[gmx-users] multiple processor running of gromacs-4.0.4

[Mark Abraham]

Jianhui Tian wrote:
> 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.

Those messages are generic failure messages from the MPI system. The 
stack trace therein suggests you should read the stderr and/or log file 
to get some diagnostic information from GROMACS. Possibly your system is 
blowing up because you've started from an unsuitable configuration.

> 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?

Wouldn't think so. However because you have no cut-offs, there will be 
no advantage to DD because there is no data locality - every processor 
needs the position of every atom. mdrun -pd may work. It strikes me as 
possible that this scenario doesn't work in parallel on GROMACS.

> 2. Can wen use restraints when use multiple processors?

Yes.

> 3. If a molecule is "divided" into two parts in domain decomposition, 
> will this be a problem for simulation?

No, that's routine.

Mark

> 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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