# GPU utilization and MPI **URL:** \ **Category:** User discussions\ **Created:** [February 2, 2021, 12:36pm UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528 "2021-02-02T12:36:32Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![arnab\_1](https://avatars.discourse-cdn.com/v4/letter/a/0ea827/32.png) [@arnab\_1](https://gromacs.bioexcel.eu/u/arnab_1)\ **Post date:** [February 2, 2021, 12:36pm UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/1 "2021-02-02T12:36:32Z")
GROMACS version: 2021 GROMACS modification: Yes/No Here post your question Hi, I have NVIDIA Geforce GTX 1660 super,6GB which is CUDA enabled. During the GROMACS installation I used DGMX\_GPU=cuda in command line. Now, I am running a 20ns job by using simple command gmx mdrun -s topol-nvt.tpr -deffnm nvt. How do I confirm that job is using GPU? or is there anything else need to write in command line? Another query, can I use MPI and GPU simultaneously for increasing the efficiency? ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [February 2, 2021, 12:55pm UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/2 "2021-02-02T12:55:00Z")
> [@arnab\_1](#): > > How do I confirm that job is using GPU? or is there anything else need to write in command line? Take a look at the log file. There you will find a hardware detection report as well as a hardware usage and task assignment report which will indicate whether you are using a GPU and which of the computations are offloaded. To check GPU utilization use the `nvidia-smi` tool. > [@arnab\_1](#): > > Another query, can I use MPI and GPU simultaneously for increasing the efficiency? If you have a single GPU, you have no need for MPI. In addition, GROMACS has a built-in MPI (called thread-MPI) which allows MPI-type parallelization as long as you run on a single node. ---
**Author:** ![arnab\_1](https://avatars.discourse-cdn.com/v4/letter/a/0ea827/32.png) [@arnab\_1](https://gromacs.bioexcel.eu/u/arnab_1)\ **Post date:** [February 3, 2021, 5:43am UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/3 "2021-02-03T05:43:15Z")
Thank you so much for your information. I will check my log file. Is there anything additional need to write to command line for GPU utilization? ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [February 3, 2021, 3:31pm UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/4 "2021-02-03T15:31:05Z")
> [@arnab\_1](#): > > Is there anything additional need to write to command line for GPU utilization? That depends on your use-case; see [https://manual.gromacs.org/current/user-guide/mdrun-performance.html#node-level-parallelization-via-gpu-offloading-and-thread-mpi](https://manual.gromacs.org/current/user-guide/mdrun-performance.html#node-level-parallelization-via-gpu-offloading-and-thread-mpi) and [https://manual.gromacs.org/current/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node](https://manual.gromacs.org/current/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node) ---
**Author:** ![arnab\_1](https://avatars.discourse-cdn.com/v4/letter/a/0ea827/32.png) [@arnab\_1](https://gromacs.bioexcel.eu/u/arnab_1)\ **Post date:** [February 4, 2021, 6:22am UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/5 "2021-02-04T06:22:14Z")
Okay, Thanks a lot! ---
**Author:** ![arnab\_1](https://avatars.discourse-cdn.com/v4/letter/a/0ea827/32.png) [@arnab\_1](https://gromacs.bioexcel.eu/u/arnab_1)\ **Post date:** [February 4, 2021, 12:19pm UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/6 "2021-02-04T12:19:09Z")
Dear pszilard, I have checked my log file where I found **GROMACS version: 2020.1-Ubuntu-2020.1-1** **Precision: Single** **Memory model:64bit** **MPI library : thread\_mpi** **OpenMP support : enabled (GMX\_OPENMP\_MAX\_THREADS = 64)** **GPU support: disabled.** Then I reinstall the gromacs with command: **cmake … -DGMX\_BUILD\_OWN\_FFTW=ON -DGMX\_GPU=CUDA -DGMX\_MPI=ON** After that when I am trying to run using **gmx mdrun … -nb gpu -pme gpu** the system is showing the following: **Inconsistency in user input:** **Nonbonded interactions on the GPU were requested with -nb gpu, but the GROMACS binary has been build without GPU support.Either run without selecting GPU options or recompile GROMACS with GPU support enabled.** Now What can be done to solve this? ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [February 4, 2021, 4:59pm UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/7 "2021-02-04T16:59:33Z")
> [@arnab\_1](#): > > I have checked my log file where I found > **GROMACS version: 2020.1-Ubuntu-2020.1-1** > **Precision: Single** > **Memory model:64bit** > **MPI library : thread\_mpi** > **OpenMP support : enabled (GMX\_OPENMP\_MAX\_THREADS = 64)** > **GPU support: disabled.** That was GROMACS provided as an Ubuntu package built without GPU support. > [@arnab\_1](#): > > After that when I am trying to run using **gmx mdrun … -nb gpu -pme gpu** > the system is showing the following: > **Inconsistency in user input:** > **Nonbonded interactions on the GPU were requested with -nb gpu, but the GROMACS binary has been build without GPU support.Either run without selecting GPU options or recompile GROMACS with GPU support enabled.** > Now What can be done to solve this? That suggests that you still do not have GPU support. Have you checked your log? ---
**Author:** ![arnab\_1](https://avatars.discourse-cdn.com/v4/letter/a/0ea827/32.png) [@arnab\_1](https://gromacs.bioexcel.eu/u/arnab_1)\ **Post date:** [February 5, 2021, 9:08am UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/8 "2021-02-05T09:08:59Z")
Yeah I have checked my log after getting your suggestion. I found that run was performed completely without GPU support and it took near about 6 hours for 20 ns run. Then I reinstall the GROMACS package and able to enable the GPU support. I run following command _gmx mdrun -s topol-nvt.tpr -deffnm nvt -nb gpu_ for the same system what I used before. This time it has been taken 9 hours for the similar 20 ns run. I was wondering that why it has taken so long time in spite of getting GPU support? ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [February 5, 2021, 2:55pm UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/9 "2021-02-05T14:55:30Z")
Please share you log files and some information about the simulated system, otherwise it is hard to assess the performance of your simulations. ---
**Author:** ![arnab\_1](https://avatars.discourse-cdn.com/v4/letter/a/0ea827/32.png) [@arnab\_1](https://gromacs.bioexcel.eu/u/arnab_1)\ **Post date:** [February 5, 2021, 4:15pm UTC](https://gromacs.bioexcel.eu/t/gpu-utilization-and-mpi/1528/10 "2021-02-05T16:15:12Z")
![IMG_20210205_111848](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/9e5b30d43f21225a349078e9e0e8862cedb5df9a.jpeg) ![IMG_20210205_111725 (1)](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/c995989e60044d98a33bbc58d2025b2035fccaa6.jpeg) I have shared two screenshots of the log file because presently I don’t have the access the computer for the sharing the log file. Kindly look these images and I will share you tomorrow the original file. Here I am simulating the Ionic Liquid. Thanks a lot for your kind concern.