topic Re: Re:ifx: missing clang_rt.msan to link Fortran program in debug build type in Intel® Fortran Compiler

ifx: missing clang_rt.msan to link Fortran program in debug build type

MehdiChinoune — Fri, 13 Oct 2023 09:47:49 GMT

Since approximately 4 months my project started failing with debug build type:

[38/40] Linking Fortran shared library src/libtdcs_e_2e.so FAILED: src/libtdcs_e_2e.so : && /opt/intel/oneapi/compiler/2023.2.1/linux/bin/ifx -fPIC -warn all -stand f18 -standard-semantics -xHost -g -check all -fpe-all=0 -traceback -ipo -ipo -shared -nofor-main -Wl,-soname,libtdcs_e_2e.so -o src/libtdcs_e_2e.so src/CMakeFiles/tdcs_e_2e.dir/conhyp.F90.o src/CMakeFiles/tdcs_e_2e.dir/conhyp_h.F90.o src/CMakeFiles/tdcs_e_2e.dir/constants.F90.o src/CMakeFiles/tdcs_e_2e.dir/fdcs_e2e.F90.o src/CMakeFiles/tdcs_e_2e.dir/fdcs_e2e_h.F90.o src/CMakeFiles/tdcs_e_2e.dir/input.F90.o src/CMakeFiles/tdcs_e_2e.dir/input_h.F90.o src/CMakeFiles/tdcs_e_2e.dir/integration.F90.o src/CMakeFiles/tdcs_e_2e.dir/integration_h.F90.o src/CMakeFiles/tdcs_e_2e.dir/special_functions.F90.o src/CMakeFiles/tdcs_e_2e.dir/special_functions_h.F90.o src/CMakeFiles/tdcs_e_2e.dir/trigo.F90.o src/CMakeFiles/tdcs_e_2e.dir/trigo_h.F90.o src/CMakeFiles/tdcs_e_2e.dir/utils.F90.o src/CMakeFiles/tdcs_e_2e.dir/utils_h.F90.o && : ifx: warning #10182: disabling optimization; runtime debug checks enabled ld: cannot find -lclang_rt.msan: No such file or directory

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

Barbara_P_Intel — Fri, 13 Oct 2023 14:41:54 GMT

"-check all" includes "-check uninit". WIth ifx 2023.2.x "-check uninit" is enabled for the first time. "-check uninit" did nothing in earlier versions.

Do you have the HPC Toolkit installed? The toolkit includes the msan (LLVM memory sanitizer) libraries you need. If not, do that and try again.

If you have the HPC Toolkit installed, please run "echo $LIBRARY_PATH" and report it here.

If you are blocked from developing, "-check all,nouninit" is a workaround for you while we determine what the issue is in your environment.

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

MehdiChinoune — Fri, 13 Oct 2023 15:22:40 GMT

Yes, I am using HPC Toolkit through APT by installing

$ wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \ | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null $ echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list $ sudo apt update $ sudo apt install --no-install-recommends -y intel-oneapi-compiler-fortran $ source /opt/intel/oneapi/setvars.sh

echo $LIBRARY_PATH:

/opt/intel/oneapi/mpi/2021.10.0//libfabric/lib:/opt/intel/oneapi/mpi/2021.10.0//lib/release:/opt/intel/oneapi/mpi/2021.10.0//lib:/opt/intel/oneapi/compiler/2023.2.1/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/compiler/2023.2.1/linux/lib

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

Barbara_P_Intel — Fri, 13 Oct 2023 19:48:22 GMT

Thanks for the information!

I checked with the compiler developer who works on the uninitialized variable feature. He suggests removing /opt/intel/oneapi/compiler/2023.2.1/linux/compiler/lib/intel64_lin from LIBRARY_PATH. There is a known issue that might be related to what you are seeing.

Please let me know how that works for you.

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

MehdiChinoune — Sat, 14 Oct 2023 04:02:33 GMT

Removing /opt/intel/oneapi/compiler/2023.2.1/linux/compiler/lib/intel64_lin from LIBRARY_PATH (andLD_LIBRARY_PATH) doesn't fix the issue.

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

Barbara_P_Intel — Mon, 16 Oct 2023 14:04:45 GMT

Okay...

Can you please post a reproducer?

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

MehdiChinoune — Mon, 16 Oct 2023 15:11:37 GMT

This is my project https://github.com/MehdiChinoune/tdcs-e-2e

It uses CMake as a buildsystem.

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

Barbara_P_Intel — Mon, 16 Oct 2023 15:52:58 GMT

What OS are you using?

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

MehdiChinoune — Mon, 16 Oct 2023 16:48:29 GMT

Ubuntu 22.04 through GitHub Actions.

Re:ifx: missing clang_rt.msan to link Fortran program in debug build type

Barbara_P_Intel — Mon, 16 Oct 2023 18:51:33 GMT

Thank you for the OS info.

I should have been more specific. Do you have a minimal reproducer? For example, do you have the same linker problem with a "Hello World" program?

Re: Re:ifx: missing clang_rt.msan to link Fortran program in debug build type

MehdiChinoune — Mon, 16 Oct 2023 19:53:10 GMT

I will try to minimize it and post it later.

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

MehdiChinoune — Mon, 23 Oct 2023 12:12:08 GMT

A minimal reproducer:

main.f90

program test print*, "Hello" end program

$ echo "${LIBRARY_PATH}" /opt/intel/oneapi/mpi/2021.10.0//libfabric/lib:/opt/intel/oneapi/mpi/2021.10.0//lib/release:/opt/intel/oneapi/mpi/2021.10.0//lib:/opt/intel/oneapi/compiler/2023.2.1/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/compiler/2023.2.1/linux/lib $ LIBRARY_PATH="${LIBRARY_PATH/"/opt/intel/oneapi/compiler/2023.2.1/linux/compiler/lib/intel64 _lin"/}" $ echo "${LIBRARY_PATH}" /opt/intel/oneapi/mpi/2021.10.0//libfabric/lib:/opt/intel/oneapi/mpi/2021.10.0//lib/release:/opt/intel/oneapi/mpi/2021.10.0//lib::/opt/intel/oneapi/compiler/2023.2.1/linux/lib $ ifx -check all main.f90 ld: cannot find /opt/intel/oneapi/compiler/2023.2.1/linux/compiler/lib/intel64_lin/msan/for_main.o: No such file or directory ld: cannot find -lclang_rt.msan: No such file or directory

Re: ifx: missing clang_rt.msan to link Fortran program in debug build type

Ron_Green — Mon, 23 Oct 2023 21:20:12 GMT

-check all,nouninit

does fix the problem, correct?

Unfortunately the memory sanitizer files needed by ifx were packaged with our C++ compiler. If you install the dpc++/c++ compiler this will also fix the issue.

A point to keep in mind - if your application uses external libraries, like MKL or NetCDF, HDF5, Lapack, etc those libraries will have to be built with -check uninit or -fsanitize=memory with icx.

Probably easier to disable uninit for now. Even the 2024.0 version to be released soon has memory sanitizer problems. We have a redesign going into 2024.1, but that release is in the first quarter of 2024.

These new technologies are painful. but eventually we'll get it right.