<div style="line-height:1.7;color:#000000;font-size:14px;font-family:arial"> Dear all,<br><br>I am trying to use the checkpoint file for the MDrun which war crashed.<br>However, the following error file was obtained in my log file:<br><br>Reading file md_0_2.tpr, VERSION 4.5.5 (single precision)<br><br>Reading checkpoint file state.cpt generated: Tue Nov 8 08:06:42 2011<br><br><br>starting mdrun 'Protein in water'<br>20000000 steps, 20000.0 ps (continuing from step 1685550, 1685.5 ps).<br>[a02c31n06.pdc.kth.se:20072] 7 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics<br>[a02c31n06.pdc.kth.se:20072] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages<br><br>-------------------------------------------------------<br>Program mdrun, VERSION 4.5.3<br>Source code file: ../../../gromacs-4.5.3/src/gmxlib/futil.c, line: 459<br><br>File input/output error:<br>state_step1714850.cpt<br>For more informati
on and tips for troubleshooting, please check the GROMACS<br>website at http://www.gromacs.org/Documentation/Errors<br>-------------------------------------------------------<br><br>"Good Music Saves your Soul" (Lemmy)<br><br>Error on node 0, will try to stop all the nodes<br>Halting parallel program mdrun on CPU 0 out of 8<br><br>gcq#311: "Good Music Saves your Soul" (Lemmy)<br><br>--------------------------------------------------------------------------<br>MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD<br>with errorcode -1.<br><br>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>You may or may not see output from other processes, depending on<br>exactly when Open MPI kills them.<br>--------------------------------------------------------------------------<br>--------------------------------------------------------------------------<br>mpirun has exited due to process rank 0 with PID 20073 on<br>node a02c31n06.pdc.kth.se exiting withou
t calling "finalize". This may<br>have caused other processes in the application to be<br>terminated by signals sent by mpirun (as reported here).<br>--------------------------------------------------------------------------<br>~ <br><br>Anyone can help me with this problem? <br>Thanks so much,<br>Xianqiang<br><br><div>--<br><span class="Apple-style-span" style="font-family: Arial,Helvetica; line-height: normal;"><div><span class="Apple-style-span" style="f
ont-family: Arial,Helvetica; line-height: normal;">Xianqiang Sun</span></div><div><span class="Apple-style-span" style="font-family: Arial,Helvetica; line-height: normal;"><br></span></div><div>Email: xianqiang@theochem.kth.se</div>Division of Theoretical Chemistry and Biology <br>School of Biotechnology <br>Royal Institute of Technology<br>S-106 91 Stockholm, Sweden</span>
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