# Keywords in command line for getting good performance in gromacs **URL:** \ **Category:** User discussions\ **Tags:** mdrun, mdrun-performance, mdrun-parallelization\ **Created:** [October 27, 2023, 11:24am UTC](https://gromacs.bioexcel.eu/t/keywords-in-command-line-for-getting-good-performance-in-gromacs/7486 "2023-10-27T11:24:06Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![SarthakTrivedi](https://avatars.discourse-cdn.com/v4/letter/s/58956e/32.png) [@SarthakTrivedi](https://gromacs.bioexcel.eu/u/SarthakTrivedi)\ **Post date:** [October 27, 2023, 11:24am UTC](https://gromacs.bioexcel.eu/t/keywords-in-command-line-for-getting-good-performance-in-gromacs/7486/1 "2023-10-27T11:24:06Z")
I am trying to run gromacs 2023.2 gpu on HPC. I am getting super slow performance in HPC. I run the calculation for the test purpose on 8 cores for 10 mins only. **The projected steps of calculation is about 15,000 in 10 minuites** , unfortunately couldn’t get performance upto mark. The script file and the last comments in output file are as shown below. **SLURM SCRIPT FILE** **#!/bin/bash** **#SBATCH -N 1** **#SBATCH --ntasks-per-node=8** **#SBATCH --gres=gpu:A100-SXM4:1** **#SBATCH --partition=testp** **#SBATCH --time=00:10:00** **#SBATCH --error=error\_test.%J.err** **#SBATCH --output=output\_test.%J.out** **echo “Starting at `date`”** **echo “Running on hosts: $SLURM\_NODELIST”** **echo “Running on $SLURM\_NNODES nodes.”** **echo “Running $SLURM\_NTASKS tasks.”** **echo “Job id is $SLURM\_JOBID”** **echo “Job submission directory is : $SLURM\_SUBMIT\_DIR”** **cd $SLURM\_SUBMIT\_DIR** **source /opt/hpcx-v2.9.0-gcc-MLNX\_OFED\_LINUX-5.4-1.0.3.0-ubuntu20.04-x86\_64/env.sh** **source /nlsasfs/home/groupiiiv/sarthakt/software\_cdac/gromacs-2023.2/install/bin/GMXRC** **mpirun -mca pml ucx -x UCX\_NET\_DEVICES -np 8 /nlsasfs/home/groupiiiv/sarthakt/software\_cdac/gromacs-2023.2/build/bin/gmx\_mpi mdrun -ntomp 4 --deffnm md\_0\_10 -cpi md\_0\_10.cpt -noappend** **OUTPUT FILE** **Started mdrun on rank 0 Thu Oct 26 11:14:28 2023** \*\* Step Time\*\* \*\* 0 0.00000\*\* \*\* Energies (kJ/mol)\*\* \*\* Bond U-B Proper Dih. Improper Dih. CMAP Dih.\*\* \*\* 5.17908e+03 1.42265e+04 1.66364e+04 8.73544e+02 -8.25547e+02\*\* \*\* LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.\*\* \*\* 5.15878e+03 7.27696e+04 8.95562e+04 -1.15064e+06 3.48482e+03\*\* \*\* Potential Kinetic En. Total Energy Conserved En. Temperature\*\* \*\* -9.43579e+05 1.87862e+05 -7.55718e+05 -7.55674e+05 3.01866e+02\*\* \*\* Pressure (bar) Constr. rmsd\*\* \*\* 2.79474e+02 2.98607e-06\*\* **DD step 99 load imb.: force 5.3%** **step 600: timed with pme grid 56 56 56, coulomb cutoff 1.200: 65983.2 M-cycles** **step 800: timed with pme grid 48 48 48, coulomb cutoff 1.400: 58358.5 M-cycles** **step 1000: timed with pme grid 44 44 44, coulomb cutoff 1.527: 60890.5 M-cycles** **step 1200: timed with pme grid 40 40 40, coulomb cutoff 1.680: 60729.1 M-cycles** **step 1400: timed with pme grid 36 36 36, coulomb cutoff 1.866: 58230.7 M-cycles** **step 1400: the maximum allowed grid scaling limits the PME load balancing to a coulomb cut-off of 1.866** **step 1600: timed with pme grid 36 36 36, coulomb cutoff 1.866: 60691.8 M-cycles** **step 1800: timed with pme grid 40 40 40, coulomb cutoff 1.680: 56804.9 M-cycles** **step 2000: timed with pme grid 42 42 42, coulomb cutoff 1.600: 61399.7 M-cycles** **Received the TERM signal, stopping within 100 steps** THANK ALL OF YOU IN ADVANCE. FEEL FREE TO ASK MORE DETAILS, SO THAT I CAN START MY CALCULATIONS HAPPILY. :D GROMACS version: GROMACS modification: Yes/No Here post your question **CAN ANYONE SUGGEST ME THE SOLUTIONS TO ENHANCE PERFORMANCE?** ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [October 27, 2023, 1:21pm UTC](https://gromacs.bioexcel.eu/t/keywords-in-command-line-for-getting-good-performance-in-gromacs/7486/2 "2023-10-27T13:21:46Z")
