Dear Roland,
We need to run the GROMACS on the base of the nodes of our cluster (in
order to use all computational resources of the cluster), that's why we
need MPI (instead of using thread or OpenMP within the SMP node).
I can run simple MPI examples, so I guess the problem on the
implementation of the Gromacs.
Regads,
Hrach
On 4/27/11 11:29 PM, Roland Schulz wrote:
This seems to be a problem with your MPI library. Test to see whether
other MPI programs don't have the same problem. If it is not GROMACS
specific please ask on the mailinglist of your MPI library. If it only
happens with GROMACS be more specific about what your setup is (what
MPI library, what hardware, ...).
Also you could use the latest GROMACS 4.5.x. It has built in thread
support and doesn't need MPI as long as you only run on n cores within
one SMP node.
Roland
On Wed, Apr 27, 2011 at 2:13 PM, Hrachya Astsatryan <hr...@sci.am
<mailto:hr...@sci.am>> wrote:
Dear Mark Abraham & all,
We used another benchmarking systems, such as d.dppc on 4
processors, but we have the same problem (1 proc use about 100%,
the others 0%).
After for a while we receive the following error:
Working directory is /localuser/armen/d.dppc
Running on host wn1.ysu-cluster.grid.am
<http://wn1.ysu-cluster.grid.am>
Time is Fri Apr 22 13:55:47 AMST 2011
Directory is /localuser/armen/d.dppc
____START____
Start: Fri Apr 22 13:55:47 AMST 2011
p2_487: p4_error: Timeout in establishing connection to remote
process: 0
rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32
p2_487: (301.160156) net_send: could not write to fd=5, errno = 32
p0_32738: p4_error: net_recv read: probable EOF on socket: 1
p3_490: (301.160156) net_send: could not write to fd=6, errno = 104
p3_490: p4_error: net_send write: -1
p3_490: (305.167969) net_send: could not write to fd=5, errno = 32
p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32
p1_483: p4_error: net_recv read: probable EOF on socket: 1
rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32
p1_483: (311.171875) net_send: could not write to fd=5, errno = 32
Fri Apr 22 14:00:59 AMST 2011
End: Fri Apr 22 14:00:59 AMST 2011
____END____
We tried new version of Gromacs, but receive the same error.
Please, help us to overcome the problem.
With regards,
Hrach
On 4/22/11 1:41 PM, Mark Abraham wrote:
On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote:
Dear all,
I would like to inform you that I have installed the
gromacs4.0.7 package on the cluster (nodes of the cluster
are 8 core Intel, OS: RHEL4 Scientific Linux) with the
following steps:
yum install fftw3 fftw3-devel
./configure --prefix=/localuser/armen/gromacs --enable-mpi
Also I have downloaded gmxbench-3.0 package and try to run
d.villin to test it.
Unfortunately it wok fine until np is 1,2,3, if I use more
than 3 procs I receive low CPU balancing and the process
in hanging.
Could you, please, help me to overcome the problem?
Probably you have only four physical cores (hyperthreading is
not normally useful), or your MPI is configured to use only
four cores, or these benchmarks are too small to scale usefully.
Choosing to do a new installation of a GROMACS version that is
several years old is normally less productive than the latest
version.
Mark
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