TJ Mustard wrote:
On January 25, 2011 at 2:08 PM Mark Abraham <mark.abra...@anu.edu.au> wrote:
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
Mark and all,
First thank you for all our help. What you suggested last time helped
considerably with our jobs/calculations. I have learned that using the
standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel)
and have made these my new standard for future jobs. We chose to use the
smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we
understand why we need these standard settings. Now what I see to be our
problem is that our machines have some sort of variable we cannot
account for. If I am blind to my error, please show me. I just don't
understand why one computer works while the other does not. We have
recompiled gromacs 4.5.3 single precission on our cluster, and still
have this problem.
I know the feeling all too well. PowerPC jobs crash instantly, on our cluster,
despite working beautifully on our lab machines. There's a bug report about
that one, but I haven't heard anything about AMD failures. It remains a
possibility that something beyond your control is going on. To explore a bit
further:
1. Do the systems in question crash immediately (i.e., step zero) or do they run
for some 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:
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.
4. Are the compilers the same on the iMac vs. AMD cluster?
-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
========================================
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