-----Original Messages-----
From:"Du, Yu" <d...@sioc.ac.cn>
Sent Time:2017-10-11 21:55:38 (Wednesday)
To: GMX-user <gromacs.org_gmx-users@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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