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On 26/01/2011 5:50 AM, TJ Mustard wrote:
<blockquote
cite="mid:1326883969.24193.1295981410881.JavaMail.open-xchange@oxusgw01.lxa.perfora.net"
type="cite">
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<p style="margin: 0px;">Hi all,</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I am running MD/FEP on a protein-ligand
system with gromacs 4.5.3 and FFTW 3.2.2.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">My iMac will run the job (over 4000 steps,
till I killed it) at 4fs steps. (I am using heavy H)</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Once I put this on our groups AMD Cluster
the jobs fail even with 2fs steps. (with thousands of lincs
errors)</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">We have recompiled the clusters gromacs
4.5.3 build, with no change. I know the system is the same since
I copied the job from the server to my machine, to rerun it.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">What is going on? Why can one machine run
a job perfectly and the other cannot? I also know there is
adequate memory on both machines.</p>
</blockquote>
<br>
You've posted this before, and I made a number of diagnostic
suggestions. What did you learn?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1326883969.24193.1295981410881.JavaMail.open-xchange@oxusgw01.lxa.perfora.net"
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<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Below is my command sequence:</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">echo
==============================================================================================================================<br>
date >>RNAP-C.joblog<br>
echo g453s-grompp -f em.mdp -c RNAP-C_b4em.gro -p RNAP-C.top -o
RNAP-C_em.tpr<br>
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f em.mdp -c
RNAP-C_b4em.gro -p RNAP-C.top -o RNAP-C_em.tpr<br>
date >>RNAP-C.joblog<br>
echo g453s-mdrun -v -s RNAP-C_em.tpr -c RNAP-C_after_em.gro -g
emlog.log -cpo state_em.cpt -nt 2<br>
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s
RNAP-C_em.tpr -c RNAP-C_after_em.gro -g emlog.log -cpo
stat_em.cpt -nt 2<br>
date >>RNAP-C.joblog<br>
echo g453s-grompp -f pr.mdp -c RNAP-C_after_em.gro -p RNAP-C.top
-o RNAP-C_pr.tpr<br>
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f pr.mdp -c
RNAP-C_after_em.gro -p RNAP-C.top -o RNAP-C_pr.tpr<br>
echo g453s-mdrun -v -s RNAP-C_pr.tpr -e pr.edr -c
RNAP-C_after_pr.gro -g prlog.log -cpo state_pr.cpt -nt 2 -dhdl
dhdl-pr.xvg<br>
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s
RNAP-C_pr.tpr -e pr.edr -c RNAP-C_after_pr.gro -g prlog.log -cpo
state_pr.cpt -nt 2 -dhdl dhdl-pr.xvg<br>
date >>RNAP-C.joblog<br>
echo g453s-grompp -f md.mdp -c RNAP-C_after_pr.gro -p RNAP-C.top
-o RNAP-C_md.tpr<br>
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f md.mdp -c
RNAP-C_after_pr.gro -p RNAP-C.top -o RNAP-C_md.tpr<br>
date >>RNAP-C.joblog<br>
echo g453s-mdrun -v -s RNAP-C_md.tpr -o RNAP-C_md.trr -c
RNAP-C_after_md.gro -g md.log -e md.edr -cpo state_md.cpt -nt 2
-dhdl dhdl-md.xvg<br>
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s
RNAP-C_md.tpr -o RNAP-C_md.trr -c RNAP-C_after_md.gro -g md.log
-e md.edr -cpo state_md.cpt -nt 2 -dhdl dhdl-md.xvg<br>
date >>RNAP-C.joblog<br>
echo g453s-grompp -f FEP.mdp -c RNAP-C_after_md.gro -p
RNAP-C.top -o RNAP-C_fep.tpr<br>
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f FEP.mdp -c
RNAP-C_after_md.gro -p RNAP-C.top -o RNAP-C_fep.tpr<br>
date >>RNAP-C.joblog<br>
echo g453s-mdrun -v -s RNAP-C_fep.tpr -o RNAP-C_fep.trr -c
RNAP-C_after_fep.gro -g fep.log -e fep.edr -cpo state_fep.cpt
-nt 2 -dhdl dhdl-fep.xvg<br>
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s
RNAP-C_fep.tpr -o RNAP-C_fep.trr -c RNAP-C_after_fep.gro -g
fep.log -e fep.edr -cpo state_fep.cpt -nt 2 -dhdl dhdl-fep.xvg</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I can add my .mdps but I do not think they
are the problem since I know it works on my personal iMac.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Thank you,</p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px
0px;">TJ Mustard<br>
Email: <a class="moz-txt-link-abbreviated" href="mailto:mustardt@onid.orst.edu">mustardt@onid.orst.edu</a></p>
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