标题: 求助：跑md测量PMF跑了一会报错 [打印本页] 作者Author: wanzongliang 时间: 2023-11-15 09:25 标题: 求助：跑md测量PMF跑了一会报错 请教各位老师，我在跑md测量PMF，用的是十个窗口并行跑，跑了十四万步之后出现问题，以下是报错内容
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
starting mdrun 'ions system'
500000000 steps, 500000.0 ps.
step 140000, will finish Sat Dec 16 15:35:32 2023
-------------------------------------------------------
Program: gmx mdrun, version 2022.6
Source file: src/gromacs/fileio/enxio.cpp (line 1121)
MPI rank: 8 (out of 10)
File input/output error:
Cannot write energy file; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 8 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
我通过报错检查了权限和磁盘空间均没有问题
09:01:42-yang7@login4:0$ ls -l
total 407
-rw-r--r-- 1 yang7 yang1 205376 Nov 14 17:53 awh.edr
-rw-r--r-- 1 yang7 yang1 24904 Nov 14 17:49 awh.log
-rw-r--r-- 1 yang7 yang1 0 Nov 14 17:39 awh_pullf.xvg
-rw-r--r-- 1 yang7 yang1 0 Nov 14 17:39 awh_pullx.xvg
lrwxr-xr-x 1 yang7 yang1 10 Nov 14 17:39 awh.tpr -> ../awh.tpr
-rw-r--r-- 1 yang7 yang1 186980 Nov 14 17:52 awh.xtc
09:01:46-yang7@login4:0$ ls
awh.edr awh.log awh_pullf.xvg awh_pullx.xvg awh.tpr awh.xtc
09:02:16-yang7@login4:0$ cd ..
09:02:18-yang7@login4:test2$ df -h
Filesystem Size Used Avail Use% Mounted on
/dev/md127p3 491G 90G 376G 20% /
tmpfs 32G 22M 32G 1% /dev/shm
/dev/md127p1 485M 38M 422M 9% /boot
df: `/dev/shm/FlexNetFs.79903': Transport endpoint is not connected
nodev_parastor_10.2.36.1-1_parastor
1.4P 620T 687T 48% /work1
nodev_parastor_10.2.86.1-1_parastor
1.5P 1004T 441T 70% /work2