GROMACS 2020.4 - gmx binary hangs
I built Gromacs 2020.04 on a Ubuntu 20.04 machine using gcc-8.4.0. Using the following command:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/home/anthony/gcc-8.4.0/bin/gcc -DCMAKE_CXX_COMPILER=/home/anthony/gcc-8.4.0/bin/g++ -DGMX_SIMD=AVX2_256 -DGMX_DOUBLE=off
then I type “make” and everything appears to build fine (i.e. there are no errors)
However if I run “make check” then several of the tests fail due to timeout reasons (output of make check is attached)check.log Below are the list of the tests that failed:
The following tests FAILED: 30 - GmxAnaTest (Timeout) 38 - TrajectoryAnalysisUnitTests (Timeout) 39 - EnergyAnalysisUnitTests (Timeout) 44 - MdrunModulesTests (Timeout) 45 - MdrunIOTests (Timeout) 46 - MdrunTests (Timeout) 47 - MdrunNonIntegratorTests (Timeout) 48 - MdrunTpiTests (Timeout)
I decided to proceed with installation anyway (“make install”). The command “gmx” (with no options or inputs) produces the expected terminal output. However, instead of terminating and the Bash shell prompt reappearing; the program hangs. If I run “gmx pdb2gmx” the program produces the expected output and terminates normally (does NOT hang). if I run however “gmx pdb2gmx -f 1ubq.pdb -o 1ubq.gro -p 1ubq.top” select force field “8” and water model “1” when prompted, the program executes as normal, produces the relevant files (which appear at a cursory glance, correct) and then hangs.
I have tried several different settings and compiled with a couple different versions of GCC. I even tried the 2020.1 version binaries that are distributed through the Ubuntu software repositories and they still have this same exact issue.
My machine uses a AMD RYZEN 5 3600X six core processor and a NVDIA GeForce RTX 2070 graphics card. However none of my compilations tried to utilize the graphics card.