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本帖最后由 jimulation 于 2020-12-31 20:41 编辑
在虚拟机里用gmx2019.6生成了tpr文件，放到广州超算平台上用gpu版的gmx2019.6跑，单结点配置是4块V100加28核心CPU。尝试了多种提交指令，遇到了几种错误如下：
1.yhrun -N 1 -n 4 ...... -ntomp 6 -gpu_id 0123 -nb gpu -pme gpu -npme 1 -bonded gpu
报错：Inconsistency in user input:Bonded interactions on the GPU were required, but not supported for these simulation settings. Change your settings, or do not require using GPUs.
2.yhrun -N 1 -n 4 ...... -ntomp 6 -gpu_id 0123 -nb gpu -pme gpu -npme 1 -bonded cpu
报错：Step 100: The total potential energy is nan, which is not finite. The LJ and electrostatic contributions to the energy are 0 and 0, respectively. A non-finite potential energy can be caused by overlapping interactions in bonded interactions or very large or Nan coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology.
3.yhrun -N 1 -n 4 ...... -ntomp 6 -gpu_id 0123
报错：80 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.
4.yhrun -N 1 -n 2 ...... -ntomp 6 -gpu_id 0123
报错：step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate.
以上，问题1：为什么采用nb/npme/bonded选项，会出现不同的错误？其中有什么内部机制么？
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将-n选项改为1，仅使用一个rank，则可以正常运行，如5~7；但指定了-bonded gpu又会出错，如8：
5.yhrun -N 1 -n 1 ...... -ntomp 16 -gpu_id 0123（63ns/day)log文件提示：1 GPU selected for this run. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node: PP:0,PME:0. PP tasks will do (non-perturbed) short-ranged interactions on the GPU, PME tasks will do all aspects on the GPU）
6.yhrun -N 1 -n 1 ...... -ntomp 24 -gpu_id 0123（66ns/day，log文件提示同5）
7.yhrun -N 1 -n 1 ...... -ntomp 28 -gpu_id 0123（61ns/day，log文件提示同5）
8.yhrun -N 1 -n 1 ...... -ntomp 24 -gpu_id 0123 -nb gpu -pme gpu -npme 1 -bonded gpu（报错，同1）
以上，问题2：为何改用一个rank就能正常运行，但-bonded还是不能手动指定？
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还有一个问题3：采用纯CPU计算时，-n或-ntmpi设置rank数，-ntomp设置每个rank的线程数(http://bbs.keinsci.com/thread-13861-1-1.html)，二者乘积是总核数。那么采用GPU/CPU混合计算时，gpu是如何被划分的？比如只有一块GPU，-ntmpi设为4，-ntomp设为6，若1个pme rank在GPU上计算，其线程数指什么？剩余3个rank在CPU上计算，则CPU一共是24核还是18核参与运算？
问题比较多，求解答，非常感谢！
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发表于 Post on 2020-12-31 20:41:20
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楼主 Author
现在不行了