Hi Mark,<br><br>You are right that treating electrostatics and vdw without cutoff and use multiple processors to speed up doesn't make any sense. <br>Using cutoff for electrostatics and vdw without using pbc and pme, the system can't run on parallel (using flag -pd doesn't work either), but works on single node.<br>
Using cutoff for electrostatics and vdw with pbc and pme, the system can run on parallel.<br>Thanks for the clarifications.<br><br>Jianhui<br>
<br>
Jianhui Tian wrote:<br>
> Hi,<br>
><br>
> I have a small system of fullerene ball with waters. I want to<br>
> simulation the system without pbc and pme, treating the coulomb and vdw<br>
> without cutoff. The system can be run on single processor. But when I<br>
> try to run it with multiple processors, it can't proceed. I am including<br>
> the error message at the end of this mail.<br>
<br>
Those messages are generic failure messages from the MPI system. The<br>
stack trace therein suggests you should read the stderr and/or log file<br>
to get some diagnostic information from GROMACS. Possibly your system is<br>
blowing up because you've started from an unsuitable configuration.<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>
<br>
Wouldn't think so. However because you have no cut-offs, there will be<br>
no advantage to DD because there is no data locality - every processor<br>
needs the position of every atom. mdrun -pd may work. It strikes me as<br>
possible that this scenario doesn't work in parallel on GROMACS.<br>
<br>
> 2. Can wen use restraints when use multiple processors?<br>
<br>
Yes.<br>
<br>
> 3. If a molecule is "divided" into two parts in domain decomposition,<br>
> will this be a problem for simulation?<br>
<br>
No, that's routine.<br>
<br>
Mark<br>
<br>
> Thanks for any suggestion about this error message.<br>
><br>
> logfile:----------------------<div id=":9f" class="ii gt">----------------------------------------------------<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<br>
> /data/disk04/tianj/trp_remd_091012/equilibrium/test/trp_full_run1.tpr,<br>
> 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]<br>
> /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]<br>
> /usr/local/gromacs-4.0.4/bin/mdrun_sm(dd_bonded_cg_distance+0x36c)<br>
> [0x45ff53]<br>
> [compute-1-12:08033] [ 6]<br>
> /usr/local/gromacs-4.0.4/bin/mdrun_sm(init_domain_decomposition+0x780)<br>
> [0x44d10c]<br>
> [compute-1-12:08033] [ 7]<br>
> /usr/local/gromacs-4.0.4/bin/mdrun_sm(mdrunner+0x89c) [0x429f6e]<br>
> [compute-1-12:08033] [ 8]<br>
> /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)<br>
> [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<br>
> exited on signal 11 (Segmentation fault).<br>
> 1 additional process aborted (not shown)<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
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