Fatal error: Failed to lock: annealing.log. Already running simulation?

User discussions
1

GROMACS version: 2019.6
GROMACS modification: No
Hello everyone, I am a beginner with GROMACS, and here is the problem I met.
I want to run my check point file to continue my simulation, and there is the command I used:

srun gmx_mpi mdrun -s ./annealing.tpr -cpi ./annealing.cpt -deffnm annealing

I am sure that in my folder there are all files that I needed, and I didn’t delect any files:

-rw-r--r-- 1 u7501910 TRI112363    7288612 Mar 21 15:51 annealing.cpt
-rw-r--r-- 1 u7501910 TRI112363     419396 Mar 21 15:51 annealing.edr
-rw-r--r-- 1 u7501910 TRI112363     482645 Mar 20 14:56 annealing.log
-rw-r--r-- 1 u7501910 TRI112363       1465 Mar  7 17:54 annealing.mdp
-rw-r--r-- 1 u7501910 TRI112363    7288612 Mar 21 15:51 annealing_prev.cpt
-rw-r--r-- 1 u7501910 TRI112363    7438420 Mar  7 17:55 annealing.tpr
-rw-r--r-- 1 u7501910 TRI112363 1138969924 Mar 21 15:39 annealing.xtc
-rw-r--r-- 1 u7501910 TRI112363   20948472 Mar  7 17:53 compressed.gro
-rw-r--r-- 1 u7501910 TRI112363         93 Mar  7 17:55 gentpr.sh
-rw-r--r-- 1 u7501910 TRI112363    7883728 Mar 12 08:54 gmx.stderr14545553
-rw-r--r-- 1 u7501910 TRI112363    1118926 Mar 17 13:08 gmx.stderr14667908
-rw-r--r-- 1 u7501910 TRI112363          0 Mar  8 08:54 gmx.stdout14545553
-rw-r--r-- 1 u7501910 TRI112363      47488 Mar 17 13:00 gmx.stdout14667908
-rw-r--r-- 1 u7501910 TRI112363      11062 Mar  7 17:55 mdout.mdp
drwxr-xr-x 3 u7501910 TRI112363       4096 Mar  7 17:52 P10.ff
-rw-r--r-- 1 u7501910 TRI112363     147458 Mar  7 17:52 P10.top
-rw-r--r-- 1 u7501910 TRI112363        545 Mar 18 14:07 subgmx.sh

However, there was an error message after I executed the above-mentioned command:

Program:     gmx mdrun, version 2019.6
Source file: src/gromacs/fileio/checkpoint.cpp (line 2435)

Fatal error:
Failed to lock: annealing.log. Already running simulation?

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Although I do have annealing.log in my folder, the error message said Failed to lock: annealing.log..
Is there anyone that has met the same issue? I am here waiting for your kind help.

2

I got this error when I mistakenly run the same simulation in two different jobs in a HPC cluster, so that the jobs where talking over each other and writing to the same trajectory/log/edr/etc files. Are you sure you are not running the same simulation in different jobs?

3

Hello, obZehn,
Thank you for the reply. I am sure that I ran this simulation after the previous one, which was totally done, and at that time, there was no other GROMACS job. This might not be the reason why I was faced with error. Still thanks to your generous sharing of experience!