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

[Jianhui Tian]

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)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091019/d978d1e5/attachment.html>