[gmx-users] parallel run hangs (not crashed)

[David van der Spoel]

chris.neale at utoronto.ca wrote:
> I am running a system of 185K atoms. The structure is energy minimized and the
> dynamics run appears to be going smoothly until it just hangs. The job still
> exists on the first node, but none of the 4 nodes are doing any work and I don't
> get any error messages.
> 
> The trajectory looks good and no step.***.pdb files were created.
> 
Are you sure you want comm_mode = angular ? It seems ike you have a 
periodic system.


Are you sure you want to run this system without constraints?

If the processes are still there you can kill -HUP them and they should 
terminate gracefully, writing all files etc.



> My only clue is that an energy file was created but was empty -- and should have
> some data based on nstenergy=10000
> 
> The last portion of output to my mdrun_mpi -g log file was:
>            Step           Time         Lambda
>           26300       52.60000        0.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
>     8.77749e+04    1.66791e+05    6.40224e+04    7.13528e+04    6.57086e+03
>           LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
>     1.01403e+05    1.73522e+05   -3.08556e+03   -2.51895e+06   -1.65998e+06
>  Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
>     5.65104e+03   -3.50492e+06    5.44080e+05   -2.96084e+06    2.99289e+02
>  Pressure (bar)
>     3.40970e+01
> 
> My commands were:
> 
> GROMPP:
> ${ED}/grompp -np 4 -f grompp_md.mdp -n ${MOL}.ndx -c ${MOL}_m.gro -p ${MOL}.top
> -o ${MOL}_mm.tpr > output.mm_grompp
> 
> MDRUN_MPI:
> ${ED}/mdrun_mpi -np 4 -nice 4 -s ${MOL}_mm.tpr -o ${MOL}_mm.trr -c ${MOL}_mm.gro
> -g output.mm_mdrun -v -deffnm run1g 2> output.mm_mdrun_e
> 
> LAM SCRIPT:
> #!/bin/sh
> PATH=.:/work/lam/bin:$PATH
> LAMRSH="ssh -x"
> export LAMRSH PATH
> cd ${MYDIR}
> lamboot -v lamhosts
> mpirun N ${MYDIR}/run.sh
> lamhalt
> 
> And my mdp file was:
> title               =  seriousMD
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES_LIPID -DPOSRES_PAGP -DPOSRES_LDA -DPOSRES_XSOL
> integrator          =  md
> nsteps              =  50000
> tinit               =  0
> dt                  =  0.002
> comm_mode           =  angular
> nstcomm             =  1
> comm_grps           =  System
> nstxout             =  10000
> nstvout             =  10000
> nstfout             =  10000
> nstlog              =  100
> nstlist             =  10
> nstenergy           =  10000
> nstxtcout           =  250
> ns_type             =  grid
> pbc                 =  xyz
> coulombtype         =  PME
> fourierspacing      =  0.15
> pme_order           =  4
> vdwtype             =  switch
> rvdw_switch         =  0.9
> rvdw                =  1.0
> rlist               =  1.1
> DispCorr            =  no
> Pcoupl              =  Berendsen
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.
> tcoupl              =  nose-hoover
> tc_grps             =  Protein_LDA   XSOL_SOL_NA+   POPE
> tau_t               =  0.05          0.05           0.05
> ref_t               =  300.          300.           300.
> annealing           =  no            no             no
> gen_vel             =  yes
> gen_temp            =  300.          300.           300.
> gen_seed            =  9896
> constraints         =  hbonds
> constraint_algorithm=  shake
> shake_tol           =  0.0001
> 
> Thanks.
> Chris.
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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