Hello CP2K community,
I am trying to run a molecular dynamics calculation on CP2K (version: 2024.2). My reaction system has one trans-stilbene and one 2-bromophenol in an explicit DMF (89 molecules) environment in a 30*20*20 box.
I receive the following error when I try to run this calculation using cp2k.ssmp or cp2k.psmp -np 4:
*********************
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7fc2efbd35af in ???
#1 0x7fc2efc2c949 in ???
#2 0x15cf3d1 in __topology_connectivity_util_MOD_topology_connectivity_pack
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/topology_connectivity_util.F:204
#3 0x15b1f6c in __topology_MOD_topology_control
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/topology.F:211
#4 0xad4531 in __cp_subsys_methods_MOD_cp_subsys_create
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/cp_subsys_methods.F:161
#5 0x1a4eb3d in __fist_environment_MOD_fist_init
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/fist_environment.F:168
#6 0xb1b010 in __fist_main_MOD_fist_create_force_env
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/fist_main.F:98
#7 0xb140e2 in __f77_interface_MOD_create_force_env
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/f77_interface.F:802
#8 0x472895 in cp2k_run
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/start/cp2k_runs.F:313
#9 0x47748e in __cp2k_runs_MOD_run_input
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/start/cp2k_runs.F:968
#10 0x47121d in cp2k
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/start/cp2k.F:379
#11 0x412a7c in main
at /common/software/install/manual/cp2k/2024.2-ompi-4.1.5/src/start/cp2k.F:44
Segmentation fault
*****************************
My input file is given below, and the necessary files are attached to the email:
**************************
&GLOBAL
PROJECT_NAME "tb-2brphoh-in-DMF-FFMD-equi-NPT-300K"
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NPT_I
STEPS 200000
TIMESTEP [fs] 0.5
TEMPERATURE [K] 300
&BAROSTAT
PRESSURE [bar] 1.0
&END BAROSTAT
&THERMOSTAT
TYPE NOSE
REGION GLOBAL
&NOSE
LENGTH 3
TIMECON 1000
&END NOSE
&END THERMOSTAT
&END MD
&END MOTION
&FORCE_EVAL
METHOD FIST
STRESS_TENSOR ANALYTICAL
&MM
&FORCEFIELD
PARMTYPE CHM
PARM_FILE_NAME ~/ff-parameters/charmm/toppar/par_all36_cgenff.prm
&SPLINE
RCUT_NB 10.0
EMAX_SPLINE 1.0E06
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA 0.44
GMAX 36
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
ABC 29.8939 20.0440 20.0440
ALPHA_BETA_GAMMA 90 90 90
SYMMETRY TETRAGONAL_BC
&END CELL
&TOPOLOGY
COORD_FILE_NAME ./tb-2brphoh-in-DMF.pdb
COORD_FILE_FORMAT PDB
CONN_FILE_NAME ./tb-2brphoh-in-DMF.psf
CONN_FILE_FORMAT PSF
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
********************************
I have been struggling to figure out where the problem is and how I can fix it. I have tried increasing the available memory and cores, but it didn't help.
Could anyone please help me work this problem out? I would really appreciate your time and help.
Thanks a lot,
Akanksha