Hi,
I’m trying to run a programme using kspace_style pppm but I get a long Segmentation fault. I have compiled and linked using mpicxx and the FFTW library.
Any tips how to do this correctly?
Sam
Hi,
Just though I’d add some more information about this fault. I’ve compiled using mpicxx and the fftw3 library (at least after compiling I didn’t get any error messages). I also tried changing the OMP_NUM_THREADS environment variable to 1, but no luck.
Here is the input file and the error file after running mpiexec.
Would be very grateful to receive some help with this one. I’m having to use the Ewald style which is slower than the PPPM style.
Yours
Sam
— in.chain
FENE beadspring benchmark
units lj
atom_style full
special_bonds fene
read_restart restart.7000000.equil
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff * 30.0 1.5 1.0 1.0
set type 1 charge 1.0
set type 2 charge 1.0
set type 3 charge 1.0
set type 4 charge -1.0
pair_style lj/cut/coul/long 2.5 10.0
pair_coeff * * 1.0 1.0
pair_modify shift yes
kspace_style pppm 1.0e-4
fix 1 all npt temp 1.0 1.0 100.0 iso 0.0 0.0 1000.0
thermo 10
timestep 0.012
minimize 1.0e-4 1.0e-8 1000 100000
run 10
— error file
[pn004:21398] *** Process received signal ***
[pn004:21404] *** Process received signal ***
[pn004:21399] *** Process received signal ***
[pn004:21399] Signal: Segmentation fault (11)
[pn004:21399] Signal code: Address not mapped (1)
[pn004:21399] Failing at address: 0x100000001
[pn004:21400] *** Process received signal ***
[pn004:21400] Signal: Segmentation fault (11)
[pn004:21400] Signal code: Address not mapped (1)
[pn004:21400] Failing at address: 0x1
[pn004:21401] *** Process received signal ***
[pn004:21401] Signal: Segmentation fault (11)
[pn004:21401] Signal code: Address not mapped (1)
[pn004:21401] Failing at address: 0x100000001
[pn004:21402] *** Process received signal ***
[pn004:21402] Signal: Segmentation fault (11)
[pn004:21402] Signal code: Address not mapped (1)
[pn004:21402] Failing at address: 0x1
[pn004:21404] Signal: Segmentation fault (11)
[pn004:21404] Signal code: Address not mapped (1)
[pn004:21404] Failing at address: 0x100000000
[pn004:21398] Signal: Segmentation fault (11)
[pn004:21398] Signal code: Address not mapped (1)
[pn004:21398] Failing at address: 0x100000001
[pn004:21399] [ 0] /lib64/libpthread.so.0 [0x3abce0ebe0]
[pn004:21399] [ 1] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS4PPPMC1EPNS_6LAMMPSEiPPc+0x1e7) [0x75a2e7]
[pn004:21399] [ 2] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Force13create_kspaceEiPPcPKc+0x43f) [0x601eff]
[pn004:21399] [ 3] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input15execute_commandEv+0x1966) [0x61a1d6]
[pn004:21399] [ 4] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input4fileEv+0x2ea) [0x6175aa]
[pn004:21399] [ 5] /home/sam/lammps/lmp_platon(main+0x94) [0x62cc84]
[pn004:21399] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3abbe1d994]
[pn004:21399] [ 7] /home/sam/lammps/lmp_platon(_ZNSt8ios_base4InitD1Ev+0x39) [0x46f649]
[pn004:21399] *** End of error message ***
[pn004:21400] [ 0] /lib64/libpthread.so.0 [0x3abce0ebe0]
[pn004:21400] [ 1] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS4PPPMC1EPNS_6LAMMPSEiPPc+0x1e7) [0x75a2e7]
[pn004:21400] [ 2] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Force13create_kspaceEiPPcPKc+0x43f) [0x601eff]
[pn004:21400] [ 3] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input15execute_commandEv+0x1966) [0x61a1d6]
[pn004:21400] [ 4] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input4fileEv+0x2ea) [0x6175aa]
[pn004:21400] [ 5] /home/sam/lammps/lmp_platon(main+0x94) [0x62cc84]
[pn004:21400] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3abbe1d994]
[pn004:21400] [ 7] /home/sam/lammps/lmp_platon(_ZNSt8ios_base4InitD1Ev+0x39) [0x46f649]
[pn004:21400] *** End of error message ***
[pn004:21401] [ 0] /lib64/libpthread.so.0 [0x3abce0ebe0]
[pn004:21401] [ 1] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS4PPPMC1EPNS_6LAMMPSEiPPc+0x1e7) [0x75a2e7]
[pn004:21401] [ 2] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Force13create_kspaceEiPPcPKc+0x43f) [0x601eff]
