[gmx-users] Help: Gromacs Installation

[Hrachya Astsatryan]

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 <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
>     <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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