From: Yu, Tao (tao.yu.1_at_und.edu)
Date: Fri Feb 28 2020 - 16:10:20 CST
Hi,
Our university just installed the Linux-x86_64-ibverbs-smp<https://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1546> (InfiniBand plus shared memory, no MPI needed) on our local cluster. There is no problem to run with a single core. But when I started to test running with 16 cores, the output indicated it was still using "1" cpu.
I tried to submit the job either with or without mpirun, but the result is the same. One 1 cpu was used.
Please give me some help here.
The script I was using was attached in below
#!/bin/bash
#####Number of nodes
#SBATCH --nodes=1
#SBATCH --partition=talon
#SBATCH --ntasks-per-node=16
#SBATCH --workdir=.
#####SBATCH -o slurm_run_%j_output.txt
#####SBATCH -e slurm_run_%j_error.txt
#SBATCH -s
#SBATCH --time=00:10:00
cd $SLURM_SUBMIT_DIR
srun -n $SLURM_NTASKS hostname | sort -u > $SLURM_JOB_ID.hosts
module load intel/mpi/64
mpirun /share/apps/namd/namd2.13/namd2 pc.conf > pc.log
**************************************************************************
The output where indicated "1" cpu was using:
ENERGY: 0 482.9967 1279.0637 1052.3094 78.2784 -71938.7727 7732.6846 0.0000 0.0000 11869.2504 -49444.1894 298.3828 -61313.4398 -49399.0775 298.3828 79.3838 81.2849 193787.4555 79.3838 81.2849
OPENING EXTENDED SYSTEM TRAJECTORY FILE
LDB: ============= START OF LOAD BALANCING ============== 2.06838
LDB: ============== END OF LOAD BALANCING =============== 2.06856
LDB: =============== DONE WITH MIGRATION ================ 2.06971
LDB: ============= START OF LOAD BALANCING ============== 8.05131
LDB: ============== END OF LOAD BALANCING =============== 8.05246
LDB: =============== DONE WITH MIGRATION ================ 8.05289
Info: Initial time: 1 CPUs 0.150798 s/step 0.872672 days/ns 236.934 MB memory
LDB: ============= START OF LOAD BALANCING ============== 9.55101
LDB: ============== END OF LOAD BALANCING =============== 9.55108
LDB: =============== DONE WITH MIGRATION ================ 9.5515
LDB: ============= START OF LOAD BALANCING ============== 15.3206
LDB: ============== END OF LOAD BALANCING =============== 15.3217
LDB: =============== DONE WITH MIGRATION ================ 15.3221
Info: Initial time: 1 CPUs 0.144713 s/step 0.837461 days/ns 237.516 MB memory
LDB: ============= START OF LOAD BALANCING ============== 22.4754
LDB: ============== END OF LOAD BALANCING =============== 22.4766
LDB: =============== DONE WITH MIGRATION ================ 22.477
Info: Initial time: 1 CPUs 0.143573 s/step 0.830862 days/ns 237.516 MB memory
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