CPU load much greater than number of CPU cores #4

New issue

Open

opened 2025-10-14 17:42:52 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:42:52 -06:00

Owner

Originally created by @prehensilecode on 11/29/2021

We are running VinaLC 1.3.0 on a cluster. Each node of the cluster has 48 CPU cores (without hyperthreading).

Normally, MPI programs which run 48 ranks per node lead to a CPU load value of about 48 on a node. However, VinaLC shows loads of 376 and higher.

Here is output from sinfo on our cluster showing fully occupied nodes running other programs (load about 48) and nodes running VinaLC (load about 380). Also listed are idle nodes (load about 0).

NODELIST      NODES PART       STATE CPUS   MEMORY FREE_MEM    S:C:T WEIGHT AVAIL_FE CPU_LOAD REASON
node008           1 def*   allocated   48   192000   170670   2:24:1      1   (null)    48.11 none
node009           1 def*   allocated   48   192000   160213   2:24:1      1   (null)    48.53 none
node010           1 def*   allocated   48   192000   170534   2:24:1      1   (null)    48.05 none
node011           1 def*   allocated   48   192000   157785   2:24:1      1   (null)    48.20 none
node012           1 def*   allocated   48   192000   158713   2:24:1      1   (null)    48.31 none
node013           1 def*   allocated   48   192000   171179   2:24:1      1   (null)   383.06 none
node014           1 def*   allocated   48   192000   171062   2:24:1      1   (null)   376.39 none
node015           1 def*   allocated   48   192000   164768   2:24:1      1   (null)   382.84 none
node016           1 def*   allocated   48   192000   127381   2:24:1      1   (null)   375.93 none
node017           1 def*   allocated   48   192000   176273   2:24:1      1   (null)   383.30 none
node018           1 def*        idle   48   192000   182161   2:24:1      1   (null)     0.00 none
node019           1 def*        idle   48   192000   183423   2:24:1      1   (null)     0.02 none
node020           1 def*        idle   48   192000   183192   2:24:1      1   (null)     0.00 none
node021           1 def*        idle   48   192000   181539   2:24:1      1   (null)     0.01 none

The VinaLC jobs were run with sbatch, using OpenMPI with Slurm integration:

#SBATCH --nodes=2
#SBATCH --ntasks-per-node=48
#SBATCH --cpus-per-task=1
...
mpirun vinalc --recList recList.txt --ligList ligList.txt --geoList geoList.txt

*Originally created by @prehensilecode on 11/29/2021* We are running VinaLC 1.3.0 on a cluster. Each node of the cluster has 48 CPU cores (without hyperthreading). Normally, MPI programs which run 48 ranks per node lead to a CPU load value of about 48 on a node. However, VinaLC shows loads of 376 and higher. Here is output from `sinfo` on our cluster showing fully occupied nodes running other programs (load about 48) and nodes running VinaLC (load about 380). Also listed are idle nodes (load about 0). ``` NODELIST NODES PART STATE CPUS MEMORY FREE_MEM S:C:T WEIGHT AVAIL_FE CPU_LOAD REASON node008 1 def* allocated 48 192000 170670 2:24:1 1 (null) 48.11 none node009 1 def* allocated 48 192000 160213 2:24:1 1 (null) 48.53 none node010 1 def* allocated 48 192000 170534 2:24:1 1 (null) 48.05 none node011 1 def* allocated 48 192000 157785 2:24:1 1 (null) 48.20 none node012 1 def* allocated 48 192000 158713 2:24:1 1 (null) 48.31 none node013 1 def* allocated 48 192000 171179 2:24:1 1 (null) 383.06 none node014 1 def* allocated 48 192000 171062 2:24:1 1 (null) 376.39 none node015 1 def* allocated 48 192000 164768 2:24:1 1 (null) 382.84 none node016 1 def* allocated 48 192000 127381 2:24:1 1 (null) 375.93 none node017 1 def* allocated 48 192000 176273 2:24:1 1 (null) 383.30 none node018 1 def* idle 48 192000 182161 2:24:1 1 (null) 0.00 none node019 1 def* idle 48 192000 183423 2:24:1 1 (null) 0.02 none node020 1 def* idle 48 192000 183192 2:24:1 1 (null) 0.00 none node021 1 def* idle 48 192000 181539 2:24:1 1 (null) 0.01 none ``` The VinaLC jobs were run with `sbatch`, using OpenMPI with Slurm integration: ``` #SBATCH --nodes=2 #SBATCH --ntasks-per-node=48 #SBATCH --cpus-per-task=1 ... mpirun vinalc --recList recList.txt --ligList ligList.txt --geoList geoList.txt ```

No labels

No milestone

No project

No assignees

1 participant

Notifications

Due date

The due date is invalid or out of range. Please use the format "yyyy-mm-dd".

No due date set.

Dependencies

No dependencies set.

Reference: github/VinaLC#4

No description provided.

Rows
Columns