# Gormacs installation-enabling GPU **URL:** \ **Category:** User discussions\ **Tags:** gpu, installation-error\ **Created:** [October 25, 2021, 8:17pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029 "2021-10-25T20:17:03Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![shivu](https://avatars.discourse-cdn.com/v4/letter/s/bbce88/32.png) [@shivu](https://gromacs.bioexcel.eu/u/shivu)\ **Post date:** [October 25, 2021, 8:17pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/1 "2021-10-25T20:17:04Z")
GROMACS version: 2021.3 GROMACS modification: Yes/No Here post your question Hi, i have recently installed Gromacs on ubuntu platform. I used following to cmake: cmake .. -DGMX\_BUILD\_OWN\_FFTW=ON -DREGRESSIONTEST\_DOWNLOAD=ON -DGMX\_MPI=on -DGMX\_GPU=CUDA -DMPI\_C\_COMPILER=mpicc -DGMX\_MPI=on I am getting following error at the end: /usr/bin/ld: ../../../../lib/libmdrun\_test\_infrastructure.a(moduletest.cpp.o): undefined reference to symbol ‘MPI\_Barrier’ /usr/bin/ld: /usr/lib/x86\_64-linux-gnu/libmpich.so: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[3]: \*\*\* [src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make:113: bin/mdrun-tpi-test] Error 1 make[2]: \*\*\* [CMakeFiles/Makefile2:6646: src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/all] Error 2 make[1]: \*\*\* [CMakeFiles/Makefile2:2713: CMakeFiles/check.dir/rule] Error 2 make: \*\*\* [Makefile:249: check] Error 2 I did “make install” after this. running an md job is giving me following error: gmx mdrun -deffnm md\_0\_1 -nb gpu GROMACS version: 2021.3 Precision: mixed Memory model: 64 bit MPI library: thread\_mpi OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 64) GPU support: disabled SIMD instructions: AVX\_512 FFT library: fftw-3.3.8-sse2-avx-avx2-avx2\_128-avx512 RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /usr/bin/cc GNU 9.3.0 C compiler flags: -mavx512f -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 9.3.0 C++ compiler flags: -mavx512f -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp Running on 1 node with total 20 cores, 40 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) Gold 6230 CPU @ 2.10GHz Family: 6 Model: 85 Stepping: 7 Number of AVX-512 FMA units: 2 * * * ## Please let me know how to resolve the issue and best use the GPU capabilities. Thank you ---
**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:** [October 25, 2021, 10:31pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/2 "2021-10-25T22:31:13Z")
There is no error in your output, but I assume it stated that your binary does not have GPU support. That’s because you build without GPU support as you can see from the " GPU support: disabled" in the version header. Make sure to pass `-DGMX_GPU=` and specify your GPU platform (CUDA or OpenCL). Secondly, your install commands should build an MPI build, but that seems to fail, then you run the `gmx mdrun` binary which is not an MPI binary (because " MPI library: thread\_mpi" indicates it is not using lib-MPI). If you want to run multi-node, make sure you have a functioning MPI build. ---
**Author:** ![shivu](https://avatars.discourse-cdn.com/v4/letter/s/bbce88/32.png) [@shivu](https://gromacs.bioexcel.eu/u/shivu)\ **Post date:** [October 27, 2021, 12:58pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/3 "2021-10-27T12:58:13Z")
Hi Thank you for the reply. I used this command to do cmake: cmake … -DGMX\_BUILD\_OWN\_FFTW=ON -DREGRESSIONTEST\_DOWNLOAD=ON -DGMX\_MPI=on -DGMX\_GPU=CUDA -DMPI\_C\_COMPILER=mpicc -DGMX\_MPI=on I specified CUDA for -DGMX\_GPU Please see and guide how to best use the GPU capabilities. Thank you ---
**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:** [October 27, 2021, 4:04pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/4 "2021-10-27T16:04:39Z")
If you did that your binary should report “GPU support: CUDA” in the `gmx --version` output. Have you verified that it does? ---
**Author:** ![shivu](https://avatars.discourse-cdn.com/v4/letter/s/bbce88/32.png) [@shivu](https://gromacs.bioexcel.eu/u/shivu)\ **Post date:** [October 27, 2021, 8:16pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/5 "2021-10-27T20:16:44Z")
> [@pszilard](#): > > `gmx --version` Hi Thanks again. I checked my system for CUDA. ==\> when I give command: “nvidia-smi”, following is the output: ±----------------------------------------------------------------------------+ | NVIDIA-SMI 495.29.05 Driver Version: 495.29.05 CUDA Version: 11.5 | |-------------------------------±---------------------±---------------------+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |===============================+======================+======================| | 0 