长时间工作的nohup命令

时间:2016-02-17 14:50:05

标签: nohup sbatch

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       
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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

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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

0 个答案:

没有答案