Reaxff example of CHO

Dear All:

Hello every one

When I was running the example of CHO given by lammps , I only changed the total running step of the input file and it will always stop at around 6000 step.

Does anybody know why it is?

i cannot reproduce it. what is your LAMMPS version? how did you run the input? what is the error message when LAMMPS stops?

axel.

Dear Dr. Axel Kohlmeyer:

My lammps version is 28Mar17.

I use qsub to submit the input file:

#!/bin/sh

#!/bin/sh

#QSUB -queue L4cpu

#QSUB -node 1

#QSUB -mpi 24

#QSUB -omp 1

#QSUB -place pack

#QSUB -over false

#PBS -l walltime=120:00:00

#PBS -N example-peiyu

cd $PBS_O_WORKDIR

nprocs=24

mpijob -np 24 /home/k0247/k024721/lammps/src/lmp_mpi < in.CHO > out

The input file is:

units real

atom_style charge

read_data data.CHO

pair_style reax/c lmp_control

pair_coeff * * ffield.reax.cho H C O

neighbor 2 bin

neigh_modify every 10 delay 0 check no

fix 1 all nve

fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq

fix 3 all temp/berendsen 500.0 500.0 100.0

thermo 10

timestep 0.25

dump 1 all atom 10 dump.reax.cho

run 8000000

The error file is:

MPT ERROR: Rank 4(g:4) received signal SIGSEGV(11).

Process ID: 14477, Host: r1i5n14, Program: /home/k0247/k024721/lammps/src/lmp_mpi

MPT Version: HPE MPT 2.19 12/07/18 05:28:30

MPT: --------stack traceback-------

MPT: Attaching to program: /proc/14477/exe, process 14477

MPT: Try: zypper install -C “debuginfo(build-id)=ee481d1b77962a972d43ae9a656f46b79b4a7453”

MPT: (no debugging symbols found)…done.

MPT: [Thread debugging using libthread_db enabled]

MPT: Using host libthread_db library “/lib64/libthread_db.so.1”.

MPT: Try: zypper install -C “debuginfo(build-id)=6d0a9685aa9de88e259cd40ae81316c65faa9186”

MPT: (no debugging symbols found)…done.

MPT: Try: zypper install -C “debuginfo(build-id)=70c4ab148421271723d2815a44dbf3aac3ff9015”

MPT: (no debugging symbols found)…done.

MPT: Try: zypper install -C “debuginfo(build-id)=d175e6f6e2c3e226b969c42aae541f39289018a0”

MPT: (no debugging symbols found)…done.

MPT: Try: zypper install -C “debuginfo(build-id)=1f0d403ad82efd28a9bc5003bc7ea703239ea09d”

MPT: (no debugging symbols found)…done.

MPT: Try: zypper install -C “debuginfo(build-id)=1b206daf4bd10c39f57644078bad773f8a02b9e8”

MPT: (no debugging symbols found)…done.

MPT: Try: zypper install -C “debuginfo(build-id)=baf5f44e44a3777c9f305f87dd31b3bf608157a4”

MPT: (no debugging symbols found)…done.

MPT: Try: zypper install -C “debuginfo(build-id)=8903371f3159db6d82fb81f64154e3d272888523”

MPT: (no debugging symbols found)…done.

MPT: Try: zypper install -C “debuginfo(build-id)=a9c9a6309b08729440240fb0b19855a3cc5eef72”

MPT: (no debugging symbols found)…done.

MPT: Try: zypper install -C “debuginfo(build-id)=64c277cdb888f64f47291cb237fc7b5dc4c0dac4”

MPT: (no debugging symbols found)…done.

MPT: 0x00002aaaab238385 in waitpid () from /lib64/libpthread.so.0

MPT: warning: File “/home/app/gcc/5.4.0/lib64/libstdc++.so.6.0.21-gdb.py” auto-loading has been declined by your `auto-load safe-path’ set to “$debugdir:$datadir/auto-load”.

