# GROMACS 2020.4 installation problem **URL:** \ **Category:** User discussions\ **Created:** [October 11, 2020, 11:46am UTC](https://gromacs.bioexcel.eu/t/gromacs-2020-4-installation-problem/946 "2020-10-11T11:46:10Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![zorba](https://avatars.discourse-cdn.com/v4/letter/z/aca169/32.png) [@zorba](https://gromacs.bioexcel.eu/u/zorba)\ **Post date:** [October 11, 2020, 11:46am UTC](https://gromacs.bioexcel.eu/t/gromacs-2020-4-installation-problem/946/1 "2020-10-11T11:46:11Z")
GROMACS version: 2020.4 GROMACS modification: No Hi everybody, I’m trying to install the CPU+GPU version of GROMACS 2020.4 on a Ryzen 3700X machine running under an updated UBUNTU 20.04/CUDA 11.1 (nvidia 455 driver). During make check I encounter the following errors: The following tests FAILED: 5 - MdlibUnitTest (Failed) 10 - EwaldUnitTests (Failed) 12 - GpuUtilsUnitTests (Failed) Errors while running CTest make[3]: \*\*\* [CMakeFiles/run-ctest-nophys.dir/build.make:77: CMakeFiles/run-ctest-nophys] Error 8 make[2]: \*\*\* [CMakeFiles/Makefile2:3522: CMakeFiles/run-ctest-nophys.dir/all] Error 2 make[1]: \*\*\* [CMakeFiles/Makefile2:2660: CMakeFiles/check.dir/rule] Error 2 make: \*\*\* [Makefile:346: check] Error 2 More precisely: …/gromacs-2020.4/build/bin/mdlib-test: symbol lookup error: …/gromacs-2020.4/build/bin/mdlib-test: undefined symbol: \_ZN3gmx4test20integrateLeapFrogGpuEPNS0\_16LeapFrogTestDataEi …/gromacs-2020.4/build/bin/ewald-test: undefined symbol: _Z27pme\_gpu\_get\_real\_grid\_sizesPK6PmeGpuPN3gmx11BasicVectorIiEES5_ …/gromacs-2020.4/build/bin/gpu\_utils-test: symbol lookup error: …/gromacs-2020.4/build/bin/gpu\_utils-test: undefined symbol: \_Z18isHostMemoryPinnedPKv Is there any solution for the above or should I ignore it? I thank you in advance. Best. ---
**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 12, 2020, 3:19pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2020-4-installation-problem/946/2 "2020-10-12T15:19:44Z")
This is not expected and it is quite unusual, please post the commands you used to configure and build GROMACS. ---
**Author:** ![jbender](https://avatars.discourse-cdn.com/v4/letter/j/ebca7d/32.png) [@jbender](https://gromacs.bioexcel.eu/u/jbender)\ **Post date:** [November 19, 2020, 9:36pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2020-4-installation-problem/946/3 "2020-11-19T21:36:34Z")
Hi, I am experiencing the same behavior when building 2020.2 under Ubuntu 20.04 on a Ryzen 3700X with the nvidia 455 driver. My procedure was as follows: ``` tar xfz gromacs-2020.2.tar.gz cd gromacs-2020.2 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on make make check ``` More information on the system: ``` nvcc --version 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 gcc --version gcc (Ubuntu 8.4.0-3ubuntu2) 8.4.0 g++ --version g++ (Ubuntu 8.4.0-3ubuntu2) 8.4.0 uname -a Linux marvin 5.4.0-54-generic #60-Ubuntu SMP Fri Nov 6 10:37:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian Address sizes: 43 bits physical, 48 bits virtual CPU(s): 16 On-line CPU(s) list: 0-15 Thread(s) per core: 2 Core(s) per socket: 8 Socket(s): 1 NUMA node(s): 1 Vendor ID: AuthenticAMD CPU family: 23 Model: 113 Model name: AMD Ryzen 7 3700X 8-Core Processor ``` Can I provide any more information to locate the error? Thanks for you help! **Update** : I can confirm that this also happens with gromacs 2020.4 plus I now also get an error in the GmxPreprocessTests: ``` The following tests FAILED: 5 - MdlibUnitTest (Failed) 10 - EwaldUnitTests (Failed) 12 - GpuUtilsUnitTests (Failed) 31 - GmxPreprocessTests (Failed) ``` With the respective output being ``` 5/59 Test #5: MdlibUnitTest .......................***Failed 0.00 sec /home/aretaon/progs/gromacs-2020.4/build/bin/mdlib-test: symbol lookup error: /home/aretaon/progs/gromacs-2020.4/build/bin/mdlib-test: undefined symbol: _ZN3gmx4test20integrateLeapFrogGpuEPNS0_16LeapFrogTestDataEi 10/59 Test #10: EwaldUnitTests ......................***Failed 0.00 sec /home/aretaon/progs/gromacs-2020.4/build/bin/ewald-test: symbol lookup error: /home/aretaon/progs/gromacs-2020.4/build/bin/ewald-test: undefined symbol: _Z13pme_gpu_solvePK6PmeGpuP9t_complex12GridOrderingb 12/59 Test #12: GpuUtilsUnitTests ...................