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Hi,<br><br>Are the crashes with plain 4.0.4, or 4.0.4 with PLUMED?<br>I have not heard of crashes in 4.0.4 with particle decomposition,<br>so it might have to do with the link with PLUMED.<br><br>Have you tried running 4.0.4 in single processor?<br><br>If plain Gromacs 4.0.4 crahes on your system with PD,<br>please file a report on bugzilla.gromacs.org and attach the tpr file.<br><br>Berk<br><br>> Date: Wed, 6 May 2009 20:23:56 +0530<br>> From: suman@sscu.iisc.ernet.in<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] problem with particle decomposition in gromacs 4.0.4<br>> <br>> Hi,<br>> <br>> I am trying particle decomposition with gromacs 4.0.4 for a small<br>> polymer (20 atoms) in SPC/E water. Unfortunately every run crashes at<br>> the very beginning without any useful error message, when I use<br>> version 4.0.4 with option -pd. Whereas everything remaining same it's<br>> still running fine in version 3.3.3. I have tried 4, 8, 16 nodes with<br>> the same result. How do I troubleshoot this? I need to use the<br>> particle decomposition method since the PLUMED plugin to perform<br>> metadynamics supports only pd as of now.<br>> <br>> Here are the last few lines from the log, stderr and stdout files:<br>> <br>> log:<br>> ============================================<br>> Center of mass motion removal mode is Linear<br>> We have the following groups for center of mass motion removal:<br>> 0: rest<br>> <br>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak<br>> Molecular dynamics with coupling to an external bath<br>> J. Chem. Phys. 81 (1984) pp. 3684-3690<br>> -------- -------- --- Thank You --- -------- --------<br>> ==============================================<br>> <br>> stderr:<br>> ==============================================<br>> Getting Loaded...<br>> Reading file c20.G53a6.eq.gmx404.tpr, VERSION 4.0.4 (single precision)<br>> Loaded with Money<br>> <br>> starting mdrun 'Protein in water'<br>> 2500000 steps, 5000.0 ps.<br>> ===============================================<br>> <br>> stdout:<br>> ===============================================<br>> /opt/gridengine/default/spool/compute-0-4/active_jobs/5329.1/pe_hostfile<br>> ibc4<br>> ibc4<br>> ibc4<br>> ibc4<br>> rank 2 in job 1 compute-0-4.local_46551 caused collective abort of all ranks<br>> exit status of rank 2: killed by signal 9<br>> rank 1 in job 1 compute-0-4.local_46551 caused collective abort of all ranks<br>> exit status of rank 1: killed by signal 9<br>> =================================================<br>> <br>> Thanks for any suggestion.<br>> <br>> <br>> Best regards,<br>> Suman.<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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