[gmx-users] simulation killed

Mon Jan 30 12:25:48 CET 2012

On 30/01/2012 9:56 PM, murat özçelik wrote:
> hi! lina my script this.... please tell me where is wrong.......thanks....

Probably your use of -maxwarn is erroneous, unless you can write down 
why it is valid.

Mark

>
>
> #!/bin/bash
>
> # Set some environment variables
> FREE_ENERGY=/home/mkiytak/Free_Energy1
> echo "Free energy home directory set to $FREE_ENERGY"
>
> MDP=$FREE_ENERGY/MDP
> echo ".mdp files are stored in $MDP"
>
> LAMBDA=0
>
> # A new directory will be created for each value of lambda and
> # at each step in the workflow for maximum organization.
>
> mkdir Lambda_$LAMBDA
> cd Lambda_$LAMBDA
>
> #################################
> # ENERGY MINIMIZATION 1: STEEP  #
> #################################
> echo "Starting minimization for lambda = $LAMBDA..."
>
> mkdir EM_1
> cd EM_1
>
> # Iterative calls to grompp and mdrun to run the simulations
>
> grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro 
> -p $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>
> mdrun -nt 8 -deffnm min$LAMBDA
>
>
> ############################# ####
> # ENERGY MINIMIZATION 2: L-BFGS #
> #################################
>
> cd ../
> mkdir EM_2
> cd EM_2
>
> grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p 
> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>
> # Run L-BFGS in serial (cannot be run in parallel)
>
> mdrun -nt 1 -deffnm min$LAMBDA
>
> echo "Minimization complete."
>
>
>
> #####################
> # NVT EQUILIBRATION #
> #####################
> echo "Starting constant volume equilibration..."
>
> cd ../
> mkdir NVT
> cd NVT
>
> grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p 
> $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3
>
> mdrun -nt 8 -deffnm nvt$LAMBDA
>
> echo "Constant volume equilibration complete."
>
>
>
> #####################
> # NPT EQUILIBRATION #
> #####################
> echo "Starting constant pressure equilibration..."
>
> cd ../
> mkdir NPT
> cd NPT
>
> grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p 
> $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr 
> -maxwarn 3
>
> mdrun -nt 8 -deffnm npt$LAMBDA
>
> echo "Constant pressure equilibration complete."
>
>
> #################
> # PRODUCTION MD #
> #################
> echo "Starting production MD simulation..."
>
> cd ../
> mkdir Production_MD
> cd Production_MD
>
> grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro 
> -p $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o 
> md$LAMBDA.tpr -maxwarn 3
>
> mdrun -nt 8 -deffnm md$LAMBDA
>
> echo "Production MD complete."
>
> # End
> echo "Ending. Job completed for lambda = $LAMBDA"
>
> > Date: Mon, 30 Jan 2012 13:54:18 +0800
> > Subject: Re: [gmx-users] simulation killed
> > From: lina.lastname at gmail.com
> > To: gmx-users at gromacs.org
> >
> > On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik <mehmet63900 at hotm 
> ail.com> wrote:
> > > hi again.... capacity of my harddisk 600 GB.... ? try again ..the 
> program
> > > gave me below message...
> > >
> > > Reading file md0.tpr, VERSION 4.5.4 (single precision)
> > > Starting 8 threads
> > >
> > > NOTE: The load imbalance in PME FFT and solve is 1211%.
> > >       For optimal PME load balancing
> > >       PME grid_x (1152) and grid_y (1152) should be divisible by
> > > #PME_nodes_x (8)
> > >       and PME grid_y (1152) and grid_z (1152) should be divisible by
> > > #PME_nodes_y (1)
> > >
> > >
> > > Making 1D domain decomposition 8 x 1 x 1
> > > starting mdrun 'Protein in water'
> >
> > > 2500000 steps,   5000.0 ps.
> > > ./job_0.sh: line 95: 15777 Killed                   mdrun -nt 8 
> -deffnm
> >
> > What's inside your job_0.sh?
> >
> > something wrong your script.
> >
> > > md$LAMBDA
> > >
> > > Production MD complete.
> > > Ending. Job completed for lambda = 0
> > > mkiytak at babil:~/JOB1$
> > >
> > >
> > > How can I solve this problem....thanks for your help.....
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >> Date: Sun, 29 Jan 2012 10:43:53 -0600
