# Gromacs 2025.3 installation, make check regression tests /complex failed **URL:** \ **Category:** User discussions\ **Tags:** installation-error\ **Created:** [November 6, 2025, 2:51pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2025-3-installation-make-check-regression-tests-complex-failed/12871 "2025-11-06T14:51:14Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Marie](https://avatars.discourse-cdn.com/v4/letter/m/bc8723/32.png) [@Marie](https://gromacs.bioexcel.eu/u/Marie)\ **Post date:** [November 6, 2025, 2:51pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2025-3-installation-make-check-regression-tests-complex-failed/12871/1 "2025-11-06T14:51:14Z")
GROMACS version: 2025.3 GROMACS modification: No g ++ 13.30, Mpirun 4.1.6, cmake 3.28.3, Cuda 13.0.48, Python 3.12.3 My flags are > cmake .. -DGMX\_GPU=CUDA DGMX\_BUILD\_OWN\_FFTW=ON -DREGRESSIONTEST\_DOWNLOAD=ON when I run > make check I get that regressiontest/complex failed (as shown below). All other test are passed. I would really like some advise on how to proceed for finding out, what I did wrong. Thank you! /Marie > 93/94 Test #93: regressiontests/complex …\*\*\*Failed 375.93 sec > Re-running aminoacids using only CPU-based non-bonded kernels > Re-running aminoacids using CPU-based update > Re-running awh\_multidim using only CPU-based non-bonded kernels > Re-running awh\_multidim using CPU-based update > Re-running butane using only CPU-based non-bonded kernels > Re-running butane using CPU-based update > Re-running dd121 using only CPU-based non-bonded kernels > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -nb cpu -notunepme \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > Re-running distance\_restraints using only CPU-based non-bonded kernels > Re-running distance\_restraints using CPU-based update > Re-running ethyleenglycol using only CPU-based non-bonded kernels > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > Re-running ethyleenglycol using CPU-based update > Re-running field using only CPU-based non-bonded kernels > Re-running field using CPU-based update > Re-running nacl using only CPU-based non-bonded kernels > Re-running nacl using CPU-based update > > Abnormal return value for ’ gmx mdrun -nb cpu -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn-energy-groups for nbnxn-energy-groups > Re-running nbnxn-free-energy using only CPU-based non-bonded kernels > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > Re-running nbnxn-free-energy using CPU-based update > Re-running nbnxn-free-energy-vv using only CPU-based non-bonded kernels > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > Re-running nbnxn-ljpme-geometric using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-geometric/nb-cpu for nbnxn-ljpme-geometric-nb-cpu > Re-running nbnxn-ljpme-geometric using CPU-based update > Re-running nbnxn-ljpme-LB using only CPU-based non-bonded kernels > Re-running nbnxn-ljpme-LB-geometric using only CPU-based non-bonded kernels > Re-running nbnxn-vdw-force-switch using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn-vdw-force-switch/nb-cpu for nbnxn-vdw-force-switch-nb-cpu > Re-running nbnxn-vdw-force-switch using CPU-based update > Re-running nbnxn-vdw-potential-switch using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn-vdw-potential-switch/nb-cpu for nbnxn-vdw-potential-switch-nb-cpu > Re-running nbnxn-vdw-potential-switch using CPU-based update > Re-running nbnxn-vdw-potential-switch-argon using only CPU-based non-bonded kernels > Re-running nbnxn-vdw-potential-switch-argon using CPU-based update > Re-running nbnxn\_pme using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn\_pme/nb-cpu for nbnxn\_pme-nb-cpu > Re-running nbnxn\_pme using CPU-based update > Re-running nbnxn\_pme\_order5 using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn\_pme\_order5/nb-cpu for nbnxn\_pme\_order5-nb-cpu > Re-running nbnxn\_pme\_order5 using CPU-based