[gmx-users] Help: Gromacs Installation
hrach at sci.am
Wed Apr 27 20:13:30 CEST 2011
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.
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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