Paymon Pirzadeh wrote:
Regarding the problems I have on running protein system in parallel
(runs without output), When I run pure water system, everything is fine,
I have tested pure water systems 8 times larger than my protein system.
while the former runs fine, the latter has problems. I have also tested
pure water systems with approximately same number of sites in .gro file
as in my protein .gro file, and with the same input file in terms of
spitting outputs; they are fine.I would like to know what happens to
GROMACS when a protein is added to the system. The cluster admin has not
get back to me, but I still want to check there is no problem with my
setup! (although my system runs fine in serial mode).
Regards,
There's no known reason why similarly-sized simulations where the only
change is between water+protein and water-only would have problems with
producing output in the absence of a crash (probably integration error
from bad equilibration). Check that your protein+water .tpr file will
run correctly elsewhere than your cluster. Check for inhomogeneities in
your cluster - if possible submit the two job types to the same physical
nodes. Equilibrate better.
Mark
On Fri, 2009-08-28 at 16:41 -0400, Justin A. Lemkul wrote:
Payman Pirzadeh wrote:
There is sth strange about this problem which I suspect it might be due to
the mdp file and input. I can run the energy minimization without any
problems (I submit the job and it apparently works using the same submission
script)! But as soon as I prepare the tpr file for MD run, then I run into
this run-without-output trouble.
Again I paste my mdp file below (I want to run an NVT run):
There isn't anything in the .mdp file that suggests you wouldn't get any output.
The output of mdrun is buffered, so depending on your settings, you may have
more frequent output during energy minimization. There may be some problem with
the MPI implementation in buffering and communicating data properly. That's a
bit of a guess, but it could be happening.
Definitely check with the cluster admin to see if there are any error messages
reported for the jobs you submitted.
Another test you could do to force a huge amount of data would be to set all of
your outputs (nstxout, nstxtcout, etc) = 1 and run a much shorter simulation (to
prevent massive data output!); this would force more continuous data through the
buffer.
-Justin
cpp = cpp
include = -I../top
define = -DPOSRES
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 3000000 ;3 ns
comm_mode = linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy = 5000
nstxtcout = 1500
nstvout = 5000
nstfout = 5000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist = 0.9
pbc = xyz
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
;epsilon_r = 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft = yes
; Temperature coupling
tcoupl = v-rescale
ld_seed = -1
tc-grps = System
tau_t = 0.1
ref_t = 275
; Pressure Coupling
Pcoupl = no
;Pcoupltype = isotropic
;tau_p = 1.0
;compressibility = 5.5e-5
;ref_p = 1.0
gen_vel = yes
gen_temp = 275
gen_seed = 173529
constraint-algorithm = Lincs
constraints = all-bonds
lincs-order = 4
Regards,
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: August 27, 2009 3:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: wierd behavior of mdrun
Vitaly V. Chaban wrote:
Then I believe you have problems with MPI.
Before I experienced something alike on our old system - serial
version worked OK but parallel one failed. The same issue was with
CPMD by the way. Another programs worked fine. I didn't correct that
problem...
On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pirzadeh<ppirz...@ucalgary.ca>
wrote:
Yes,
it works when it is run on one processor interactively!
That's fine, but it doesn't mean the problem is with the parallelism, as
Vitaly suggests. If your cluster filesystem isn't configured properly,
you will observe these symptoms. Since the submission script was the
same, MPI worked previously, so isn't likely to be the problem...
Mark
On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote:
I made a .tpr file for my md run without any problems (using the bottom
mdp file). My job submission script is also the same thing I used for
other jobs which had no problems. But now when I submit this .tpr file,
only an empty log file is generated! The qstat of the cluster shows
that
the job is running, also the processors are 100% engaged while I have
no
outputs!
A standard guess: what about trying to run the single-processor job on
the same cluster? Does it run OK?
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