huifang liu wrote:
Hello, everybody,
I recently installed FFTW-3.0.1, mpich-1.2.7 and Gromacs 3.3.3 on my
workstation with two 8-cords CPUs. I think i installed them correctly,
beause it runs normally with other parellel MD software. It also went
nomorally when i run mdrun command in gromacs with 4 nodes. The problem
is it doesn't run with when it is up to 8 nodes. In fact, i only change
the '-np 4' to '-np 8' in both grompp and mdrun commmand. When i typed
the 'top' command, it shows there are only two node are running. And
after a little while, it stopped run with the follow error:
p7_19858: p4_error: Timeout in establishing connection to remote process: 0
p5_19808: p4_error: Timeout in establishing connection to remote process: 0
p6_19832: p4_error: Timeout in establishing connection to remote process: 0
p0_19710: (324.359375) net_recv failed for fd = 9
p0_19710: p4_error: net_recv read, errno = : 104
In addition, it runs very well, when i use '-np 5'
So how is your MPI environment configured?
Mark
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