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Performance Discrepancy between Slurm and Direct mpirun for VASP Jobs.

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Performance Discrepancy between Slurm and Direct mpirun for VASP Jobs.

Posted: Fri May 24, 2024 1:49 pm
by hszhao.cn@gmail.com
Dear VASP Team and Users,

I am experiencing a significant performance discrepancy when running the same VASP job through the Slurm scheduler compared to running it directly with mpirun. I am hoping for some insights or advice on how to resolve this issue.

System, slurm and vasp information:

Code: Select all

$ inxi -CMmS
System:
  Host: x13dai-t Kernel: 6.5.0-18-generic arch: x86_64 bits: 64 Desktop: GNOME
    v: 42.9 Distro: Ubuntu 22.04.4 LTS (Jammy Jellyfish)
Machine:
  Type: Unknown System: Supermicro product: Super Server v: 0123456789
    serial: 0123456789
  Mobo: Supermicro model: X13DAI-T v: 1.01 serial: WM23AS002622
    UEFI: American Megatrends LLC. v: 2.1 date: 12/14/2023
Memory:
  System RAM: total: 512 GiB available: 503.52 GiB used: 15.5 GiB (3.1%)
  Array-1: capacity: 6 TiB note: check slots: 16 modules: 16
    EC: Single-bit ECC
  Device-1: P1-DIMMA1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-2: P1-DIMMB1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-3: P1-DIMMC1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-4: P1-DIMMD1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-5: P1-DIMME1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-6: P1-DIMMF1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-7: P1-DIMMG1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-8: P1-DIMMH1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-9: P2-DIMMA1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-10: P2-DIMMB1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-11: P2-DIMMC1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-12: P2-DIMMD1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-13: P2-DIMME1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-14: P2-DIMMF1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-15: P2-DIMMG1 type: DDR5 size: 32 GiB speed: 4800 MT/s
  Device-16: P2-DIMMH1 type: DDR5 size: 32 GiB speed: 4800 MT/s
CPU:
  Info: 2x 48-core model: Intel Xeon Platinum 8488C bits: 64 type: MT MCP SMP
    cache: L2: 2x 96 MiB (192 MiB)
  Speed (MHz): avg: 876 min/max: 800/3800 cores: 1: 800 2: 800 3: 800 4: 800
    5: 800 6: 800 7: 800 8: 800 9: 800 10: 800 11: 800 12: 800 13: 800 14: 800
    15: 800 16: 800 17: 800 18: 800 19: 800 20: 800 21: 800 22: 800 23: 800
    24: 795 25: 800 26: 800 27: 800 28: 800 29: 800 30: 800 31: 800 32: 800
    33: 800 34: 800 35: 800 36: 800 37: 887 38: 800 39: 800 40: 3100 41: 800
    42: 800 43: 2222 44: 800 45: 2500 46: 800 47: 800 48: 800 49: 800 50: 800
    51: 800 52: 800 53: 800 54: 800 55: 800 56: 800 57: 800 58: 800 59: 800
    60: 800 61: 800 62: 800 63: 800 64: 800 65: 800 66: 800 67: 800 68: 800
    69: 800 70: 800 71: 800 72: 800 73: 800 74: 800 75: 800 76: 800 77: 800
    78: 800 79: 800 80: 800 81: 800 82: 800 83: 800 84: 800 85: 800 86: 800
    87: 800 88: 800 89: 800 90: 800 91: 800 92: 800 93: 800 94: 800 95: 800
    96: 800 97: 800 98: 800 99: 800 100: 800 101: 800 102: 800 103: 800
    104: 800 105: 800 106: 800 107: 800 108: 800 109: 800 110: 800 111: 800
    112: 800 113: 800 114: 800 115: 800 116: 2400 117: 800 118: 800 119: 800
    120: 800 121: 800 122: 800 123: 800 124: 800 125: 800 126: 800 127: 800
    128: 800 129: 800 130: 800 131: 3800 132: 2400 133: 1200 134: 800 135: 800
    136: 800 137: 800 138: 800 139: 800 140: 800 141: 800 142: 2500 143: 801
    144: 800 145: 800 146: 800 147: 800 148: 800 149: 800 150: 800 151: 800
    152: 800 153: 800 154: 800 155: 800 156: 800 157: 800 158: 800 159: 800
    160: 800 161: 800 162: 800 163: 800 164: 800 165: 800 166: 800 167: 800
    168: 800 169: 800 170: 800 171: 800 172: 800 173: 800 174: 800 175: 1021
    176: 800 177: 800 178: 800 179: 800 180: 800 181: 800 182: 1500 183: 800
    184: 800 185: 800 186: 800 187: 800 188: 800 189: 800 190: 800 191: 800
    192: 800
Slurm Version: 21.08.5
VASP version: 6.4.3

Job Submission Script:

