[gmx-users] Fw: Potassium channel EM Segmentation fault
Du, Yu
duyu at sioc.ac.cn
Wed Oct 11 16:55:21 CEST 2017
Thanks for Mark's prompt reply.
I find there indeed are overlapping potassiums from each chain and I remove the extra potassiums then EM succeeds.
Yu
> -----Original Messages-----
> From: "Mark Abraham" <mark.j.abraham at gmail.com>
> Sent Time: 2017-10-11 22:12:29 (Wednesday)
> To: gmx-users at gromacs.org, GMX-user <gromacs.org_gmx-users at maillist.sys.kth.se>
> Cc:
> Subject: Re: [gmx-users] Fw: Potassium channel EM Segmentation fault
>
> Hi,
>
> This is probably a case of
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up and I suggest
> you consider some of the investigation approaches documented there.
>
> Mark
>
> On Wed, Oct 11, 2017 at 4:07 PM Du, Yu <duyu at sioc.ac.cn> wrote:
>
> >
> >
> >
> > -----Original Messages-----
> > From:"Du, Yu" <duyu at sioc.ac.cn>
> > Sent Time:2017-10-11 21:55:38 (Wednesday)
> > To: GMX-user <gromacs.org_gmx-users at maillist.sys.kth.se>
> > Cc:
> > Subject: Potassium channel EM Segmentation fault
> >
> > Dear GMX Users,
> >
> >
> > Keyword: metal, energy minimization, segmentation fault
> >
> >
> > I have pinpointed the source of EM error. EM succeeds only without
> > potassiums.
> >
> >
> > I used PDB 1r3j and changed the TL to K.
> > You can download the my 1r3j here and reproduce the error like this.
> >
> >
> > $gmx pdb2gmx -f 1r3j_kchannel.pdb -o 1r3j.gro -ignh -water tip3p
> > $gmx grompp -f minim.mdp -c 1r3j.gro -p topol.top -o em.tpr
> > $mpirun -np 20 gmx_mpi mdrun -ntomp 1 -s em.tpr
> >
> >
> > Thanks for any solutions.
> >
> >
> > ######################The minim.mdp file######################
> > define=-DPOSRES
> > ; Parameters describing what to do, when to stop and what to save
> > integrator = steep ; Algorithm (steep = steepest descent minimization)
> > emtol = 1000.0 ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > emstep = 0.01 ; Energy step size
> > nsteps = 50000 ; Maximum number of (minimization) steps to perform
> >
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist = 1 ; Frequency to update the neighbor list and long
> > range forces
> > cutoff-scheme = verlet
> > ns_type = grid ; Method to determine neighbor list (simple, grid)
> > rlist = 1.2 ; Cut-off for making neighbor list (short range
> > forces)
> > coulombtype = PME ; Treatment of long range electrostatic
> > interactions
> > rcoulomb = 1.2 ; Short-range electrostatic cut-off
> > rvdw = 1.2 ; Short-range Van der Waals cut-off
> > pbc = xyz ; Periodic Boundary Conditions
> > ###################################END##########################
> >
> >
> > ############################EM Error############################
> >
> > Steepest Descents:
> > Tolerance (Fmax) = 1.00000e+03
> > Number of steps = 50000
> > [gpu-new:22930] *** Process received signal ***
> > [gpu-new:22930] Signal: Segmentation fault (11)
> > [gpu-new:22930] Signal code: Address not mapped (1)
> > [gpu-new:22930] Failing at address: 0xfffffffe01bf6dd0
> > [gpu-new:22930] [ 0] /lib64/libpthread.so.0[0x383660f710]
> > [gpu-new:22930] [ 1]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6c36f)[0x2b1966ebe36f]
> > [gpu-new:22930] [ 2]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6d65f)[0x2b1966ebf65f]
> > [gpu-new:22930] [ 3]
> > /home/duyu/software/gcc-4.9.4/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b196d7a58cf]
> > [gpu-new:22930] [ 4]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_Z17nbnxn_put_on_gridP12nbnxn_searchiPA3_fiPfS3_iifPKiS2_iPiiP16nbnxn_atomdata_t+0xecd)[0x2b1966ec28fd]
> > [gpu-new:22930] [ 5]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(dd_partition_system+0x2c67)[0x2b19661ed6b7]
> > [gpu-new:22930] [ 6]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe0379d)[0x2b1966e5579d]
> > [gpu-new:22930] [ 7]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx8do_steepEP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiP11gmx_vsite_tP10gmx_constriP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP9t_mdatomsP6t_nrnbP13gmx_wallcycleP9gmx_edsamP10t_forcereciiiP12gmx_membed_tffimP23gmx_walltime_accounting+0x353)[0x2b1966e69aa3]
> > [gpu-new:22930] [ 8]
> > gmx_mpi(_ZN3gmx8mdrunnerEP12gmx_hw_opt_tP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiPiiiffPKcfSE_SE_SE_SE_iliiiiiifffim+0x190a)[0x4101ca]
> > [gpu-new:22930] [ 9] gmx_mpi(_Z9gmx_mdruniPPc+0x1766)[0x421516]
> > [gpu-new:22930] [10]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x2a3)[0x2b19661a5693]
> > [gpu-new:22930] [11] gmx_mpi(main+0x7c)[0x40cd3c]
> > [gpu-new:22930] [12] /lib64/libc.so.6(__libc_start_main+0xfd)[0x383621ed1d]
> > [gpu-new:22930] [13] gmx_mpi[0x40cb79]
> > [gpu-new:22930] *** End of error message ***
> > --------------------------------------------------------------------------
> > mpirun noticed that process rank 0 with PID 0 on node gpu-new exited on
> > signal 11 (Segmentation fault).
> > --------------------------------------------------------------------------
> > ###################################END##########################
> >
> >
> > --
> > Du, Yu
> > PhD Student,
> > Shanghai Institute of Organic Chemistry
> > 345 Ling Ling Rd., Shanghai, China.
> > Zip: 200032, Tel: (86) 021 5492 5275
> >
> > --
> > Du, Yu
> > PhD Student,
> > Shanghai Institute of Organic Chemistry
> > 345 Ling Ling Rd., Shanghai, China.
> > Zip: 200032, Tel: (86) 021 5492 5275
> > --
> > Gromacs Users mailing list
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--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275
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