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Hi,<br><br>This bug has been fixed in 4.0.3,<br>but I forgot about it when writing the release notes.<br><br>Berk<br><br>> From: ydubief@uvm.edu<br>> To: gmx-users@gromacs.org<br>> Date: Tue, 20 Jan 2009 08:53:15 -0500<br>> Subject: [gmx-users] deform option in parallel with Gromacs 4.0.2<br>> <br>> Hi,<br>> <br>> I am running stress simulations of vesicles and lipid bilayer <br>> membranes, which work on one processor but fail when using multiple <br>> processors. The simulations run Marrink's CGMD model with Gromacs <br>> 4.0.2 (sorry I am unable to upgrade until next week) on openmpi and <br>> mpich. The simulations run fine with the deform option set to zero for <br>> all six components but crashes for 2 processors or more. Here is an <br>> example of what I get on a mac with openmpi (fink package of gromacs):<br>> [ip138195:37938] *** Process received signal ***<br>> [ip138195:37938] Signal: Segmentation fault (11)<br>> [ip138195:37938] Signal code: Address not mapped (1)<br>> [ip138195:37938] Failing at address: 0x8fe830<br>> [ip138195:37938] [ 0] 2 libSystem.B.dylib <br>> 0x925882bb _sigtramp + 43<br>> [ip138195:37938] [ 1] 3 ??? <br>> 0xffffffff 0x0 + 4294967295<br>> [ip138195:37938] [ 2] 4 libgmx_mpi.5.dylib <br>> 0x003d24f1 do_nonbonded + 1361<br>> [ip138195:37938] *** End of error message ***<br>> [ip138195:37939] *** Process received signal ***<br>> [ip138195:37939] Signal: Segmentation fault (11)<br>> [ip138195:37939] Signal code: Address not mapped (1)<br>> [ip138195:37939] Failing at address: 0xfb890<br>> [ip138195:37939] [ 0] 2 libSystem.B.dylib <br>> 0x925882bb _sigtramp + 43<br>> [ip138195:37939] [ 1] 3 ??? <br>> 0xffffffff 0x0 + 4294967295<br>> [ip138195:37939] [ 2] 4 libgmx_mpi.5.dylib <br>> 0x003d24f1 do_nonbonded + 1361<br>> [ip138195:37939] *** End of error message ***<br>> mpiexec noticed that job rank 0 with PID 37938 on node <br>> ip138195.uvm.edu exited on signal 11 (Segmentation fault).<br>> 1 additional process aborted (not shown)<br>> I have checked the wiki, manuals and searched this list but I can't <br>> find any report of bugs nor an indication that I am doing something <br>> wrong. It seems that there might be a bug associated with the deform <br>> option in parallel.<br>> Thanks for any insight, advice on this.<br>> <br>> .<br>> --<br>> Yves Dubief, Ph.D., Assistant Professor<br>> Graduate program coordinator<br>> University of Vermont, School of Engineering<br>> Mechanical Engineering Program<br>> 201 D Votey Bldg, 33 Colchester Ave, Burlington, VT 05405<br>> Tel: (1) 802 656 1930 Fax: (1) 802 656 3358<br>> Also:<br>> Vermont Advanced Computing Center<br>> 206 Farrell Hall, 210 Colchester Ave, Burlington, VT 05405<br>> Tel: (1) 802 656 9830 Fax: (1) 802 656 9892<br>> email: ydubief@uvm.edu<br>> web: http://www.uvm.edu/~ydubief/<br>> <br>> <br>> <br>> <br>> <br>> <br>> <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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