[gmx-users] Re: wierd behavior of mdrun

[Payman Pirzadeh]

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):

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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