TJ Mustard wrote:
<snip>
> 1. Do the systems in question crash immediately (i.e., step zero) or
do they run
> for some time?
>
Step 0, every time.
> 2. If they give you even a little bit of output, you can analyze
which energy
> terms, etc go haywire with the tips listed here:
>
All I have seen on these is LINCS Errors and Water molecules unable to
be settled.
But I will check this out right now, and email if I smell trouble.
>
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>
> That would help in tracking down any potential bug or error.
>
> 3. Is it just the production runs that are crashing, or everything?
If EM isn't
> even working, that smells even buggier.
Awesome question here, we have seen some weird stuff. Sometimes the
cluster will give us segmentation faults, then it will fail on our
machines or sometimes not on our iMacs. I know weird! If EM starts on
the cluster it will finish. Where we have issues is in positional
restraint (PR) and MD and MD/FEP. It doesn't matter if FEP is on or off
in a MD (although we are using SD for these MD/FEP runs).
Does "sometimes" refer to different simulations, or multiple invocations of the
same simulation system? If you're referencing the fact that system A works
while system B doesn't, we're talking apples and oranges and it's irrelevant to
the diagnosis (and perhaps some systems simply require greater finesse or a
different protocol). If one system continually fails on one system and works on
another, that's what we need to be discussing. Sorry if I've missed something,
I'm just getting confused.
>
> 4. Are the compilers the same on the iMac vs. AMD cluster?
No I am using x86_64-apple-darwin10 GCC 4.4.4 and the cluster is using
x86_64-redhat-linux 4.1.2 GCC.
Well, I know that for years weird behavior has been attributed to the gcc-4.1.x
series, including the famous warning on the downloads page:
"WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These
compilers come with recent Linux distributions like Fedora 5/6 etc."
I don't know if those issues were ever resolved (some error in Gromacs that
wasn't playing nice with gcc, or vice versa).
I just did a quick yum search and there doesn't seem to be a newer GCC.
We know you are going to cmake but we have yet to get it implemented on
our cluster successfully.
The build system is irrelevant. You still need a reliable C compiler, whether
using autoconf or cmake.
-Justin
Thank you,
TJ Mustard
>
> -Justin
>
> >
> >
> > Now I understand that my iMac works, but it only has 2 cpus and the
> > cluster has 320. Since we are running our jobs via a Bennet's
Acceptance
> > Ratio FEP with 21 lambda windows, using just one 2 cpu machine would
> > take too long. Especially since we wish to start pseudo high throughput
> > drug testing.
> >
> >
> >
> >
> >
> > In my .mdp files now, the only changes are:
> >
> > (the default setting is on the right of the ";")
> >
> >
> >
> >
> >
> > define = ; =
> >
> > ; RUN CONTROL PARAMETERS
> > integrator = sd ; = md
> > ; Start time and timestep in ps
> > tinit = 0 ; = 0
> > dt = 0.004 ; = 0.001
> > nsteps = 750000 ; = 0 (this one depends on the
> > window and particular part of our job)
> >
> > ; OUTPUT CONTROL OPTIONS
> > ; Output frequency for coords (x), velocities (v) and forces (f)
> > nstxout = 10000 ; = 100 (to save on disk space)
> > nstvout = 10000 ; = 100
> >
> >
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype = PME ; = Cutoff
> > rcoulomb-switch = 0 ; = 0
> > rcoulomb = 1 ; = 1
> > ; Relative dielectric constant for the medium and the reaction field
> > epsilon_r = 1 ; = 1
> > epsilon_rf = 1 ; = 1
> > ; Method for doing Van der Waals
> > vdw-type = Cut-off ; = Cut-off
> > ; cut-off lengths
> > rvdw-switch = 0 ; = 0
> > rvdw = 1 ; = 1
> > ; Spacing for the PME/PPPM FFT grid
> > fourierspacing = 0.12 ; = 0.12
> > ; EWALD/PME/PPPM parameters
> > pme_order = 4 ; = 4
> > ewald_rtol = 1e-05 ; = 1e-05
> > ewald_geometry = 3d ; = 3d
> > epsilon_surface = 0 ; = 0
> > optimize_fft = yes ; = no
> >
> >
> >
> > ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> > ; Temperature coupling
> > tcoupl = v-rescale ; = No
> > nsttcouple = -1 ; = -1
> > nh-chain-length = 10 ; = 10
> > ; Groups to couple separately
> > tc-grps = System ; =
> > ; Time constant (ps) and reference temperature (K)
> > tau-t = 0.1 ; =
> > ref-t = 300 ; =
> > ; Pressure coupling
> > Pcoupl = Parrinello-Rahman ; = No
> > Pcoupltype = Isotropic
> > nstpcouple = -1 ; = -1
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > tau-p = 1 ; = 1
> > compressibility = 4.5e-5 ; =
> > ref-p = 1.0 ; =
> >
> >
> >
> > ; OPTIONS FOR BONDS
> > constraints = all-bonds ; = none
> > ; Type of constraint algorithm
> > constraint-algorithm = Lincs ; = Lincs
> >
> >
> >
> > ; Free energy control stuff
> > free-energy = yes ; = no
> > init-lambda = 0.00 ; = 0
> > delta-lambda = 0 ; = 0
> > foreign_lambda = 0.05 ; =
> > sc-alpha = 0.5 ; = 0
> > sc-power = 1.0 ; = 0
> > sc-sigma = 0.3 ; = 0.3
> > nstdhdl = 1 ; = 10
> > separate-dhdl-file = yes ; = yes
> > dhdl-derivatives = yes ; = yes
> > dh_hist_size = 0 ; = 0
> > dh_hist_spacing = 0.1 ; = 0.1
> > couple-moltype = LGD ; =
> > couple-lambda0 = vdw-q ; = vdw-q
> > couple-lambda1 = none ; = vdw-q
> > couple-intramol = no ; = no
> >
> >
> >
> >
> >
> > Some of these change due to positional restraint md and energy
minimization.
> >
> >
> >
> > All of these settings have come from either tutorials, papers or
peoples
> > advice.
> >
> >
> >
> > If it would be advantageous I can post my entire energy minimization,
> > positional restraint, md, and FEP mdp files.
> >
> >
> >
> > Thank you,
> >
> > TJ Mustard
> >
> >
> >
> >
> >
> >>>
> >>>
> >>> 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 <mailto:musta...@onid.orst.edu>
> >>>
> >>
> >
> >
> > TJ Mustard
> > Email: musta...@onid.orst.edu
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>
TJ Mustard
Email: musta...@onid.orst.edu
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