Quadro RTX 4000 On | 00000000:17:00.0 On | N/A | | 30% 41C P8 17W / 125W | 274MiB / 7974MiB | 5% Default | | | | N/A | ±------------------------------±---------------------±---------------------+ I re did the cmake command: ==\> “cmake … -DGMX\_GPU=CUDA” output: – The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;–enable-avx;–enable-avx2;–enable-avx512 – Configuring done – Generating done – Build files have been written to: /home/mypc/Documents/software/gromacs-2021.3/build ==\> after this I gave: “make” output: [1%] Built target fftwBuild [1%] Built target scanner [2%] Generating release version information [2%] Built target release-version-info [4%] Built target tng\_io\_obj [4%] Built target tng\_io\_zlib [4%] Built target lmfit\_objlib [5%] Built target thread\_mpi [25%] Built target linearalgebra [26%] Built target modularsimulator [93%] Built target libgromacs [94%] Built target gmxapi [95%] Built target nblib [95%] Built target methane-water-integration [95%] Built target argon-forces-integration [95%] Built target gtest [95%] Built target gmock [98%] Built target testutils [100%] Built target gmx\_objlib [100%] Built target mdrun\_objlib [100%] Built target view\_objlib [100%] Built target gmx ==\> followed by “make check” output: [0%] Built target mdrun\_objlib [0%] Built target scanner [1%] Generating release version information [1%] Built target release-version-info [2%] Built target fftwBuild [3%] Built target tng\_io\_obj [3%] Built target tng\_io\_zlib [3%] Built target lmfit\_objlib [4%] Built target thread\_mpi [18%] Built target linearalgebra [19%] Built target modularsimulator [67%] Built target libgromacs [68%] Built target gmx\_objlib [68%] Built target view\_objlib [68%] Built target gmx [68%] Built target gmxtests [68%] Built target gtest [68%] Built target gmock [70%] Built target testutils [70%] Built target mdrun\_test\_infrastructure [71%] Built target gmxapi [72%] Built target workflow-details-test [73%] Built target nblib [73%] Built target nblib\_test\_infrastructure [74%] Built target nblib-setup-test [74%] Built target methane-water-integration [74%] Built target argon-forces-integration [74%] Built target nblib-integrator-test [75%] Built target nblib-integration-test [75%] Built target nblib-tests [75%] Built target nblib-listed-forces-test [75%] Built target nblib-util-test [75%] Built target testutils-mpi-test [75%] Built target testutils-test [75%] Built target utility-mpi-test [77%] Built target utility-test [77%] Linking CXX executable …/…/…/…/bin/mdlib-test [78%] Built target mdlib-test [79%] Built target awh-test [79%] Built target density\_fitting\_applied\_forces-test [79%] Built target applied\_forces-test [79%] Built target listed\_forces-test [79%] Built target onlinehelp-test-shared [80%] Built target commandline-test [81%] Built target domdec-mpi-test [81%] Built target domdec-test [82%] Built target ewald-test [82%] Built target fft-test [82%] Linking CXX executable …/…/…/…/bin/gpu\_utils-test [82%] Built target gpu\_utils-test [83%] Built target hardware-test [84%] Built target math-test [84%] Built target mdrunutility-test-shared [84%] Built target mdrunutility-mpi-test [84%] Built target mdrunutility-test [85%] Built target mdspan-test [85%] Built target mdtypes-test [85%] Built target onlinehelp-test [86%] Built target options-test [86%] Built target pbcutil-test [86%] Built target random-test [86%] Built target restraintpotential-test [86%] Built target table-test [86%] Built target taskassignment-test [86%] Built target topology-test [86%] Built target pull-test [87%] Built target simd-test [87%] Built target compat-test [87%] Built target gmxana-test [88%] Built target pdb2gmx3-test [88%] Built target pdb2gmx2-test [88%] Built target pdb2gmx1-test [89%] Built target gmxpreprocess-test [89%] Built target correlations-test [89%] Built target analysisdata-test-shared [89%] Built target analysisdata-test [90%] Built target coordinateio-test [91%] Built target trajectoryanalysis-test [91%] Built target energyanalysis-test [92%] Built target tool-test [92%] Built target fileio-test [93%] Built target selection-test [93%] Linking CXX executable …/…/…/…/bin/mdrun-tpi-test /usr/bin/ld: …/…/…/…/lib/libmdrun\_test\_infrastructure.a(moduletest.cpp.o): undefined reference to symbol ‘MPI\_Barrier’ /usr/bin/ld: /usr/lib/x86\_64-linux-gnu/libmpich.so: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[3]: \*\*\* [src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make:113: bin/mdrun-tpi-test] Error 1 make[2]: \*\*\* [CMakeFiles/Makefile2:6646: src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/all] Error 2 make[1]: \*\*\* [CMakeFiles/Makefile2:2713: