On 26/01/2011 5:50 AM, TJ Mustard wrote:
Hi all,
I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and
FFTW 3.2.2.
My iMac will run the job (over 4000 steps, till I killed it) at 4fs
steps. (I am using heavy H)
Once I put this on our groups AMD Cluster the jobs fail even with 2fs
steps. (with thousands of lincs errors)
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.
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.
You've posted this before, and I made a number of diagnostic
suggestions. What did you learn?
Mark
Below is my command sequence:
echo
==============================================================================================================================
date >>RNAP-C.joblog
echo g453s-grompp -f em.mdp -c RNAP-C_b4em.gro -p RNAP-C.top -o
RNAP-C_em.tpr
/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
date >>RNAP-C.joblog
echo g453s-mdrun -v -s RNAP-C_em.tpr -c RNAP-C_after_em.gro -g
emlog.log -cpo state_em.cpt -nt 2
/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
date >>RNAP-C.joblog
echo g453s-grompp -f pr.mdp -c RNAP-C_after_em.gro -p RNAP-C.top -o
RNAP-C_pr.tpr
/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
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
/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
date >>RNAP-C.joblog
echo g453s-grompp -f md.mdp -c RNAP-C_after_pr.gro -p RNAP-C.top -o
RNAP-C_md.tpr
/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
date >>RNAP-C.joblog
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
/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
date >>RNAP-C.joblog
echo g453s-grompp -f FEP.mdp -c RNAP-C_after_md.gro -p RNAP-C.top -o
RNAP-C_fep.tpr
/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
date >>RNAP-C.joblog
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
/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
I can add my .mdps but I do not think they are the problem since I
know it works on my personal iMac.
Thank you,
TJ Mustard
Email: musta...@onid.orst.edu
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