If you are running on 8 cores of a single node, there is no reason to use MPI. You are also specifying 8 MPI tasks with 4 OpenMP threads per task, so you’re probably just overloading the hardware. `gmx mdrun -nt 8` is sufficient if using 8 cores. Also note that `mdrun` is still doing some tuning of cutoffs so the performance report will not be accurate. You need to run for a larger number of steps and should use `-resethway` to reset the timing calculation to omit the tuning part. ---
**Author:** ![SarthakTrivedi](https://avatars.discourse-cdn.com/v4/letter/s/58956e/32.png) [@SarthakTrivedi](https://gromacs.bioexcel.eu/u/SarthakTrivedi)\ **Post date:** [October 27, 2023, 1:40pm UTC](https://gromacs.bioexcel.eu/t/keywords-in-command-line-for-getting-good-performance-in-gromacs/7486/3 "2023-10-27T13:40:58Z")
Thank you sir for your immediate response. I will try your advice and update you soon. Thank you so much again. Regards, Sarthak ---
**Author:** ![Yogesh](https://avatars.discourse-cdn.com/v4/letter/y/49beb7/32.png) [@Yogesh](https://gromacs.bioexcel.eu/u/Yogesh)\ **Post date:** [November 23, 2025, 1:35pm UTC](https://gromacs.bioexcel.eu/t/keywords-in-command-line-for-getting-good-performance-in-gromacs/7486/4 "2025-11-23T13:35:48Z")
Hi all, Related to the issue addressed above I am getting the term signal error regularly, for now I have tried my production runs with nohup gmx mdrun -s step7.tpr -v -deffnm step7 nohup mpirun -np 4 gmx\_mpi mdrun -s step7.tpr -deffnm step7\_1 -ntomp 16 -gpu\_id 0123 nohup mpirun -np 3 gmx\_mpi mdrun -s step7.tpr -deffnm step7\_1 -ntomp 12 -gpu\_id 012 Although we are in process of creating slurm Workload Management system, I expect trial run to complete smoothly. Can you please guide me with the right flags for simulation system with 214297 atoms. Also, Previously i never felt the need of specifying GPUs for -nb -pme etc tags. please suggest if i should use them ideally? I am using gromacs 2025 and below are our cluster details $ lscpu lscpu Architecture: x86\_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 112 On-line CPU(s) list: 0-111 Thread(s) per core: 2 Core(s) per socket: 28 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 106 Model name: Intel(R) Xeon(R) Gold 6330 CPU @ 2.00GHz Stepping: 6 CPU MHz: 2000.000 CPU max MHz: 3100.0000 CPU min MHz: 800.0000 BogoMIPS: 4000.00 Virtualization: VT-x L1d cache: 48K L1i cache: 32K L2 cache: 1280K L3 cache: 43008K NUMA node0 CPU(s): 0-27,56-83 NUMA node1 CPU(s): 28-55,84-111 $ lspci | grep -i --color ‘vga|3d|2d’ 04:00.0 VGA compatible controller: ASPEED Technology, Inc. ASPEED Graphics Family (rev 41) 0a:00.0 3D controller: NVIDIA Corporation GA102GL [A10] (rev a1) 0b:00.0 3D controller: NVIDIA Corporation GA102GL [A10] (rev a1) 0e:00.0 3D controller: NVIDIA Corporation GA102GL [A10] (rev a1) 12:00.0 3D controller: NVIDIA Corporation GA102GL [A10] (rev a1) 21:00.0 3D controller: NVIDIA Corporation GA102GL [A10] (rev a1) 22:00.0 3D controller: NVIDIA Corporation GA102GL [A10] (rev a1) 25:00.0 3D controller: NVIDIA Corporation GA102GL [A10] (rev a1) 29:00.0 3D controller: NVIDIA Corporation GA102GL [A10] (rev a1) 6a:00.0 Non-Volatile memory controller: Intel Corporation NVMe DC SSD [3DNAND, Sentinel Rock Controller] 6b:00.0 Non-Volatile memory controller: Intel Corporation NVMe DC SSD [3DNAND, Sentinel Rock Controller]