"make check" Test 1 fails for Gromacs 2022

GROMACS version: 2022
GROMACS modification: No

I just followed the normal non-GPU installation instructions and in “make check” Test 1 fails with this error message:

Error in user input:
Invalid command-line options
In command-line option -s
File ‘dummyfilename.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -s
Option specified multiple times

Seems like a typo in the command in the regression test script or a missing file.

That sounds like something that would be consistent and easily reproducible, but my “make check” clears the first test with no problems.

Hello,

can you check that your regression test archive is complete? I haven’t run into this while preparing the release.

Cheers

Paul

P.s.: Sorry for the previous misplaced post I deleted, was working on the wrong thread.

I ran the regression tests manually from the separate package and it checks out fine on both CPU-only and GPU builds.

How do I check everything is present and correct in the automatically downloaded test archive?

The downloads page has md5sum hashes:
https://manual.gromacs.org/documentation/2022/download.html
You can use them to confirm that the downloaded archive is complete and intact (not corrupt).

Once you extract the archive, it’s harder to prove. I’ve extracted the archive and created a list of checksums of all the files in it. If you have a version of the md5sum command that supports it, you can easily confirm that yours match mine using the “-c” option to the md5sum command.
regressiontests-2022-contents.md5.log (100.2 KB)

Hello!

I am experiencing the identical problem when running make check for 2022. When I do “./gmxtest.pl all” using the manually downloaded regression tests, it did not report (to my eyes) any error. However, the output was so verbose that I could not tell (again to my untrained eyes) what it was doing. How do I know that manual regression tests indeed passed and that the failed Test 1 in make check is not an actual problem?

Many thanks for your advice,
Gregory

Hello,

you can use perl gmxtest.pl all -xml to reduce the output from the regression tests. I think the issue must be with the way we are configuring the automated run of the tests with CTest that is invoked by make test. If the tests pass when run manually it shouldn’t be an error. If you can, please just add the error text here, it will help in debugging if this is an actual issue.

Cheers

Paul

Hi Paul,

Thanks for the response. I tried your suggestion with the following output:

Re-running aminoacids using only CPU-based non-bonded kernels
Re-running awh_multidim using only CPU-based non-bonded kernels
Re-running butane using only CPU-based non-bonded kernels
Re-running dd121 using only CPU-based non-bonded kernels
Re-running distance_restraints using only CPU-based non-bonded kernels
Re-running ethyleenglycol using only CPU-based non-bonded kernels
Re-running field using only CPU-based non-bonded kernels
Re-running nacl using only CPU-based non-bonded kernels
Re-running nbnxn-free-energy using only CPU-based non-bonded kernels
Re-running nbnxn-free-energy-vv using only CPU-based non-bonded kernels
Re-running nbnxn-ljpme-geometric using only CPU-based non-bonded kernels
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
Re-running nbnxn-vdw-potential-switch using only CPU-based non-bonded kernels
Re-running nbnxn-vdw-potential-switch-argon using only CPU-based non-bonded kernels
Re-running nbnxn_pme using only CPU-based non-bonded kernels
Re-running nbnxn_pme_order5 using only CPU-based non-bonded kernels
Re-running nbnxn_pme_order6 using only CPU-based non-bonded kernels
Re-running nbnxn_rf using only CPU-based non-bonded kernels
Re-running nbnxn_rzero using only CPU-based non-bonded kernels
Re-running nbnxn_vsite using only CPU-based non-bonded kernels
Re-running nst_mismatch using only CPU-based non-bonded kernels
Re-running octahedron using only CPU-based non-bonded kernels
Re-running orientation-restraints using only CPU-based non-bonded kernels
Re-running orientation-restraints using CPU-based PME
Re-running position-restraints using only CPU-based non-bonded kernels
Re-running pr-vrescale using only CPU-based non-bonded kernels
Re-running pull_constraint using only CPU-based non-bonded kernels
Re-running pull_cylinder using only CPU-based non-bonded kernels
Re-running pull_geometry_angle using only CPU-based non-bonded kernels
Re-running pull_geometry_angle-axis using only CPU-based non-bonded kernels
Re-running pull_geometry_dihedral using only CPU-based non-bonded kernels
Re-running sw using only CPU-based non-bonded kernels
Re-running swap_x using only CPU-based non-bonded kernels
Re-running swap_y using only CPU-based non-bonded kernels
Re-running swap_z using only CPU-based non-bonded kernels
Re-running tip4p using only CPU-based non-bonded kernels
Re-running tip4pflex using only CPU-based non-bonded kernels
Re-running urea using only CPU-based non-bonded kernels
Re-running walls using only CPU-based non-bonded kernels
All 89 complex tests PASSED
Re-running coulandvdwsequential_coul using only CPU-based non-bonded kernels
Re-running coulandvdwsequential_vdw using only CPU-based non-bonded kernels
Re-running coulandvdwtogether using only CPU-based non-bonded kernels
Re-running expanded using only CPU-based non-bonded kernels
Re-running relative using only CPU-based non-bonded kernels
Re-running relative-position-restraints using only CPU-based non-bonded kernels
Re-running restraints 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 simtemp using only CPU-based non-bonded kernels
Re-running transformAtoB using only CPU-based non-bonded kernels
Re-running vdwalone using only CPU-based non-bonded kernels
All 20 freeenergy tests PASSED
All 12 rotation tests PASSED
All 0 extra tests PASSED
All 7 essential dynamics tests PASSED

I would like your advice on whether the line about mdrun not using the requested number of ranks (near the end) is okay.

Thanks again,
Gregory

Hello Gregory,

the message with the number of ranks is just from the test script to tell you that the system is too small to run on all 8 ranks, so it will do it instead on a number that is known to work. So nothing to worry about.

Looks like all is fine, and the tests also worked well with the available GPU.

Cheers

Paul

Many thanks for your advice, Paul!