hongyibaixue 发表于 2015-1-31 15:58:25

在超算上运行并行版Gromacs出现如下提示

* Hwloc has encountered what looks like an error from the operating system.
*
* object intersection without inclusion!
* Error occurred in topology.c line 594
*
* Please report this error message to the hwloc user's mailing list,
* along with the output from the hwloc-gather-topology.sh script.这是第一个提示,也就是说openmpi可能有问题,对吗?但是超算上的MPI是主机早都编译好的,我前段时间用超算做并行模拟的时候,完全没问题啊。为什么现在提示这个错误????
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starting mdrun 'Protein in water'
20000000 steps,40000.0 ps.
step 0

step   30: timed with pme grid 100 100 100, coulomb cutoff 1.000: 8465.0 M-cycles

step   50: timed with pme grid 84 84 84, coulomb cutoff 1.170: 8763.5 M-cycles

step   70: timed with pme grid 72 72 72, coulomb cutoff 1.365: 7046.3 M-cycles

step   90: timed with pme grid 64 64 64, coulomb cutoff 1.536: 7913.3 M-cycles

step110: timed with pme grid 80 80 80, coulomb cutoff 1.229: 8378.4 M-cycles

step130: timed with pme grid 72 72 72, coulomb cutoff 1.365: 7962.1 M-cycles

            optimal pme grid 72 72 72, coulomb cutoff 1.365
imb F 81% pme/F 2.53 step 200, will finish Fri Jun5 14:31:37 2015
imb F 80% pme/F 2.44 step 300, will finish Mon Jun1 22:43:18 2015
imb F 88% pme/F 2.72 step 400, will finish Sun May 31 03:16:06 2015 第二个问题是,前几天使用超算做并行的MD模拟,三天就可以运算完成。但这几天   模拟 同样的文件,却需要5个月才能结束?这是怎么回事?哪里出问题了?

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