update > Re-running nbnxn\_pme\_order6 using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn\_pme\_order6/nb-cpu for nbnxn\_pme\_order6-nb-cpu > Re-running nbnxn\_pme\_order6 using CPU-based update > Re-running nbnxn\_rf using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn\_rf/nb-cpu for nbnxn\_rf-nb-cpu > Re-running nbnxn\_rf using CPU-based update > Re-running nbnxn\_rzero using only CPU-based non-bonded kernels > Re-running nbnxn\_rzero using CPU-based update > Re-running nbnxn\_vsite using only CPU-based non-bonded kernels > Re-running nst\_mismatch using only CPU-based non-bonded kernels > Re-running nst\_mismatch using CPU-based update > Re-running octahedron using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in octahedron/nb-cpu for octahedron-nb-cpu > Re-running octahedron using CPU-based update > Re-running orientation-restraints using only CPU-based non-bonded kernels > Re-running position-restraints using only CPU-based non-bonded kernels > Re-running position-restraints using CPU-based update > Re-running pr-vrescale using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in pr-vrescale/nb-cpu for pr-vrescale-nb-cpu > Re-running pr-vrescale using CPU-based update > Re-running pull\_constraint using only CPU-based non-bonded kernels > Re-running pull\_cylinder using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in pull\_cylinder/nb-cpu for pull\_cylinder-nb-cpu > Re-running pull\_cylinder using CPU-based update > Re-running pull\_geometry\_angle using only CPU-based non-bonded kernels > Re-running pull\_geometry\_angle using CPU-based update > Re-running pull\_geometry\_angle-axis using only CPU-based non-bonded kernels > Re-running pull\_geometry\_angle-axis using CPU-based update > Re-running pull\_geometry\_dihedral using only CPU-based non-bonded kernels > Re-running pull\_geometry\_dihedral using CPU-based update > Re-running sw using only CPU-based non-bonded kernels > Re-running swap\_x using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in swap\_x/nb-cpu for swap\_x-nb-cpu > Re-running swap\_y using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in swap\_y/nb-cpu for swap\_y-nb-cpu > Re-running swap\_z using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in swap\_z/nb-cpu for swap\_z-nb-cpu > Re-running tip4p using only CPU-based non-bonded kernels > Re-running tip4pflex using only CPU-based non-bonded kernels > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in tip4pflex/nb-cpu for tip4pflex-nb-cpu > Re-running urea using only CPU-based non-bonded kernels > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -notunepme -nb cpu \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > Re-running urea using CPU-based update > Re-running walls using only CPU-based non-bonded kernels > Re-running walls using CPU-based update > 15 out of 115 complex tests FAILED > > ```auto > Start 94: regressiontests/essentialdynamics > > ``` > > 94/94 Test #94: regressiontests/essentialdynamics … Passed 25.71 sec > > 99% tests passed, 1 tests failed out of 94 > > Label Time Summary: > GTest = 662.01 sec_proc (90 tests) > IntegrationTest = 357.41 sec_proc (29 tests) > MpiTest = 452.11 sec_proc (21 tests) > QuickGpuTest = 142.36 sec_proc (23 tests) > SlowGpuTest = 902.36 sec_proc (16 tests) > SlowTest = 288.30 sec_proc (14 tests) > UnitTest = 16.29 sec\*proc (47 tests) > > Total Test time (real) = 760.76 sec > > The following tests FAILED: > 93 - regressiontests/complex (Failed) > Errors while running CTest > make[3]: \*\*\* [CMakeFiles/run-ctest-nophys.dir/build.make:71: CMakeFiles/run-ctest-nophys] Error 8 > make[2]: \*\*\* [CMakeFiles/Makefile2:3383: CMakeFiles/run-ctest-nophys.dir/all] Error 2 > make[1]: \*\*\* [CMakeFiles/Makefile2:3416: CMakeFiles/check.dir/rule] Error 2 > make: \*\*\* [Makefile:628: check] Error 2 ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [November 11, 2025, 11:34am UTC](https://gromacs.bioexcel.eu/t/gromacs-2025-3-installation-make-check-regression-tests-complex-failed/12871/2 "2025-11-11T11:34:31Z")
