color:#111111;">Dear users,<br><br>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. <br><br>First I have some questions:<br><br>1. I probably should start the openmpi before using the mpirun, right?<br>2. If so, how do I start it? (the mpdboot is abscent)<br>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.<br><br>The 1st command line I used:<br><br> mpirun.openmpi -np 8 /usr/local/bin/mdrun -s pr.tpr -v <br><br>The 1st error:<br><br>orted: symbol lookup error: orted: undefined symbol: orte_daemon<br> [user:shell]
[0,0,0] ORTE_ERROR_LOG: Timeout in file base/pls_base_orted_cmds.c at line 275<br>[user:shell] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line 1166<br>[user:shell] [0,0,0] ORTE_ERROR_LOG: Timeout in file errmgr_hnp.c at line 90<br>[user:shell] ERROR: A daemon on node FB-Xeon01 failed to start as expected.<br>[user:shell] ERROR: There may be more information available from<br>[user:shell] ERROR: the remote shell (see above).<br>[user:shell] ERROR: The daemon exited unexpectedly with status 127.<br>[user:shell] [0,0,0] ORTE_ERROR_LOG: Timeout in file base/pls_base_orted_cmds.c at line 188<br>[user:shell] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line 1198<br>--------------------------------------------------------------------------<br>mpirun.openmpi was unable to cleanly terminate the daemons for this job. Returned value Timeout instead of
ORTE_SUCCESS.<br>--------------------------------------------------------------------------<br><br>The 2nd command:<br><br> mpirun -np 8 /usr/local/bin/mdrun -s pr.tpr -v<br><br>The 2nd error:<br><br> mpirun: symbol lookup error: mpirun: undefined symbol: orted_cmd_line<br><br>The command "mdrun -s pr.tpr -v" if fine, though it uses only one node...<br><br><br>Thanks a lot for any clarification!<br><br><div>Ricardo. <br><div style="font-family: times new roman,new york,times,serif; font-size: 14pt;"><br><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 8pt;" lang="PT-BR">---</span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 8pt;"
lang="PT-BR"> <font size="1"> </font></span></p><font size="1">Ricardo O. S. Soares , MsC.<br>Group of Biological Physics - Department of Physics & Chemistry<br>Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.<br>Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil.<br>Phone: +55 16 36024840.</font><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><br><span style="font-size: 8pt;" lang="PT-BR"></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 8pt;" lang="PT-BR"><a rel="nofollow">ross_usp@yahoo.com.br</a>,<a rel="nofollow">rsoares@fcfrp.usp.br</a></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 8pt;" lang="PT-BR"> </span></p> <br></div></div><div><br></div></div><br>
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