# MdrunModulesTests timeout on Gromacs 2021, gcc 10.2.1 **URL:** \ **Category:** User discussions\ **Created:** [January 28, 2021, 11:48pm UTC](https://gromacs.bioexcel.eu/t/mdrunmodulestests-timeout-on-gromacs-2021-gcc-10-2-1/1506 "2021-01-28T23:48:52Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![rmera](https://avatars.discourse-cdn.com/v4/letter/r/a3d4f5/32.png) [@rmera](https://gromacs.bioexcel.eu/u/rmera)\ **Post date:** [January 28, 2021, 11:48pm UTC](https://gromacs.bioexcel.eu/t/mdrunmodulestests-timeout-on-gromacs-2021-gcc-10-2-1/1506/1 "2021-01-28T23:48:52Z")
GROMACS version: 2021 GROMACS modification: No Dear all, I am attempting to compile Gromacs 2021 (although I experienced the same problem while trying to build 2020.5). I use the following cmake call: cmake … -DGMX\_BUILD\_OWN\_FFTW=ON -DREGRESSIONTEST\_DOWNLOAD=ON -DCMAKE\_INSTALL\_PREFIX=/opt/software/gromacs-2021-nogpu -DCMAKE\_C\_COMPILER=gcc -DCMAKE\_CXX\_COMPILER=g++ -DGMX\_GPU=OFF -DGMX\_MPI=OFF -DBUILD\_SHARED\_LIBS=ON -DGMX\_HWLOC=ON What I am actually trying to do is to build a CUDA enabled version (CUDA 11.1) but I found that the problem persists without CUDA, so I thought it would be better to post the info for the CUDA-less build. The build process (cmake and make), runs without problems. When I run the tests with “make check”, the test MdrunModulesTests times out (after about 120 sec). I haven’t been able to find more information about what exactly is MdrunModulesTests checking, so I’m writing to ask how serious it is, what could be the cause of the problem, and how could I fix it. Below is some system info and the output of “gmx mdrun -version”: The system runs Fedora 32. The relevant output of “gcc --version” is: gcc (GCC) 10.2.1 20201016 (Red Hat 10.2.1-6) The output for “cat /proc/cpuinfo” is: processor : 0 vendor\_id : GenuineIntel cpu family : 6 model : 85 model name : Intel® Xeon® Gold 6130 CPU @ 2.10GHz stepping : 4 microcode : 0x2006906 cpu MHz : 3453.961 cache size : 22528 KB physical id : 0 siblings : 32 core id : 0 cpu cores : 16 apicid : 0 initial apicid : 0 fpu : yes fpu\_exception : yes cpuid level : 22 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm consta nt\_tsc art arch\_perfmon pebs bts rep\_good nopl xtopology nonstop\_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds\_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4\_1 sse4\_2 x2apic movbe popcnt tsc\_deadline\_timer aes xsave avx f16c rdrand lahf\_lm abm 3dnowprefetch cpuid\_fault epb cat\_l3 cdp\_l3 invpcid\_single pti intel\_ppin ssbd mba ibrs ibpb stibp tpr\_shadow vnmi flexpriority ept vpid ept\_ad fsgsbase tsc\_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt\_a avx512f avx512dq rdseed adx smap clflushopt clwb intel\_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm\_llc cqm\_occup\_llc cqm\_mbm\_total cqm\_mbm\_local dtherm ida arat pln pts pku ospke md\_cl ear flush\_l1d vmx flags : vnmi preemption\_timer posted\_intr invvpid ept\_x\_only ept\_ad ept\_1gb flexpriority apicv tsc\_offset vtpr mtf vapic ept vpid unrestricted\_guest vapic\_reg vid ple shadow\_vmcs pml ept\_mode\_based\_exec tsc\_scaling bugs : cpu\_meltdown spectre\_v1 spectre\_v2 spec\_store\_bypass l1tf mds swapgs taa itlb\_multihit bogomips : 4200.00 clflush size : 64 cache\_alignment : 64 address sizes : 46 bits physical, 48 bits virtual power management: (repeated for the 64 cores seen by the OS, 32 of which are real) The relevant output from “./gmx mdrun -version” (run in the build/bin directory) is: GROMACS: gmx mdrun, version 2021 Executable: /wrk/programs/gromacs-2021/build-nocuda/bin/./gmx Data prefix: /wrk/programs/gromacs-2021 (source tree) Working dir: /wrk/programs/gromacs-2021/build-nocuda/bin Command line: gmx mdrun -version GROMACS version: 2021 Verified release checksum is 3e06a5865d6ff726fc417dea8d55afd37ac3cbb94c02c54c76d7a881c49c5dd8 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/gcc GNU 10.2.1 C compiler flags: -mavx512f -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O2 -DNDEBUG C++ compiler: /usr/bin/g++ GNU 10.2.1 C++ compiler flags: -mavx512f -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O2 -DNDEBUG Cheers, Raul ---
**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:** [January 29, 2021, 3:15pm UTC](https://gromacs.bioexcel.eu/t/mdrunmodulestests-timeout-on-gromacs-2021-gcc-10-2-1/1506/2 "2021-01-29T15:15:55Z")
That’s strange, for me MdrunModulesTests executes in \<1s. Can you try to turn off OpenMP and see if that is something that contributes to the issue? Is your machine idle when you run `make check`? Also, do you not build in release mode (you have `-O2`)? ---
**Author:** ![rmera](https://avatars.discourse-cdn.com/v4/letter/r/a3d4f5/32.png) [@rmera](https://gromacs.bioexcel.eu/u/rmera)\ **Post date:** [January 30, 2021, 8:59pm UTC](https://gromacs.bioexcel.eu/t/mdrunmodulestests-timeout-on-gromacs-2021-gcc-10-2-1/1506/3 "2021-01-30T20:59:08Z")
Hi, Thanks for the answer. I have been attempting a “regular” build, with -O2. I now tested a “debug” build, without -O2, the problem persists. OpenMP does seem to play a role. If I set OMP\_THREAD\_LIMIT=1, several tests fail, but MdrunModulesTests run correctly, without timing out. An MPI build (-DGMX\_MPI=on) also runs MdrunModulesTests correctly (as well as all the other tests). As this runs 8 omp threads per MPI process, I thought setting OMP\_THREAD\_LIMIT=8 on the non-mpi build could get the test to run, but it didn’t. I don’t know how to build without openmp. For now, the MPI build passes all the tests, so I will be using that. For reference, my system is running libomp 10.0.1, libgomp 10.2.1, and openmpi 4.0.4