On Thu, Oct 15, 2009 at 1:40 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> Itamar Kass wrote: > >> Hi, >> >> Lately few of my simulations had ended up with wired output: >> >> Writing final coordinates. >> step 500000, remaining runtime: 0 s [xn068:94365] *** Process >> received signal *** >> [xn068:94365] Signal: Segmentation fault (11) >> [xn068:94365] Signal code: Address not mapped (1) >> [xn068:94365] Failing at address: 0x108ee9000 >> [xn068:94365] [ 0] 2 libSystem.B.dylib >> 0x00000000844e83fa _sigtramp + 26 >> [xn068:94365] [ 1] 3 ??? >> 0x0000000000801b78 0x0 + 8395640 >> [xn068:94365] *** End of error message *** >> >> >> In addition, the output files are not usable. We use apple with 10.5 >> (server version) and gromacs (4.0.5) is compiles using 64bit. >> >> Any idea someone? >> > > What was the command line? > mpiexec mdrun_mpi -pd -s one_GroEL_noATP_run2_for_MD6.tpr -o one_GroEL_noATP_run2_from_MD6.trr -c one_GroEL_noATP_run2_from_MD6.gro -e one_GroEL_noATP_run2 _from_MD6.edr -x one_GroEL_noATP_run2_from_MD6.xtc -g one_GroEL_noATP_run2_from_MD6.log -v -stepout 5000 I am using -pd 'cause I am using SHAKE. What's the end of the .log file? I gave the mdrun output and not the logfile 'cause there is nothing speaciel there. It write the temp, energy etc. which look OK and then stop: Step Time Lambda 499800 999.60000 0.00000 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 9.05518e+03 3.39568e+03 2.06800e+03 -2.23433e+02 8.39937e+04 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 4.54232e+05 -2.10739e+04 -3.24147e+06 -3.58373e+04 -6.38806e+04 Potential Kinetic En. Total Energy Temperature Pressure (bar) -2.80974e+06 4.96949e+05 -2.31279e+06 3.05107e+02 -3.18227e+01 Step Time Lambda 499900 999.80000 0.00000 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 9.09295e+03 3.38158e+03 2.12674e+03 -1.83503e+02 8.36385e+04 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 4.54228e+05 -2.10769e+04 -3.24015e+06 -3.55380e+04 -6.38776e+04 Potential Kinetic En. Total Energy Temperature Pressure (bar) -2.80836e+06 4.95856e+05 -2.31250e+06 3.04437e+02 -1.27131e+01 Step Time Lambda 500000 1000.00000 0.00000 Writing checkpoint, step 500000 at Wed Oct 14 17:34:47 2009 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 8.53869e+03 3.32588e+03 2.03245e+03 -2.36432e+02 8.41339e+04 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 4.57725e+05 -2.10767e+04 -3.24340e+06 -3.52958e+04 -6.38808e+04 Potential Kinetic En. Total Energy Temperature Pressure (bar) -2.80813e+06 4.96000e+05 -2.31213e+06 3.04525e+02 9.63155e+01 > What filesystem are you using? We are using MAC so this is Mac OS Extended (Journaled). > Did it fill? > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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