我用自己的笔记本电脑用ubuntu 15.10 ssh到一个集群。我需要执行一个命令,这个命令将生成大约46 GB的数据。我尝试使用sbatch
命令提交作业脚本(SLURM),但是墙上时间(一周)确实用完了,作业终止了。我使用nohup...>&output&
,但工作在9个小时内完成。
这是输出文件:
nohup: ignoring input
GROMACS: gmx mdrun, VERSION 5.0.4
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, VERSION 5.0.4
Executable: /sw/easybuild/software/MPI/intel/2016.1.150-GCC-4.9.3-2.25/impi/5.1.2.150/GROMACS/5.0.4-mt/bin/gmx
Library dir: /sw/easybuild/software/MPI/intel/2016.1.150-GCC-4.9.3-2.25/impi/5.1.2.150/GROMACS/5.0.4-mt/share/gromacs/top
Command line:
gmx mdrun -deffnm md_0_1
Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
Changing nstlist from 10 to 20, rlist from 1 to 1.03
Will use 32 particle-particle and 8 PME only ranks
This is a guess, check the performance at the end of the log file
Using 40 MPI threads
Using 1 OpenMP thread per tMPI thread
WARNING: This run will generate roughly 42640 Mb of data
starting mdrun 'Protein in water'
500000000 steps, 1000000.0 ps.
NOTE: Turning on dynamic load balancing
Received the TERM signal, stopping at the next NS step
Average load imbalance: 3.0 %
Part of the total run time spent waiting due to load imbalance: 1.9 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 %
Average PME mesh/force load: 0.866
Part of the total run time spent waiting due to PP/PME imbalance: 2.0 %
Core t (s) Wall t (s) (%)
Time: 1255999.549 31470.936 3991.0
8h44:30
(ns/day) (hour/ns)
Performance: 119.401 0.201
gcq#177: "Whatever Happened to Pong ?" (F. Black)
有人可以解释一下吗? 如果服务器的最长挂壁时间为一周,那么运行该作业的任何想法都会出现吗?
/ Elsaid