On Thu, Oct 15, 2009 at 1:40 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5">Itamar Kass wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
Lately few of my simulations had ended up with wired output:<br>
<br>
Writing final coordinates.<br>
step 500000, remaining runtime: 0 s [xn068:94365] *** Process received signal ***<br>
[xn068:94365] Signal: Segmentation fault (11)<br>
[xn068:94365] Signal code: Address not mapped (1)<br>
[xn068:94365] Failing at address: 0x108ee9000<br>
[xn068:94365] [ 0] 2 libSystem.B.dylib 0x00000000844e83fa _sigtramp + 26<br>
[xn068:94365] [ 1] 3 ??? 0x0000000000801b78 0x0 + 8395640<br>
[xn068:94365] *** End of error message ***<br>
<br>
<br>
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.<br>
<br>
Any idea someone?<br>
</blockquote>
<br></div></div>
What was the command line?<br></blockquote><div>
<br>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<br>_from_MD6.edr -x one_GroEL_noATP_run2_from_MD6.xtc -g one_GroEL_noATP_run2_from_MD6.log -v -stepout 5000<br>
<br>I am using -pd 'cause I am using SHAKE.<br><br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">What's the end of the .log file? </blockquote>
<div><br>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:<br><br> Step Time Lambda<br> 499800 999.60000 0.00000<br>
<br> Energies (kJ/mol)<br> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<br> 9.05518e+03 3.39568e+03 2.06800e+03 -2.23433e+02 8.39937e+04<br> LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl.<br>
4.54232e+05 -2.10739e+04 -3.24147e+06 -3.58373e+04 -6.38806e+04<br> Potential Kinetic En. Total Energy Temperature Pressure (bar)<br> -2.80974e+06 4.96949e+05 -2.31279e+06 3.05107e+02 -3.18227e+01<br>
<br> Step Time Lambda<br> 499900 999.80000 0.00000<br><br> Energies (kJ/mol)<br> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<br> 9.09295e+03 3.38158e+03 2.12674e+03 -1.83503e+02 8.36385e+04<br>
LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl.<br> 4.54228e+05 -2.10769e+04 -3.24015e+06 -3.55380e+04 -6.38776e+04<br> Potential Kinetic En. Total Energy Temperature Pressure (bar)<br>
-2.80836e+06 4.95856e+05 -2.31250e+06 3.04437e+02 -1.27131e+01<br><br> Step Time Lambda<br> 500000 1000.00000 0.00000<br><br>Writing checkpoint, step 500000 at Wed Oct 14 17:34:47 2009<br>
<br> Energies (kJ/mol)<br> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<br> 8.53869e+03 3.32588e+03 2.03245e+03 -2.36432e+02 8.41339e+04<br> LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl.<br>
4.57725e+05 -2.10767e+04 -3.24340e+06 -3.52958e+04 -6.38808e+04<br> Potential Kinetic En. Total Energy Temperature Pressure (bar)<br> -2.80813e+06 4.96000e+05 -2.31213e+06 3.04525e+02 9.63155e+01<br>
<br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">What filesystem are you using? </blockquote><div><br>We are using MAC so this is Mac OS Extended (Journaled).<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Did it fill?<br>
<br>
Mark<br>
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</blockquote></div><br>