24小时热门版块排行榜

返回列表

当前只显示满足指定条件的回帖，点击这里查看本话题的所有回帖

jianchuanliu

金虫 (初入文坛)

应助: 1 (幼儿园)
金币: 2036.2
散金: 10
帖子: 49
在线: 48.6小时
虫号: 2924195
注册: 2014-01-10
专业: 化学动力学

[求助] NVT时出现here is no domain decomposition for 30 nodes 已有1人参与

急！！
Gromacs！ NVT时出现here is no domain decomposition for 30 nodes that is compatible with the given box and a minimum cell size of 5.01333 nm 错误如何解决啊，我的gro和mdp文件在附件里。
做的是碳纳米管加乙醇甲醇仿真。
谢谢大神的解答！

error.png

回复此楼

» 本帖附件资源列表

欢迎监督和反馈：小木虫仅提供交流平台，不对该内容负责。
本内容由用户自主发布，如果其内容涉及到知识产权问题，其责任在于用户本人，如对版权有异议，请联系邮箱：xiaomuchong@tal.com
附件 1 : all.gro

2015-07-20 17:25:43, 437.44 K

附件 2 : nvt.mdp

2015-07-20 17:38:16, 1.72 K

» 猜你喜欢

» 本主题相关商家推荐: (我也要在这里推广)

1楼 2015-07-20 17:27:31

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

jianchuanliu

金虫 (初入文坛)

应助: 1 (幼儿园)
金币: 2036.2
散金: 10
帖子: 49
在线: 48.6小时
虫号: 2924195
注册: 2014-01-10
专业: 化学动力学

引用回帖:

2楼: Originally posted by angjzy at 2015-07-21 00:14:38
就是你模拟的时候，nodes 数目30并不能被整除，查看一下mdrun生成的log file，里面有一行
The maximum allowed number of cells is : x a y b z c % a b c 是数字
你设置的30 个nodes数目是能整除a b c就可以

log文件里你说的那行是
Initializing Domain Decomposition on 32 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 4.558 nm, LJ-14, atoms 742 1195
multi-body bonded interactions: 4.549 nm, Angle, atoms 742 1176
Minimum cell size due to bonded interactions: 5.013 nm
Guess for relative PME load: 0.06
Will use 30 particle-particle and 2 PME only nodes
This is a guess, check the performance at the end of the log file
Using 2 separate PME nodes, as guessed by mdrun
Optimizing the DD grid for 30 cells with a minimum initial size of 5.013 nm
The maximum allowed number of cells is: X 0 Y 0 Z 1

-------------------------------------------------------
Program mdrun, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/mdlib/domdec.c, line: 6913

Fatal error:
There is no domain decomposition for 30 nodes that is compatible with the given box and a minimum cell size of 5.01333 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"What's Your Definition Of Dirty ?" (G. Michael)