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On 4/28/2011 4:44 AM, Hrachya Astsatryan wrote:
<blockquote cite="mid:4DB863FD.2080201@sci.am" type="cite">
<meta content="text/html; charset=ISO-8859-1"
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Dear Roland,<br>
<br>
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).<br>
I can run simple MPI examples, so I guess the problem on the
implementation of the Gromacs.<br>
</blockquote>
<br>
I agree with Roland that the problem is likely to be in the
configuration and function of the MPI library. RHEL4, being at least
5 years old, is probably using some ancient MPI library version that
is not up to the job. This is frequently-occurring problem. Roland
asked about your MPI library... if you want free help, you'll do
yourself favours by providing answers to the questions of people who
are offering help :-)<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:4DB863FD.2080201@sci.am" type="cite"> On
4/27/11 11:29 PM, Roland Schulz wrote:
<blockquote
cite="mid:BANLkTimebqT1KTTkYjd=oGW90zE5SiMFMQ@mail.gmail.com"
type="cite">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, ...).
<div> <br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Roland<br>
<br>
<div class="gmail_quote"> On Wed, Apr 27, 2011 at 2:13 PM,
Hrachya Astsatryan <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:hrach@sci.am">hrach@sci.am</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;"> Dear Mark Abraham & all,<br>
<br>
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%).<br>
After for a while we receive the following error:<br>
<br>
Working directory is /localuser/armen/d.dppc<br>
Running on host <a moz-do-not-send="true"
href="http://wn1.ysu-cluster.grid.am" target="_blank">wn1.ysu-cluster.grid.am</a><br>
Time is Fri Apr 22 13:55:47 AMST 2011<br>
Directory is /localuser/armen/d.dppc<br>
____START____<br>
Start: Fri Apr 22 13:55:47 AMST 2011<br>
p2_487: p4_error: Timeout in establishing connection to
remote process: 0<br>
rm_l_2_500: (301.160156) net_send: could not write to
fd=5, errno = 32<br>
p2_487: (301.160156) net_send: could not write to fd=5,
errno = 32<br>
p0_32738: p4_error: net_recv read: probable EOF on
socket: 1<br>
p3_490: (301.160156) net_send: could not write to fd=6,
errno = 104<br>
p3_490: p4_error: net_send write: -1<br>
p3_490: (305.167969) net_send: could not write to fd=5,
errno = 32<br>
p0_32738: (305.371094) net_send: could not write to fd=4,
errno = 32<br>
p1_483: p4_error: net_recv read: probable EOF on socket:
1<br>
rm_l_1_499: (305.167969) net_send: could not write to
fd=5, errno = 32<br>
p1_483: (311.171875) net_send: could not write to fd=5,
errno = 32<br>
Fri Apr 22 14:00:59 AMST 2011<br>
End: Fri Apr 22 14:00:59 AMST 2011<br>
____END____<br>
<br>
We tried new version of Gromacs, but receive the same
error.<br>
Please, help us to overcome the problem.<br>
<br>
<br>
With regards,<br>
Hrach
<div>
<div class="h5"><br>
<br>
On 4/22/11 1:41 PM, Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;"> On 4/22/2011 5:40 PM,
Hrachya Astsatryan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;"> Dear all,<br>
<br>
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:<br>
<br>
yum install fftw3 fftw3-devel<br>
./configure --prefix=/localuser/armen/gromacs
--enable-mpi<br>
<br>
Also I have downloaded gmxbench-3.0 package and
try to run d.villin to test it.<br>
<br>
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.<br>
<br>
Could you, please, help me to overcome the
problem?<br>
</blockquote>
<br>
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.<br>
<br>
Choosing to do a new installation of a GROMACS
version that is several years old is normally less
productive than the latest version.<br>
<br>
Mark<br>
<br>
<br>
<br>
</blockquote>
<br>
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