CMakeFiles/check.dir/rule] Error 2 make: \*\*\* [Makefile:249: check] Error 2 it gave errors. now: “gmx --version” output: GROMACS version: 2021.3 Precision: mixed Memory model: 64 bit MPI library: thread\_mpi OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 64) GPU support: disabled SIMD instructions: AVX\_512 FFT library: fftw-3.3.8-sse2-avx-avx2-avx2\_128-avx512 RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /usr/bin/cc GNU 9.3.0 C compiler flags: -mavx512f -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 9.3.0 C++ compiler flags: -mavx512f -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp there are few errors here also in C compiler and it is still saying GPU support: disabled Please see and guide ---
**Author:** ![shivu](https://avatars.discourse-cdn.com/v4/letter/s/bbce88/32.png) [@shivu](https://gromacs.bioexcel.eu/u/shivu)\ **Post date:** [October 28, 2021, 4:50pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/6 "2021-10-28T16:50:13Z")
Please provide the best possible solution to help resolve this issue. Thank you ---
**Author:** ![shivu](https://avatars.discourse-cdn.com/v4/letter/s/bbce88/32.png) [@shivu](https://gromacs.bioexcel.eu/u/shivu)\ **Post date:** [October 29, 2021, 6:20pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/7 "2021-10-29T18:20:52Z")
Hi, I have done the complete installation again. now the gmx --version shows that GPU is supported. see below: gmx pdb2gmx --version GROMACS version: 2021.3 Verified release checksum is Precision: mixed Memory model: 64 bit MPI library: thread\_mpi OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 64) GPU support: CUDA SIMD instructions: AVX\_512 FFT library: fftw-3.3.8-sse2-avx RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /usr/bin/cc GNU 8.4.0 C compiler flags: -mavx512f -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 8.4.0 C++ compiler flags: -mavx512f -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG CUDA compiler: /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Sun\_Jul\_28\_19:07:16\_PDT\_2019;Cuda compilation tools, release 10.1, V10.1.243 CUDA compiler flags:-std=c++14;-gencode;arch=compute\_30,code=sm\_30;-gencode;arch=compute\_35,code=sm\_35;-gencode;arch=compute\_37,code=sm\_37;-gencode;arch=compute\_50,code=sm\_50;-gencode;arch=compute\_52,code=sm\_52;-gencode;arch=compute\_60,code=sm\_60;-gencode;arch=compute\_61,code=sm\_61;-gencode;arch=compute\_70,code=sm\_70;-gencode;arch=compute\_75,code=sm\_75;-gencode;arch=compute\_35,code=compute\_35;-gencode;arch=compute\_32,code=compute\_32;-use\_fast\_math;-D\_FORCE\_INLINES;-mavx512f -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG CUDA driver: 11.40 CUDA runtime: 10.10 I do see: “-Wno-missing-field-initializers” in C++ compiler section. ---
**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:** [November 2, 2021, 6:25pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/8 "2021-11-02T18:25:42Z")
> [@shivu](#): > > I have done the complete installation again. > now the gmx --version shows that GPU is supported. Good, so mdrun should now be able to utilize an NVIDIA GPU. > [@shivu](#): > > I do see: “-Wno-missing-field-initializers” in C++ compiler section. That is very much expected, it is a compiler flag used. ---
**Author:** ![shivu](https://avatars.discourse-cdn.com/v4/letter/s/bbce88/32.png) [@shivu](https://gromacs.bioexcel.eu/u/shivu)\ **Post date:** [November 3, 2021, 8:27pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/9 "2021-11-03T20:27:46Z")
Thank you for your feedback. ---
**Author:** ![LTaro](https://avatars.discourse-cdn.com/v4/letter/l/ebca7d/32.png) [@LTaro](https://gromacs.bioexcel.eu/u/LTaro)\ **Post date:** [April 3, 2022, 8:14am UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/10 "2022-04-03T08:14:50Z")
How did you fix it? ---
**Author:** ![Sajad](https://avatars.discourse-cdn.com/v4/letter/s/8491ac/32.png) [@Sajad](https://gromacs.bioexcel.eu/u/Sajad)\ **Post date:** [July 28, 2022, 8:01am UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/11 "2022-07-28T08:01:41Z")
Hi I have the same problem may you please help me? ---
**Author:** ![Vignesh](https://avatars.discourse-cdn.com/v4/letter/v/4bbf92/32.png) [@Vignesh](https://gromacs.bioexcel.eu/u/Vignesh)\ **Post date:** [September 1, 2023, 3:18pm UTC](https://gromacs.bioexcel.eu/t/gormacs-installation-enabling-gpu/3029/12 "2023-09-01T15:18:54Z")
After completing the installation with -DGMX\_GPU=CUDA (or your preference) execute the following command > source /usr/local/gromacs/bin/GMXRC After this whenever you need GPU support run the same command before starting your mdrun and proceed with your run (or verify with gmx --version)