Plugging "Epoll ADD(4) on fd 1 failed" into Google suggests this is a warning from OpenMPI that relates to its Slurm integration. It is not an AMBER issue. My parsing of the Google output got this nugget:
"When next you run, I would just add "-mca plm rsh" to your cmd line. You don't need to rebuild OMPI to avoid issues with the slurm integration. This will still allow OMPI to read the slurm allocation so it knows which nodes to use, but won't use slurm to launch the job.
If it is a slurm PMI issue, this should resolve it." from:
https://users.open-mpi.narkive.com/nVycQkzv/ompi-users-deadly-warning-epoll-add-4-on-fd-2-failed
-tec3
________________________________________
From: angad sharma <angadsharma54.gmail.com>
Sent: Monday, December 7, 2020 9:44:37 AM
To: amber.ambermd.org
Subject: [AMBER] error after simulation
I am running a simulation for DNA. I have run it, till equilibration. Ater
simulation process done i get e.65187.master-node says the following:
[warn] Epoll ADD(4) on fd 1 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
[warn] Epoll ADD(4) on fd 1 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
[warn] Epoll ADD(4) on fd 1 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
I am not able to understand this because all files which i am getting seem
correct.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 07 2020 - 13:00:05 PST