[pn004:21401] [ 3] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input15execute_commandEv+0x1966) [0x61a1d6]
[pn004:21401] [ 4] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input4fileEv+0x2ea) [0x6175aa]
[pn004:21401] [ 5] /home/sam/lammps/lmp_platon(main+0x94) [0x62cc84]
[pn004:21401] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3abbe1d994]
[pn004:21401] [ 7] /home/sam/lammps/lmp_platon(_ZNSt8ios_base4InitD1Ev+0x39) [0x46f649]
[pn004:21401] *** End of error message ***
[pn004:21402] [ 0] /lib64/libpthread.so.0 [0x3abce0ebe0]
[pn004:21402] [ 1] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS4PPPMC1EPNS_6LAMMPSEiPPc+0x1e7) [0x75a2e7]
[pn004:21402] [ 2] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Force13create_kspaceEiPPcPKc+0x43f) [0x601eff]
[pn004:21402] [ 3] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input15execute_commandEv+0x1966) [0x61a1d6]
[pn004:21402] [ 4] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input4fileEv+0x2ea) [0x6175aa]
[pn004:21402] [ 5] /home/sam/lammps/lmp_platon(main+0x94) [0x62cc84]
[pn004:21402] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3abbe1d994]
[pn004:21404] [ 0] /lib64/libpthread.so.0 [0x3abce0ebe0]
[pn004:21404] [ 1] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS4PPPMC1EPNS_6LAMMPSEiPPc+0x1e7) [0x75a2e7]
[pn004:21404] [ 2] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Force13create_kspaceEiPPcPKc+0x43f) [0x601eff]
[pn004:21404] [ 3] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input15execute_commandEv+0x1966) [0x61a1d6]
[pn004:21404] [ 4] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input4fileEv+0x2ea) [0x6175aa]
[pn004:21404] [ 5] /home/sam/lammps/lmp_platon(main+0x94) [0x62cc84]
[pn004:21404] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3abbe1d994]
[pn004:21404] [ 7] /home/sam/lammps/lmp_platon(_ZNSt8ios_base4InitD1Ev+0x39) [0x46f649]
[pn004:21404] *** End of error message ***
[pn004:21402] [ 7] /home/sam/lammps/lmp_platon(_ZNSt8ios_base4InitD1Ev+0x39) [0x46f649]
[pn004:21402] *** End of error message ***
[pn004:21398] [ 0] /lib64/libpthread.so.0 [0x3abce0ebe0]
[pn004:21398] [ 1] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS4PPPMC1EPNS_6LAMMPSEiPPc+0x1e7) [0x75a2e7]
[pn004:21398] [ 2] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Force13create_kspaceEiPPcPKc+0x43f) [0x601eff]
[pn004:21398] [ 3] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input15execute_commandEv+0x1966) [0x61a1d6]
[pn004:21398] [ 4] /home/sam/lammps/lmp_platon(_ZN9LAMMPS_NS5Input4fileEv+0x2ea) [0x6175aa]
[pn004:21398] [ 5] /home/sam/lammps/lmp_platon(main+0x94) [0x62cc84]
[pn004:21398] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3abbe1d994]
[pn004:21398] [ 7] /home/sam/lammps/lmp_platon(_ZNSt8ios_base4InitD1Ev+0x39) [0x46f649]
[pn004:21398] *** End of error message ***
Can't reproduce your problem without the restart file.
Can you run bench/in.rhodo with the current version of LAMMPS?
Steve
Sometimes I have the same error when restart and lammps versions are different.
But if I convert the restart to a data file and then use read_data instead of read_restart, everything is ok. Maybe it helps in your case.
Regards,
Grigory
2012/9/18 Steve Plimpton <[email protected]>
Yes. I can run in.rhodo funnily enough.
Then it's likely a problem with your input/restart file, not with LAMMPS.
Maybe run it under valgrind and see what it complains about.
Steve
Hi,
Then it’s likely a problem with your input/restart file
What common problem would you envisage?
not with LAMMPS.
Maybe run it under valgrind and see what it complains about.
I’m unfamiliar with valgrind. Can you please give an example of how to invoke it and what it would tell me?
Thanks
Sam
Google for valgrind and you can download it - you
just run your executable under it ... e.g. valgrind lmp_foo < in.foo
If you post your data file & input script and the crash happens
quickly, I can take a look.
Steve
HI,
I found the same thing. I had to use restart2data and remove the Velocities section in order to get it to work!
Sam