Dear Dr. Axel Kohlmeyer:
My lammps version is 28Mar17.
This is over 2 years old. There have been multiple bugfixes to the USER-REAXC package since. there is a good chance, the problem you are running into has been fixed.
you should upgrade to the latest LAMMPS version. please note, that we will most likely do a new stable release this week.
axel.
Dear Dr. Axel Kohlmeyer:
I tried latest stable version(12Dec18) but it still has the problem
I use the same submit file.
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 100
timestep 0.25
dump 1 all atom 100 dump.reax.cho
run 6000000
The error file is:
MPT ERROR: Rank 4(g:4) received signal SIGSEGV(11).
Process ID: 15910, Host: r1i6n0, Program: /work/k0247/k024721/lammps-12Dec18/src/lmp_mpi
MPT Version: HPE MPT 2.19 12/07/18 05:28:30
MPT: --------stack traceback-------
MPT: Attaching to program: /proc/15910/exe, process 15910
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 0x0000000000ad7e69 in Num_Entries (i=, l=)
MPT: at …/reaxc_list.h:44
MPT: #7 Validate_Lists (system=, lists=,
MPT: step=, N=, numH=2, comm=)
MPT: at …/reaxc_forces.cpp:153
MPT: #8 Init_Forces_noQEq (system=, control=,
MPT: data=, workspace=, lists=,
MPT: comm=) at …/reaxc_forces.cpp:313
MPT: #9 Compute_Forces (system=0x12c, control=0x2, data=0x12d,
MPT: workspace=0x36484d60 <cbkmolec_+173890720>, lists=0x2,
MPT: out_control=0x626c9a60, mpi_data=0x62215580) at …/reaxc_forces.cpp:445
MPT: #10 0x000000000083f661 in LAMMPS_NS::PairReaxC::compute (this=0x12c, eflag=2,
MPT: vflag=301) at …/pair_reaxc.cpp:529
MPT: #11 0x0000000000aceeb0 in LAMMPS_NS::Verlet::run (this=0x12c, n=2)
MPT: at …/verlet.cpp:310
MPT: #12 0x00000000004c7c69 in LAMMPS_NS::Run::command (this=0x12c, narg=2,
MPT: arg=0x12d) at …/run.cpp:183
MPT: #13 0x0000000000481599 in LAMMPS_NS::Input::command_creator<LAMMPS_NS::Run> (
MPT: lmp=0x12c, narg=2, arg=0x12d) at …/input.cpp:873
MPT: #14 0x0000000000479921 in LAMMPS_NS::Input::execute_command (this=0x12c)
MPT: at …/input.cpp:856
MPT: #15 0x0000000000476697 in LAMMPS_NS::Input::file (this=0x12c)
MPT: at …/input.cpp:243
MPT: #16 0x0000000000a26a8e in main (argc=1, argv=0x7fffffffcac8) at …/main.cpp:64
MPT: (gdb) A debugging session is active.
MPT:
MPT: Inferior 1 [process 15910] will be detached.
MPT:
MPT: Quit anyway? (y or n) [answered Y; input not from terminal]
MPT: Detaching from program: /proc/15910/exe, process 15910
MPT: -----stack traceback ends-----
MPT: On host r1i6n0, Program /work/k0247/k024721/lammps-12Dec18/src/lmp_mpi, Rank 4, Process 15910: Dumping core on signal SIGSEGV(11) into directory /work/k0247/k024721/CHOnew
MPT ERROR: MPI_COMM_WORLD rank 4 has terminated without calling MPI_Finalize()
aborting job
MPT: Received signal 11
And the output file is:
mpijob CMD : mpirun -f /tmp/mpiexec.params.k024721.15825
mpijob PARAMS : -d /work/k0247/k024721/CHOnew r1i6n0 24 omplace -nt 1
“/work/k0247/k024721/lammps-12Dec18/src/lmp_mpi”
SGI MPT Placement option