GROMACS 2023.1 25 - CommandLineUnitTests (Failed)

User discussions
1

GROMACS version: 2023.1
GROMACS modification: None

No matter what parameters I use to build GROMACS, the regression test CommandLineUnitTests always fails at ParseCommonArgsTest.HandlesCompressedFiles.

Here is the error message:

[ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
/data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/src/gromacs/commandline/tests/pargs.cpp:416: Failure
Expected equality of these values:
expectedF
Which is: “/data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.pdb.gz/ParseCommonArgsTest_HandlesCompressedFiles.pdb”
opt2fn(“-f”, nfile(), fnm)
Which is: 0x744af8
/data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/src/gromacs/commandline/tests/pargs.cpp:417: Failure
Expected equality of these values:
expectedG
Which is: “/data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.gro.Z/ParseCommonArgsTest_HandlesCompressedFiles.gro”
opt2fn(“-g”, nfile(), fnm)
Which is: 0x745038
[ FAILED ] ParseCommonArgsTest.HandlesCompressedFiles (7 ms)

I cannot resolve this error. Does anyone have an idea how to solve this problem?
Thank you in advance for your help.

2

Hi!

It looks like an issue with our tests, but a bit hard to confirm since it appears to be very compiler/environment dependent.

Could you please try editing the /data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/src/gromacs/commandline/tests/pargs.cpp file, and replacing, in line 415:

    EXPECT_EQ(expectedF, opt2fn("-f", nfile(), fnm));
    EXPECT_EQ(expectedG, opt2fn("-g", nfile(), fnm));

with

    EXPECT_EQ(expectedF.u8string(), opt2fn("-f", nfile(), fnm));
    EXPECT_EQ(expectedG.u8string(), opt2fn("-g", nfile(), fnm));

?

If my suspicion is correct and the suggestion above helps, the problem is totally harmless, and we’ll fix our tests in 2023.2.

3

Hello!

First of all, thank you for the quick reply and solution.
Unfortunately, I still get an error message.

[RUN] ParseCommonArgsTest.HandlesCompressedFiles
/data/a/lore***/GROMACS/gromacs-2023.1/gromacs-2023.1/src/gromacs/commandline/tests/pargs.cpp:422: Failure
Expected equality of these values:
  expectedF.u8string()
    Which is: "/data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.pdb.gz/ParseCommonArgsTest_HandlesCompressedFiles.pdb"
  opt2fn("-f", nfile(), fnm)
    This is: "/data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.pdb"
/data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/src/gromacs/commandline/tests/pargs.cpp:423: Fails
Expected equality of these values:
  expectedG.u8string()
    Which is: "/data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.gro.Z/ParseCommonArgsTest_HandlesCompressedFiles.gro"
  opt2fn("-g", nfile(), fnm)
    This is: "/data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.gro"
[ FAILED ] ParseCommonArgsTest.HandlesCompressedFiles (6 ms)

Unfortunately that’s not it yet, does anyone have another idea?

I have added the following Debugcode:

std::cout << "expectedF: " << expectedF.u8string() << std::endl;
std::cout << "opt2fn(\"-f\", nfile(), fnm): " << opt2fn("-f", nfile(), fnm) << std::endl;
std::cout << "expectedG: " << expectedG.u8string() << std::endl;
std::cout << "opt2fn(\"-g\", nfile(), fnm): " << opt2fn("-g", nfile(), fnm) << std::endl;

Here are the output:

expectedF: /data/a/loret***/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.pdb.gz/ParseCommonArgsTest_HandlesCompressedFiles.pdb
opt2fn("-f", nfile(), fnm): /data/a/lore***/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.pdb
expectedG: /data/a/loret***/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.gro.Z/ParseCommonArgsTest_HandlesCompressedFiles.gro
opt2fn("-g", nfile(), fnm): /data/a/lore****/GROMACS/gromacs-2023.1/gromacs-2023.1/build_create_andy_gcc9ucx_nopme_hpcx/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_HandlesCompressedFiles.gro
4

Thanks for the verbose output. opt2fn produces the correct results; the reference data in our tests is getting messed up for some reason.

What version of the compiler and OS (and whatever else you think is relevant) are you using?

5

I use GNU 9.3.1 as C and CXX compiler and my OS is CentOS7.

Here are some details how I started the build process.
Maybe it helps.

source scl_source enable devtoolset-9
load module userspace/all
load module cuda/11.8 cmake/3.25.2
load module hwloc/2.9.1

export HWLOC_ROOT=/trinity/shared/apps/tr17.10/x86_64/hwloc-2.9.1
export LD_LIBRARY_PATH=$HWLOC_ROOT/lib:$LD_LIBRARY_PATH
export CPATH=$HWLOC_ROOT/include:$CPATH

export HPCX_HOME=/trinity/home/src/hpcx-v2.14-gcc-inbox-redhat7-cuda11-gdrcopy2-nccl2.16-x86_64
Source $HPCX_HOME/hpcx-init.sh
hpcx_load

cmake …
-DGMX_HWLOC_PREFIX=$HWLOC_ROOT
-DGMX_MPI=ON
-DGMX_FFT_LIBRARY=fftw3
-DGMX_BUILD_OWN_FFTW=ON
-DGMX_GPU=CUDA
-DCMAKE_BUILD_TYPE=release
-DGMX_DOUBLE=off
-DGMX_HWLOC=ON
-DREGRESSIONTEST_DOWNLOAD=ON

Thanks again for the effort.

6

Hi! We merged the fix. GROMACS 2023.2 (soon to be released) should be working fine.