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Hi,<br><br>I don't understand why 4.0.7 gives a segv.<br><br>But 4.5-beta probably gives a segv because of a parallel problem.<br>Could you try 4.5-beta with the mdrun option -nt 1<br>and report back?<br><br>Thanks,<br><br>Berk<br><br>> Date: Fri, 13 Aug 2010 18:35:55 +0200<br>> From: jcb1@um.es<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] tpi segmentation fault<br>> <br>> Hi all.<br>> <br>> I am trying to perform a tpi (test particle insertion) calculation on a <br>> trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf <br>> cluster of Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz). I am using <br>> tpi integrator in the mdp file and the following command:<br>> <br>> $ grompp -f tpi.mdp -c 32hoa_128dmpcwrun.gro -n index_tpi.ndx -p <br>> topol_tpi.top<br>> $ mdrun -rerun 32hoa_128dmpcwrun.trr -g tpi.log<br>> <br>> I tried different versions of gromcas and for 4.0.X I got a segmentation <br>> fault getting the message:<br>> <br>> trn version: GMX_trn_file (single precision)<br>> Reading frame 0 time 0.000 Segmentation fault<br>> <br>> using a compiled version with "config --prefix <br>> /home/cerezo/Programs/gromacs4.07" + "make" + "make install". However, <br>> it works when I used a precompiled version (got with apt-get, I have <br>> kubuntu). So I guess that it may be due to a mistake during the <br>> compilation. In addition, other integrators (i.e. md, steep) work <br>> correctly with the version I've compiled. My system is and Intel(R) <br>> Core(TM)2 Quad CPU Q8400 @ 2.66GHz. Is there any trick I could try <br>> in the compilation?<br>> <br>> I also tried gromacs-4.5-betaX and it works but sometimes (apparently <br>> randomly) the calculation gets stops (as if it had entered in an <br>> infinite loop) after reading the last frame.<br>> <br>> Thanks for your attention!<br>> <br>> Javier<br>> <br>> -- <br>> Javier CEREZO BASTIDA<br>> Estudiante de Doctorado<br>> ---------------------<br>> Dpto. Química-Física<br>> Universidad de Murcia<br>> 30100 MURCIA (España)<br>> Tlf.(+34)868887434<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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> </body>
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