标题: 双分子层nvt平衡如何修改P-LINUX的最大距离 [打印本页] 作者Author: lhh2020 时间: 2021-10-28 20:39 标题: 双分子层nvt平衡如何修改P-LINUX的最大距离 想请教一下各位老师，搭建的双分子层在进行nvt平衡的时候，出现了如下这样的报错，按照这个提示，我是不是应该修改P-LINUX的最大距离就可以，如果是的话这个要通过什么方式来修改
Initializing Domain Decomposition OI 64 ranks
Dynamic load balancing: auto
Minimum cell size due to atom displacement: 0.373 nm Initial maximum distances in bonded interactions:
two-body bonded interactions: 1.140 nm, Exclusion, atoms 10999 11005 multi-body bonded interactions: 1.515 nm, G96Angler atomз 6137 6139 Minimum cell size due to bonded interactions: 1.667 nm
Maximum distance for 5 constraints, at 120 deq. anqles, al1-trans: 2.626 nm Estimated maximum distance required for P-LINCS: 2.626 nm
This distance wi11 limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/O.8 (option -dds) = 1 25
Optimizing the DD grid for 64 cells with a minimum initial size of 3.282 nm The maximum allowed number of cel1s is: X 4 Y 4 Z 2
Program: gmx mdrun, version 2020.6
Source file: src/gromacs/domdec/domdec.cpp (line 2277)
MPI rank: 0 (out of 64)
Fatal error:
There is no domain decomposition for 64 ranks that is compatible with the given box and a minimum cel1 size o£ 3.28188 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
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 作者Author: sobereva 时间: 2021-10-29 06:31
mdrun加上-ntmpi 1不用域分解
哪来的P-LINUX，明明是P-LINCS 作者Author: lhh2020 时间: 2021-10-29 15:50
老师，我mdrun加上-ntmpi 1运行后，出现了这样的提示，这个有什么方法解决吗
Program: gmx mdrun, version 2020.6
Source file: src/gromacs/taskassignment/resourcedivision.cpp (1ine 701)
MPI rank: 14(out of 64)
fatal error:
Settinq the number of thread-MPI ranks is only supported with thread-MPI and GROMACS was compiled without thread-MPI
For more information and tips for troubleshootinq, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors
application ca11ed MPI Abort (MPI COMM W0RLD، 1)- process 14 application ca11ed MPI Abort (MPI COMM W0RID, 1) - process 8
srun: Job step aborted: Waitinq up to 62 seconds for iob step to finish
slurmstepd: error: *** STEP 1314310.0 ON eb0813 CANCELLED AT 2021-10-29T15:36:43 **↓ srun: error: eb0813: tasks 0-63: Ki11ed