[gmx-users] Fw: Potassium channel EM Segmentation fault

[Mark Abraham]

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
> --
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