This is not a Gromacs issue. You should take it up with your sysadmin. Perhaps
you are seeing sporadic successes and failures due to a buggy node (or
multiple!) or perhaps you have typos in your submission script.
-Justin
Paymon Pirzadeh wrote:
OK! I tested your suggestion about frequent output. As you had
predicted, it crashed immediately. But the message I got from the
cluster was
PBS Job Id: 94865.orca1.ibb
Job Name: AFPIII_NVT275test
job deleted
Job deleted at request of r...@elder2.ibb
MOAB_INFO: job was rejected - job violates qos configuration 'job
'94865' violates MINPROC policy of 4 (R: 1, U: 0)'
This is despite the fact that in my submission script, the number of
CPUs are 8! As I had mentioned earlier, same script is used for my water
systems.
Regards,
Payman
On Fri, 2009-09-04 at 19:29 -0400, Justin A. Lemkul wrote:
Have you tried my suggestion from the last message of setting frequent output?
Could your system just be collapsing at the outset of the simulation? Setting
nstxout = 1 would catch something like this.
There is nothing special about treating a protein in parallel vs. a system of
water. Since a system of water runs just fine, it seems even more likely to me
that your system is simply crashing immediately, rather than a problem with
Gromacs or the MPI implementation.
-Justin
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,
Payman
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?
_______________________________________________
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/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/mailing_lists/users.php
_______________________________________________
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/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/mailing_lists/users.php
_______________________________________________
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/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/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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/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/mailing_lists/users.php
