[gmx-users] problem with mdrun in parallel

[huifang liu]

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'

Hope for your help. Thanks

Huifang


-- 
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University

138 Yi Xue Yuan Rd.          Tel: (86-21)54237419 (O)
Shanghai, China, 200032     Cell phone: +86-13764669357
E-mail: huifangliu1985 at gmail.com Fax: (86-21)54237264
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