[gmx-users] Re: wierd behavior of mdrun

Paymon Pirzadeh ppirzade at ucalgary.ca
Sat Sep 5 01:14:17 CEST 2009 

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-bounces at gromacs.org [mailto:gmx-users-bounces at 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<ppirzade at 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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