Hi,<br><br>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.<br>
<br>There are some of my guesses for the possible reason of the error:<br>1. Do we have to use pbc and pme to use multiple processors for simulation?<br>2. Can wen use restraints when use multiple processors?<br>3. If a molecule is "divided" into two parts in domain decomposition, will this be a problem for simulation?<br>
Thanks for any suggestion about this error message.<br><br>logfile:--------------------------------------------------------------------------<br>[0,1,1]: OpenIB on host compute-1-12.local was unable to find any HCAs.<br>
Another transport will be used instead, although this may result in <br>lower performance.<br>--------------------------------------------------------------------------<br>--------------------------------------------------------------------------<br>
[0,1,0]: OpenIB on host compute-1-12.local was unable to find any HCAs.<br>Another transport will be used instead, although this may result in <br>lower performance.<br>--------------------------------------------------------------------------<br>
NNODES=2, MYRANK=0, HOSTNAME=compute-1-12.local<br>NODEID=0 argc=13<br>NNODES=2, MYRANK=1, HOSTNAME=compute-1-12.local<br>NODEID=1 argc=13<br>.<br>.<br>.<br>.<br>Reading file /data/disk04/tianj/trp_remd_091012/equilibrium/test/trp_full_run1.tpr, VERSION 4.0 (single precision)<br>
[compute-1-12:08033] *** Process received signal ***<br>[compute-1-12:08033] Signal: Segmentation fault (11)<br>[compute-1-12:08033] Signal code: Address not mapped (1)<br>[compute-1-12:08033] Failing at address: 0xc0<br>
[compute-1-12:08033] [ 0] /lib64/libpthread.so.0 [0x378fe0de80]<br>[compute-1-12:08033] [ 1] /lib64/libc.so.6(_IO_vfprintf+0x39) [0x378f642309]<br>[compute-1-12:08033] [ 2] /lib64/libc.so.6(_IO_fprintf+0x88) [0x378f64cf68]<br>
[compute-1-12:08033] [ 3] /usr/local/gromacs-4.0.4/bin/mdrun_sm(mk_mshift+0x315) [0x516593]<br>[compute-1-12:08033] [ 4] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x45fa97]<br>[compute-1-12:08033] [ 5] /usr/local/gromacs-4.0.4/bin/mdrun_sm(dd_bonded_cg_distance+0x36c) [0x45ff53]<br>
[compute-1-12:08033] [ 6] /usr/local/gromacs-4.0.4/bin/mdrun_sm(init_domain_decomposition+0x780) [0x44d10c]<br>[compute-1-12:08033] [ 7] /usr/local/gromacs-4.0.4/bin/mdrun_sm(mdrunner+0x89c) [0x429f6e]<br>[compute-1-12:08033] [ 8] /usr/local/gromacs-4.0.4/bin/mdrun_sm(main+0x7ba) [0x4306b6]<br>
[compute-1-12:08033] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x378f61d8b4]<br>[compute-1-12:08033] [10] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x4199a9]<br>[compute-1-12:08033] *** End of error message ***<br>mpirun noticed that job rank 0 with PID 8033 on node compute-1-12.local exited on signal 11 (Segmentation fault). <br>
1 additional process aborted (not shown)<br>