***Failed 0.00 sec /home/aretaon/progs/gromacs-2020.4/build/bin/gpu_utils-test: symbol lookup error: /home/aretaon/progs/gromacs-2020.4/build/bin/gpu_utils-test: undefined symbol: _Z8findGpusP14gmx_gpu_info_t ``` The GmxProcessTests seem to have some problem with encoding (but the download was fine, I checked the md5sum). ``` [----------] 1 test from GenRestrTest [RUN] GenRestrTest.SimpleRestraintsGenerated Reading structure file Group 0 ( System) has 156 elements Group 1 ( Other) has 156 elements Group 2 ( ) has 39 elements Group 3 ( ile/3) has 36 elements Group 4 ( ���U) has 0 elements Group 5 ( �~;�U) has 7 elements Group 6 ( ) has 1 elements Group 7 ( @) has 11 elements Select a group: Select group to position restrain Selected 3: 'ile/3' /home/aretaon/progs/gromacs-2020.4/src/testutils/refdata.cpp:873: Failure In item: /Files/-o/Contents Actual: '; position restraints for ile/3 of ��;�U ``` ---
**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 20, 2020, 12:38pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2020-4-installation-problem/946/4 "2020-11-20T12:38:01Z")
Hi, I can’t reproduce either of those on a very similar setup. The symbol lookup errors are suspicious of some king of link-time issue. Have you tried to use e.g. a different CUDA version or gcc? The latter also looks strange, the group selection output looks quite different starting from “Group 2” for me. I suggest to open an issue on [https://gitlab.com/gromacs/gromacs](https://gitlab.com/gromacs/gromacs) for this as there may be a bug that is causing this. Szilárd ---
**Author:** ![jbender](https://avatars.discourse-cdn.com/v4/letter/j/ebca7d/32.png) [@jbender](https://gromacs.bioexcel.eu/u/jbender)\ **Post date:** [November 25, 2020, 3:17pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2020-4-installation-problem/946/5 "2020-11-25T15:17:48Z")
Hi Szilárd, thanks for looking into this. Eventually, I realised my mistake: I used Cuda10 and gcc8.4 together with an Ampere-GPU. So now, I switched to Cuda11.1 and gcc9.3 but failed with gromacs 2020.2 (due to [https://gitlab.com/gromacs/gromacs/-/merge\_requests/461](https://gitlab.com/gromacs/gromacs/-/merge_requests/461)). However building and checking gromacs 2020.4 worked just fine and I will continue using 2020.4. ``` Label Time Summary: GTest = 115.29 sec*proc (55 tests) IntegrationTest = 43.91 sec*proc (12 tests) MpiTest = 59.10 sec*proc (8 tests) SlowTest = 51.49 sec*proc (2 tests) UnitTest = 19.89 sec*proc (41 tests) ``` Not sure if it was the same issue for the OP, but for me this is closed. ---
**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 26, 2020, 3:30pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2020-4-installation-problem/946/6 "2020-11-26T15:30:03Z")
Thanks for the feedback. Still not sure how could the latter, GmxProcessTests test failures be related to the gcc 8 + CUDA 10 vs gcc 9 + CUDA 11.1. Have you also tried gcc 8 + CUDA 11.1? ---
**Author:** ![jbender](https://avatars.discourse-cdn.com/v4/letter/j/ebca7d/32.png) [@jbender](https://gromacs.bioexcel.eu/u/jbender)\ **Post date:** [November 28, 2020, 12:46pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2020-4-installation-problem/946/7 "2020-11-28T12:46:11Z")
Just tested gcc 8.4.0 with cuda 11.1 and gromacs 2020.04 and all tests passed during make check. Maybe it’s something with cuda10 not supporting the Ampere GPU? Not sure if this plays a role during GmcProcessTests… ---
**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 30, 2020, 3:52pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2020-4-installation-problem/946/8 "2020-11-30T15:52:19Z")
In principle, if you do not restrict the target architectures (by using `-DGMX_CUDA_TARGET_SM`), Ampere should work even when GROMACS is compiler with earlier CUDA versions (ref [https://docs.nvidia.com/cuda/ampere-compatibility-guide/index.html#verifying-ampere-compatibility-using-cuda-10-2](https://docs.nvidia.com/cuda/ampere-compatibility-guide/index.html#verifying-ampere-compatibility-using-cuda-10-2)). If you can reproducibly get failing tests with CUDA 10 on Ampere, can you please file an issue on [https://gitlab.com/gromacs/gromacs/-/issue](https://gitlab.com/gromacs/gromacs/-/issue) so we look into this (please mention both the cases that fail and those that succeed). Thanks, Szilárd