Issues running tutorial

[flbrandao]

Hi, I am trying to test the code. After installing it with no issues at a given cluster, I trying to follow the "cavity" tutorial. When executing the command "flexi parameter_flexi.ini" this is the output:

| Reading from file "parameter_flexi.ini":
Segmentation fault (core dumped)

No idea what is wrong. Do I need to execute any other command before "flexi parameter_flexi.ini"?

Thanks,
Filipe

[flexi-framework]

Hello flbrandao and thanks for checking out FLEXI!

No further commands are necessary to run FLEXI, the output Readin from file ... is the first line printed when initializing a simulation. As it crashes immediately, have the unit tests passed, which are executed at the end of the compilation?

And can you give us more information on your software stack, i.e. OS, compiler suite, versions of MPI and HDF5, etc.?

[flbrandao]

These are what I am using:

compiler/intel/2023.1.0
mpi/openmpi/4.1.5
cmake/4.2.4.intel2025

Regarding HDF5, I believe it comes from FLEXI no? This is what the cmake commands result:

$ cmake -B build --preset cavity
-- This is FLEXI (v25.10)
-- Generating with [cmake] (v4.2.4)
-- Checking git origin: https://github.com/flexi-framework/flexi.git
-- Generating for [Unix Makefiles] build system
-- Compiling on generic Linux 4.18.0-553.123.1.el8_10.x86_64 machine
-- Compiling with [IntelLLVM] (v2023.1.0) fortran compiler using [-xHost] instruction
-- Compiling with [release] build type
-- [MPI] not found in system libraries
-- Setting [HDF5] to self-build
-- Setting [HDF5] download link: https://github.com/HDFGroup/hdf5.git
-- Setting [HDF5] download tag: hdf5_1.14.5
-- Compiling with self-built [HDF5] (v1.14.5) without parallel support
-- [BLAS/Lapack] found in system libraries
-- Compiling with system [BLAS/Lapack]
-- [OpenMP] not found in system libraries
-- Compiling with [OpenMP] (v5.0)
-- Executing unit tests with 184 processes
-- Posti: building visu tool.
-- Configuring done (27.4s)
-- Generating done (0.9s)
-- Build files have been written to: /flexi/build

$ cmake --build build
[ 1%] Updating commit header with current git commit
[ 1%] Built target UpdateGitCommitHash
[ 2%] Built target stacksizelib
[ 70%] Built target libflexistaticF90
[ 71%] Built target libflexistatic
[ 71%] Built target generateUserblock
[ 72%] Building C object CMakeFiles/userblocklib.dir/bin/print_userblock.c.o
[ 73%] Linking C static library lib64/libuserblocklib.a
[ 73%] Built target userblocklib
[ 74%] Building Fortran object CMakeFiles/libflexishared.dir/src/flexilib.f90.o
[ 74%] Linking Fortran shared library lib64/libflexi.so
SUCCESS: LIBFLEXISHARED BUILD COMPLETE!
[ 74%] Built target libflexishared
[ 75%] Linking Fortran executable unitTests/bin/ReadInTools
[ 75%] Built target ReadInTools
[ 76%] Linking Fortran executable unitTests/bin/NodesAndWeights
[ 76%] Built target NodesAndWeights
[ 76%] Linking Fortran executable unitTests/bin/Vandermonde
[ 77%] Built target Vandermonde
[ 77%] Linking Fortran executable unitTests/bin/DerivativeMatrix
[ 78%] Built target DerivativeMatrix
[ 79%] Linking Fortran executable unitTests/bin/ChangeBasis
[ 79%] Built target ChangeBasis
[ 79%] Linking Fortran executable unitTests/bin/SurfInt
[ 80%] Built target SurfInt
[ 81%] Linking Fortran executable unitTests/bin/ProlongToFace
[ 82%] Built target ProlongToFace
[ 83%] Linking Fortran executable unitTests/bin/MatrixInverse
[ 84%] Built target MatrixInverse
Run unit tests
Test project /flexi/build
Start 8: MatrixInverse
Start 3: Vandermonde
Start 1: ReadInTools
Start 5: ChangeBasis
Start 7: ProlongToFace
Start 6: SurfInt
Start 4: DerivativeMatrix
Start 2: NodesAndWeights
1/8 Test #4: DerivativeMatrix ................. Passed 0.15 sec
2/8 Test #2: NodesAndWeights .................. Passed 0.15 sec
3/8 Test #3: Vandermonde ...................... Passed 0.16 sec
4/8 Test #5: ChangeBasis ...................... Passed 0.16 sec
5/8 Test #7: ProlongToFace .................... Passed 0.16 sec
6/8 Test #6: SurfInt .......................... Passed 0.16 sec
7/8 Test #1: ReadInTools ...................... Passed 0.20 sec
8/8 Test #8: MatrixInverse .................... Passed 0.25 sec

100% tests passed, 0 tests failed out of 8

Total Test time (real) = 0.26 sec
[ 84%] Built target all_tests
[ 85%] Linking Fortran executable bin/flexi
SUCCESS: FLEXI BUILD COMPLETE!
[ 86%] Built target flexi
[ 86%] Built target target_libposti
[ 88%] Built target libposti
[ 88%] Built target visutarget
[ 98%] Built target visulibF90
[ 98%] Built target visulib
[ 99%] Linking Fortran executable bin/posti_visu
SUCCESS: POSTI_VISU BUILD COMPLETE!
[100%] Built target posti_visu

[flexi-framework]

Ok, thanks for the output info.

The unit tests pass and HDF5 is indeed built by FLEXI, which happens if HDF5 is misconfigured or not installed on the system.

It seems, however, that OpenMPI is not picked up properly. Have you tried using another version or implementation (like IntelMPI)?
On some clusters, we had to set the MPI compiler wrappers explicitly, as MPI_C_COMPILER in the LUMI section of cmake/SetLibraries.txt, or via environment variables (see e.g. MPICC in .docker/fedora_42/intel/dockerfile).

And does the problem persist if you use another build type, like Debug or RelWithDebInfo?

[flbrandao]

Which debug flag should I use?

--debug-trycompile = Do not delete the try_compile build tree.
Only useful on one try_compile at a time.
--debug-output = Put cmake in a debug mode.
--debug-find = Put cmake find in a debug mode.
--debug-find-pkg=[,...]
= Limit cmake debug-find to the
comma-separated list of packages
--debug-find-var=[,...]
= Limit cmake debug-find to the
comma-separated list of result variables

[flexi-framework]

We were referring to the FLEXI-specific flag -DCMAKE_BUILD_TYPE=Debug or -DCMAKE_BUILD_TYPE=RelWithDebInfo, which sets compiler optimizations (first option in the ccmake interface). These build types should only be used for developing / testing, the default for production runs is Release.