Code: Select all

#!/usr/bin/env bash
#SBATCH -N 1
#SBATCH -D .
#SBATCH --output=%j.out
#SBATCH --error=%j.err
##SBATCH --time=2-00:00:00
#SBATCH --ntasks=36
#SBATCH --mem=64G

echo '#######################################################'
echo "date                    = $(date)" 
echo "hostname                = $(hostname -s)"
echo "pwd                     = $(pwd)"
echo "sbatch                  = $(which sbatch | xargs realpath -e)"
echo ""
echo "WORK_DIR                = $WORK_DIR"
echo "SLURM_SUBMIT_DIR        = $SLURM_SUBMIT_DIR"
echo "SLURM_JOB_NUM_NODES     = $SLURM_JOB_NUM_NODES"
echo "SLURM_NTASKS            = $SLURM_NTASKS"
echo "SLURM_NTASKS_PER_NODE   = $SLURM_NTASKS_PER_NODE"
echo "SLURM_CPUS_PER_TASK     = $SLURM_CPUS_PER_TASK"
echo "SLURM_JOBID             = $SLURM_JOBID"
echo "SLURM_JOB_NODELIST      = $SLURM_JOB_NODELIST"
echo "SLURM_NNODES            = $SLURM_NNODES"
echo "SLURMTMPDIR             = $SLURMTMPDIR"
echo '#######################################################'
echo ""

module purge > /dev/null 2>&1
module load vasp
ulimit -s unlimited
mpirun vasp_std
Performance Observation:

When running the job through Slurm:

Code: Select all

werner@x13dai-t:~/Public/hpc/servers/benchmark/Cr72_3x3x3K_350eV_10DAV$ grep LOOP OUTCAR 
      LOOP:  cpu time     14.4893: real time     14.5049
      LOOP:  cpu time     14.3538: real time     14.3621
      LOOP:  cpu time     14.3870: real time     14.3568
      LOOP:  cpu time     15.9722: real time     15.9018
      LOOP:  cpu time     16.4527: real time     16.4370
      LOOP:  cpu time     16.7918: real time     16.7781
      LOOP:  cpu time     16.9797: real time     16.9961
      LOOP:  cpu time     15.9762: real time     16.0124
      LOOP:  cpu time     16.8835: real time     16.9008
      LOOP:  cpu time     15.2828: real time     15.2921
     LOOP+:  cpu time    176.0917: real time    176.0755
When running the job directly with mpirun:

Code: Select all

werner@x13dai-t:~/Public/hpc/servers/benchmark/Cr72_3x3x3K_350eV_10DAV$ module load vasp 
werner@x13dai-t:~/Public/hpc/servers/benchmark/Cr72_3x3x3K_350eV_10DAV$ module list 

Currently Loaded Modules:
  1) lmod              3) hdf5/1.14.3-oneapi.2023.2.0                5) dftd4/main-oneapi.2023.2.0
  2) oneapi/2023.2.0   4) wannier90/develop-serial-oneapi.2023.2.0   6) vasp/6.4.3-oneapi-oneapi.2023.2.0

werner@x13dai-t:~/Public/hpc/servers/benchmark/Cr72_3x3x3K_350eV_10DAV$ mpirun -n 36 vasp_std
werner@x13dai-t:~/Public/hpc/servers/benchmark/Cr72_3x3x3K_350eV_10DAV$ grep LOOP OUTCAR 
      LOOP:  cpu time      9.0072: real time      9.0074
      LOOP:  cpu time      9.0515: real time      9.0524
      LOOP:  cpu time      9.1896: real time      9.1907
      LOOP:  cpu time     10.1467: real time     10.1479
      LOOP:  cpu time     10.2691: real time     10.2705
      LOOP:  cpu time     10.4330: real time     10.4340
      LOOP:  cpu time     10.9049: real time     10.9055
      LOOP:  cpu time      9.9718: real time      9.9714
      LOOP:  cpu time     10.4511: real time     10.4470
      LOOP:  cpu time      9.4621: real time      9.4584
     LOOP+:  cpu time    110.0790: real time    110.0739
Could you provide any insights or suggestions on what might be causing this performance issue? Are there any specific configurations or settings in Slurm that I should check or adjust to align the performance more closely with the direct mpirun execution?

The attachment is the test example used above.

Thank you for your time and assistance.

Best regards,
Zhao

Re: Performance Discrepancy between Slurm and Direct mpirun for VASP Jobs.

Posted: Fri May 24, 2024 1:52 pm
by hszhao.cn@gmail.com
See here for the related discussion.

Re: Performance Discrepancy between Slurm and Direct mpirun for VASP Jobs.

Posted: Sat May 25, 2024 1:51 am
by hszhao.cn@gmail.com
Finally, I found that the cause of the problem was that hyper-threading was enabled by default in the BIOS. If I disable
hyper-threading, I observed that the computational efficiency is consistent between using slurm and using mpirun directly. Therefore, it appears that hyper-threading should not be enabled in the BIOS when using slurm.

Regards,
Zhao

Re: Performance Discrepancy between Slurm and Direct mpirun for VASP Jobs.

Posted: Sat May 25, 2024 2:04 am
by hszhao.cn@gmail.com
Regarding the reason, I think the description here is reasonable:

It is recommended to disable processor hyper-threading. In applications that are compute-intensive rather than I/O-intensive, enabling HyperThreading is likely to decrease the overall performance of the server. Intuitively, the physical memory available per core is reduced after hyper-threading is enabled.

Regards,
Zhao

Re: Performance Discrepancy between Slurm and Direct mpirun for VASP Jobs.

Posted: Mon May 27, 2024 12:29 pm
by henrique_miranda
Thank you for the question, and thanks for following up with the answer as well (this can be helpful for other users)!
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