[gmx-users] Two machines, same job, one fails

[Mark Abraham]

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: mustardt at onid.orst.edu
>

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