Hi, I am trying particle decomposition with gromacs 4.0.4 for a small polymer (20 atoms) in SPC/E water. Unfortunately every run crashes at the very beginning without any useful error message, when I use version 4.0.4 with option -pd. Whereas everything remaining same it's still running fine in version 3.3.3. I have tried 4, 8, 16 nodes with the same result. How do I troubleshoot this? I need to use the particle decomposition method since the PLUMED plugin to perform metadynamics supports only pd as of now.
Here are the last few lines from the log, stderr and stdout files: log: ============================================ Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 -------- -------- --- Thank You --- -------- -------- ============================================== stderr: ============================================== Getting Loaded... Reading file c20.G53a6.eq.gmx404.tpr, VERSION 4.0.4 (single precision) Loaded with Money starting mdrun 'Protein in water' 2500000 steps, 5000.0 ps. =============================================== stdout: =============================================== /opt/gridengine/default/spool/compute-0-4/active_jobs/5329.1/pe_hostfile ibc4 ibc4 ibc4 ibc4 rank 2 in job 1 compute-0-4.local_46551 caused collective abort of all ranks exit status of rank 2: killed by signal 9 rank 1 in job 1 compute-0-4.local_46551 caused collective abort of all ranks exit status of rank 1: killed by signal 9 ================================================= Thanks for any suggestion. Best regards, Suman. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