> > >> From: pcl at uab.edu
> > >> To: gmx-users at gromacs.org
> > >> Subject: Re: [gmx-users] simulation killed
> > >
> > >>
> > >> something killed your job but it wasn't gromacs.
> > >> Your system has run time or memory requirements that your job 
> exceeded.
> > >>
> > >> On 2012-01-29 06:40:29PM +0200, mehmet k?ytak wrote:
> > >> > hi! all
> > >> >
> > >> > ? have to a big problem..? am doing free energy calculation for 
> a ligand
> > >> > (L
> > >> > histidine ) when ? perform mdrun .. my simulation stop ... the 
> program
> > >> > gave
> > >> > me this message..
> > >> >
> > >> > Reading file md0.tpr, VERSION 4.5.4 (single precision)
> > >> > Starting 8 threads
> > >> > Making 1D domain decomposition 8 x 1 x 1
> > > & gt; > starting mdrun 'Protein in water'
> > >
> > >> > 2500000 steps, 5000.0 ps.
> > >> > ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm
> > >> > md$LAMBDA
> > >> > Production MD complete.
> > >> > Ending. Job completed for lambda = 0
> > >> > mkiytak at babil:~/JOB1$
> > >> >
> > >> >
> > >> > my mdp file..
> > >> > ;
> > >> > ; Run control
> > >> > integrator = sd ; Langevin dynamics
> > >> > tinit = 0
> > >> > dt = 0.002
> > >> > nsteps = 2500000 ; 5 ns
> > >> > nstcomm = 100
> > >> > ; Output control
> > >> > nstxout = 500
> > >> > nstvout = 500
> > >> > nstfout = 0
> > >> > nstlog = 500
> > >> > nstenergy = 500
> > >> > nstxtcout = 0
> > >> > xtc-precision = 1000
> > >> > ; Neighborsearching and short-range nonbonded interactions
> > >> > nstlist = 10
> > >> > ns_type = grid
> > >> > pbc = xyz
> > >> > rlist = 1.0
> > >> > ; Electrostatics
> > >> > coulombtype = PME
> > >> > rcoulomb = 1.0
> > >> > ; van der Waals
> > >> > vdw-type = switch
> > >> > rvdw-switch = 0.8
> > >> > rvdw = 0.9
> > >> > ; Apply long range dispersion corrections for Energy and Pressure
> > >> > DispCorr = EnerPres
> > >> > ; Spacing for the PME/PPPM FFT grid
> > >> > fourierspacing = 0.12
> > >> > ; EWALD/PME/PPPM parameters
> > >> > pme_order = 6
> > >> > ewald_rtol = 1e-06
> > >> > epsilon_surface = 0
> > >> > optimize_fft = no
> > >> &g t; ; Temperature coupling
> > >
> > >> > ; tcoupl is implicitly handled by the sd integrator
> > >> > tc_grps = system
> > >> > tau_t = 1.0
> > >> > ref_t = 300
> > >> > ; Pressure coupling is on for NPT
> > >> > Pcoupl = Parrinello-Rahman
> > >> > tau_p = 0.5
> > >> > compressibility = 4.5e-05
> > >> > ref_p = 1.0
> > >> > ; Free energy control st uff
> > >> > free_energy = yes
> > >> > init_lambda = 0.00
> > >> > delta_lambda = 0
> > >> > foreign_lambda = 0.05
> > >> > sc-alpha = 0.5
> > >> > sc-power = 1.0
> > >> > sc-sigma = 0.3
> > >> > couple-moltype = system
> > >> > couple-lambda0 = vdw ; only van der Waals interactions
> > >> > couple-lambda1 = non e ; turn off everything, in this case
> > >
> > >> > only vdW
> > >> > couple-intramol = no
> > >> > nstdhdl = 10
> > >> > ; Do not generate velocities
> > >> > gen_vel = no
> > >> > ; options for bonds
> > >> > constraints = h-bonds ; we only have C-H bonds here
> > >> > ; Type of constraint algorithm
> > >> > constraint-algorithm = lincs
> > >> > ; Constrain the starting configuration
> > >> > ; since we are continuing from NPT
> > >> > continuation = yes
> > >> > ; Highest order in the expansion of the constraint coupling matrix
> > >> > lincs-order = 12
> > >> >
> > >> > PLEASE HELP ME... WHY THE PROGRAM STOP ( KI.LLED) SORRY FOR BAD 
> ENGLI.SH..
> > >>
> > >> > --
> > >> > gmx-users mailing list gmx-users at gromacs.org
> > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > >>
> > >>
> > >> --
> > >> =================== ===============================================
> > >> Peter C. Lai | University of Alabama-Birmingham
> > >> Programmer/Analyst | KAUL 752A
> > >> Genetics, Div. of Research | 705 South 20th Street
> > >> pcl at uab.edu | Birmingham AL 35294-4461
> > >> (205) 690-0808 |
> > >> ==================================================================
> > >>
> > >> --
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