I don’t fully understand this output. Maybe the tests fail because you are asking for too many ranks (but then our tests should handle this better). @al42and do you have an idea what is going wrong here? Anyhow, I think the issue is with the test setup, your GROMACS installation should be fine. ---
**Author:** ![al42and](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/al42and/32/1393_2.png) [@al42and](https://gromacs.bioexcel.eu/u/al42and)\ **Post date:** [November 11, 2025, 11:48am UTC](https://gromacs.bioexcel.eu/t/gromacs-2025-3-installation-make-check-regression-tests-complex-failed/12871/3 "2025-11-11T11:48:27Z")
@Marie, can you attach the files mentioned in the error messages? E.g., for > `FAILED. Check mdrun.out, md.log file(s) in pull_cylinder/nb-cpu for pull_cylinder-nb-cpu`, that would be `complex/pull_cylinder/nb-cpu/mdrun.out` and `complex/pull_cylinder/nb-cpu/md.log` ---
**Author:** ![Marie](https://avatars.discourse-cdn.com/v4/letter/m/bc8723/32.png) [@Marie](https://gromacs.bioexcel.eu/u/Marie)\ **Post date:** [November 11, 2025, 12:18pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2025-3-installation-make-check-regression-tests-complex-failed/12871/4 "2025-11-11T12:18:21Z")
[md.log](https://gromacs.bioexcel.eu/uploads/short-url/e5hzpmYNOc7cfEDHfhrY3TSWYkA.log) (19.6 KB) - pull cylinder [mdrun.txt](https://gromacs.bioexcel.eu/uploads/short-url/rEKZMURNYsA5HSWctcR4SxXMX0M.txt) (2.4 KB) - pull cylinder These are the files for 1 of the error messages, I can attach more if needed. Thank you for looking into this! ---
**Author:** ![al42and](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/al42and/32/1393_2.png) [@al42and](https://gromacs.bioexcel.eu/u/al42and)\ **Post date:** [November 11, 2025, 5:19pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2025-3-installation-make-check-regression-tests-complex-failed/12871/5 "2025-11-11T17:19:32Z")
Thanks. You can check if the errors in other files are any different, but what you attached confirms Berk’s suspicion: ```auto Fatal error: The number of ranks selected for particle-particle work (22) contains a large prime factor 11. In most cases this will lead to bad performance. Choose a number with smaller prime factors or set the decomposition (option -dd) manually. ``` @Marie: this error should be safe to ignore. You can also try adding `-DREGRESSIONTEST_EXTRA_ARGS='-nt;2'` to your CMake command; then run `make check` again; it should now run with fixed configuration, avoiding this error. @hess: CPUs with 22 threads are _fun_. We have 6 P-cores (with 2 threads each), 8 E-cores and 2 LPE-cores (with 1 thread each). Yet GROMACS incorrectly reports them as 11 cores with 2 threads each. `Package 0: [0 1] [2 3] [4 5] [6 7] [8 9] [10 11] [12 13] [14 15] [16 17] [18 19] [20 21]`. @Marie: To help us improve hardware detection for new Intel CPUs, could you run the following command in your **GROMACS source root directory**? ```auto ./src/gromacs/hardware/tests/capture-topology.sh CoreUltra9185H ``` This script will create a directory named `CoreUltra9185H` containing hardware topology information for your CPU. Please archive this directory (e.g., using `tar -czvf CoreUltra9185H.tar.gz CoreUltra9185H`) and share the resulting file with us. ---
**Author:** ![Marie](https://avatars.discourse-cdn.com/v4/letter/m/bc8723/32.png) [@Marie](https://gromacs.bioexcel.eu/u/Marie)\ **Post date:** [November 12, 2025, 11:03am UTC](https://gromacs.bioexcel.eu/t/gromacs-2025-3-installation-make-check-regression-tests-complex-failed/12871/6 "2025-11-12T11:03:30Z")
I checked the other files and they all contain the same fatal error. Good to know that it shouldn’t affect the GROMACS installation Link for [CoreUltra9185H.tar](https://drive.google.com/file/d/1sODExkLsoEH8GYd5-TfGCeWuLhmQamr2/view?usp=sharing) Thank you for your help!