[gmx-users] Help: Gromacs Installation
Mark.Abraham at anu.edu.au
Thu Apr 28 01:37:53 CEST 2011
On 4/28/2011 4:44 AM, Hrachya Astsatryan wrote:
> 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.
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
> 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.
>> On Wed, Apr 27, 2011 at 2:13 PM, Hrachya Astsatryan <hrach at sci.am
>> <mailto:hrach at 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
>> Time is Fri Apr 22 13:55:47 AMST 2011
>> Directory is /localuser/armen/d.dppc
>> 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
>> We tried new version of Gromacs, but receive the same error.
>> Please, help us to overcome the problem.
>> With regards,
>> 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.
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