MPT: To enable execution of this file add

MPT: add-auto-load-safe-path /home/app/gcc/5.4.0/lib64/libstdc++.so.6.0.21-gdb.py

MPT: line to your configuration file “/home/k0247/k024721/.gdbinit”.

MPT: To completely disable this security protection add

MPT: set auto-load safe-path /

MPT: line to your configuration file “/home/k0247/k024721/.gdbinit”.

MPT: For more information about this security protection see the

MPT: “Auto-loading safe path” section in the GDB manual. E.g., run from the shell:

MPT: info “(gdb)Auto-loading safe path”

MPT: (gdb) #0 0x00002aaaab238385 in waitpid () from /lib64/libpthread.so.0

MPT: #1 0x00002aaaabbb0d4c in mpi_sgi_system (command=) at sig.c:99

MPT: #2 MPI_SGI_stacktraceback (header=) at sig.c:340

MPT: #3 0x00002aaaabbb186b in first_arriver_handler (signo=11,

MPT: stack_trace_sem=0x2aaab3f80080) at sig.c:489

MPT: #4 0x00002aaaabbb1b0f in slave_sig_handler (signo=11,

MPT: siginfo=, extra=) at sig.c:564

MPT: #5

MPT: #6 0x0000000000a1f3c9 in Num_Entries (i=, l=)

MPT: at …/reaxc_list.h:44

MPT: #7 Validate_Lists (system=, workspace=,

MPT: lists=, step=, n=,

MPT: N=, numH=2, comm=)

MPT: at …/reaxc_forces.cpp:153

MPT: #8 Init_Forces_noQEq (system=, control=,

MPT: data=, workspace=, lists=,

MPT: out_control=, comm=)

MPT: at …/reaxc_forces.cpp:313

MPT: #9 Compute_Forces (system=0x102, control=0x2, data=0x103,

MPT: workspace=0x33f4ff34 <cbkmolec_+135175156>, lists=0x2,

MPT: out_control=0x646659c0, mpi_data=0x621caf40) at …/reaxc_forces.cpp:445

MPT: #10 0x00000000009b1f52 in LAMMPS_NS::PairReaxC::compute (this=0x102, eflag=2,

MPT: vflag=259) at …/pair_reax_c.cpp:510

MPT: #11 0x00000000006e2c1d in LAMMPS_NS::Verlet::run (this=0x102, n=2)

MPT: at …/verlet.cpp:301

MPT: #12 0x000000000052eab4 in LAMMPS_NS::Run::command (this=0x102, narg=2,

MPT: arg=0x103) at …/run.cpp:183

MPT: #13 0x00000000004863e9 in LAMMPS_NS::Input::command_creator<LAMMPS_NS::Run> (

MPT: lmp=0x102, narg=2, arg=0x103) at …/input.cpp:861

MPT: #14 0x000000000047eb81 in LAMMPS_NS::Input::execute_command (this=0x102)

MPT: at …/input.cpp:844

MPT: #15 0x000000000047b8f7 in LAMMPS_NS::Input::file (this=0x102)

MPT: at …/input.cpp:244

MPT: #16 0x0000000000a4e54e in main (argc=1, argv=0x7fffffffcad8) at …/main.cpp:44

MPT: (gdb) A debugging session is active.

MPT:

MPT: Inferior 1 [process 14477] will be detached.

MPT:

MPT: Quit anyway? (y or n) [answered Y; input not from terminal]

MPT: Detaching from program: /proc/14477/exe, process 14477

MPT: -----stack traceback ends-----

MPT: On host r1i5n14, Program /home/k0247/k024721/lammps/src/lmp_mpi, Rank 4, Process 14477: Dumping core on signal SIGSEGV(11) into directory /work/k0247/k024721/example

MPT ERROR: MPI_COMM_WORLD rank 4 has terminated without calling MPI_Finalize()

aborting job

MPT: Received signal 11

The output file is:

mpijob CMD : mpirun -f /tmp/mpiexec.params.k024721.14392

mpijob PARAMS : -d /work/k0247/k024721/example r1i5n14 24 omplace -nt 1

“/home/k0247/k024721/lammps/src/lmp_mpi”

SGI MPT Placement option