[gmx-users] about parallel run

[Justin A. Lemkul]

Mahnam wrote:
> 
> 
>  
> In God We Trust
> Hello GMX users
> I am trying to run one gromacs simulation in parallel. I have  
> successfully compiled gromacs 4  with mpi support  on a cluster with 
> x86_64 architecture with 4 cpus (intel core 2 Quad 6600).
> when I run mdrun with single-processor  ,it works  fine and everything 
> is ok, but when I run the same simulation  with 4 cpu,
> it finishs again normally and I don't  get any error messages , but my 
> protein breaks and box of sol becomes deformed.

Which (specific) version are you using?  Prior to 4.0.2 (I think), the final 
output was fragmented as a consequence of domain decomposition.  It can be 
"fixed" (i.e., molecules can be made whole again) with trjconv.

"Deformed" is a matter of perspective, and is typically an artifact of 
visualization.  You will have to describe your system in much greater detail to 
get any useful advice.

> These are first few lines of my output (on screen)

These lines just indicate the run is being split between nodes; they are not 
indicative of a problem.

-Justin

> NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain
> NODEID=3 argc=16
> NNODES=4, MYRANK=0, HOSTNAME=localhost.localdomain
> NNODES=4, MYRANK=2, HOSTNAME=localhost.localdomain
> NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain
> NODEID=2 argc=15
> NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain
> NODEID=1 argc=15
> NODEID=3 argc=15
> NODEID=0 argc=15
>  
> here is my commands and mdp file  :
> commands:
> grompp -f sp.mdp -c fprmd.gro -r fprmd.gro -p n.top -o  sp.tpr  -n n.ndx 
> -maxwarn  1000
> mpirun -np 4 mdrun -s sp.tpr -o sp.trr -c fsp.gro -g sp.log -e sp.edr -n 
> n.ndx -N 4
>  
> mdf file:
>  
> title               =  n.pdb
> restraining
> warnings            =  10
> cpp                 =  /lib/cpp
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  steep
> nsteps              =  10000
> nstcomm             =  1
> comm_mode           =  Linear
> comm_grps           =  protein
> nstxout             =  250
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.2
> coulombtype         =  PME
> rcoulomb            =  1.2
> rvdw                =  1.4
> fourierspacing      =  0.12
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  4
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
> emtol               = 10.0
> emstep              = 0.01
> 
> whould you please help me to overcome this problem. 
> Many thanks in advance for your help and your reply.
> 
> Yours truly
> Karim Mahnam
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
> P.O.box 13145-1384
> Tehran
> Iran
> http://www.ibb.ut.ac.ir/
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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

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