Hi, I have a small system of fullerene ball with waters. I want to simulation the system without pbc and pme, treating the coulomb and vdw without cutoff. The system can be run on single processor. But when I try to run it with multiple processors, it can't proceed. I am including the error message at the end of this mail.
There are some of my guesses for the possible reason of the error: 1. Do we have to use pbc and pme to use multiple processors for simulation? 2. Can wen use restraints when use multiple processors? 3. If a molecule is "divided" into two parts in domain decomposition, will this be a problem for simulation? Thanks for any suggestion about this error message. logfile:-------------------------------------------------------------------------- [0,1,1]: OpenIB on host compute-1-12.local was unable to find any HCAs. Another transport will be used instead, although this may result in lower performance. -------------------------------------------------------------------------- -------------------------------------------------------------------------- [0,1,0]: OpenIB on host compute-1-12.local was unable to find any HCAs. Another transport will be used instead, although this may result in lower performance. -------------------------------------------------------------------------- NNODES=2, MYRANK=0, HOSTNAME=compute-1-12.local NODEID=0 argc=13 NNODES=2, MYRANK=1, HOSTNAME=compute-1-12.local NODEID=1 argc=13 . . . . Reading file /data/disk04/tianj/trp_remd_091012/equilibrium/test/trp_full_run1.tpr, VERSION 4.0 (single precision) [compute-1-12:08033] *** Process received signal *** [compute-1-12:08033] Signal: Segmentation fault (11) [compute-1-12:08033] Signal code: Address not mapped (1) [compute-1-12:08033] Failing at address: 0xc0 [compute-1-12:08033] [ 0] /lib64/libpthread.so.0 [0x378fe0de80] [compute-1-12:08033] [ 1] /lib64/libc.so.6(_IO_vfprintf+0x39) [0x378f642309] [compute-1-12:08033] [ 2] /lib64/libc.so.6(_IO_fprintf+0x88) [0x378f64cf68] [compute-1-12:08033] [ 3] /usr/local/gromacs-4.0.4/bin/mdrun_sm(mk_mshift+0x315) [0x516593] [compute-1-12:08033] [ 4] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x45fa97] [compute-1-12:08033] [ 5] /usr/local/gromacs-4.0.4/bin/mdrun_sm(dd_bonded_cg_distance+0x36c) [0x45ff53] [compute-1-12:08033] [ 6] /usr/local/gromacs-4.0.4/bin/mdrun_sm(init_domain_decomposition+0x780) [0x44d10c] [compute-1-12:08033] [ 7] /usr/local/gromacs-4.0.4/bin/mdrun_sm(mdrunner+0x89c) [0x429f6e] [compute-1-12:08033] [ 8] /usr/local/gromacs-4.0.4/bin/mdrun_sm(main+0x7ba) [0x4306b6] [compute-1-12:08033] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x378f61d8b4] [compute-1-12:08033] [10] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x4199a9] [compute-1-12:08033] *** End of error message *** mpirun noticed that job rank 0 with PID 8033 on node compute-1-12.local exited on signal 11 (Segmentation fault). 1 additional process aborted (not shown)
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