OpenBLAS does not compile at Ubuntu 24.04

[Markus92]

Fresh Ubuntu 24.04 (Docker container) using Release 1.9.18.3 results in the following error:

[  3%] Performing configure step for 'OpenBLAS'
CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


CMake Warning at CMakeLists.txt:64 (message):
  CMake support is experimental.  It does not yet support all build options
  and may not produce the same Makefiles that OpenBLAS ships with.


CMake Warning (dev) at cmake/system_check.cmake:13 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "LINUX" will no longer be dereferenced when the
  policy is set to NEW.  Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  cmake/system.cmake:8 (include)
  CMakeLists.txt:67 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- GEMM multithread threshold set to 4.
-- Running getarch
-- GETARCH results:
CORE=UNKNOWN
LIBCORE=unknown
NUM_CORES=12
HAVE_MMX=1
HAVE_SSE=1
HAVE_SSE2=1
HAVE_SSE3=1
HAVE_SSSE3=1
HAVE_SSE4_1=1
HAVE_SSE4_2=1
HAVE_AVX=1
HAVE_AVX2=1
HAVE_FMA3=1
MAKE += -j 12

CMake Error at cmake/prebuild.cmake:525 (MESSAGE):
  Compiling getarch_2nd failed Change Dir:
  '/opt/minc_source/minc-toolkit-v2/build/OpenBLAS-build/getarch2_build/CMakeFiles/CMakeTmp'




  Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f
  Makefile cmTC_92781/fast

  gmake[3]: Entering directory
  '/opt/minc_source/minc-toolkit-v2/build/OpenBLAS-build/getarch2_build/CMakeFiles/CMakeTmp'


  /usr/bin/gmake -f CMakeFiles/cmTC_92781.dir/build.make
  CMakeFiles/cmTC_92781.dir/build

  gmake[4]: Entering directory
  '/opt/minc_source/minc-toolkit-v2/build/OpenBLAS-build/getarch2_build/CMakeFiles/CMakeTmp'


  Building C object CMakeFiles/cmTC_92781.dir/getarch_2nd.c.o

  /usr/bin/cc -fPIC -march=native -DGEMM_MULTITHREAD_THRESHOLD=4
  -DNO_PARALLEL_MAKE=0
  -I/opt/minc_source/minc-toolkit-v2/build/OpenBLAS-build/getarch2_build
  -I"/opt/minc_source/minc-toolkit-v2/build/OpenBLAS"
  -I"/opt/minc_source/minc-toolkit-v2/build/OpenBLAS-build" -o
  CMakeFiles/cmTC_92781.dir/getarch_2nd.c.o -c
  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c: In function
  ‘main’:

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:12:35: error:
  ‘SGEMM_DEFAULT_UNROLL_M’ undeclared (first use in this function); did
  you mean ‘XGEMM_DEFAULT_UNROLL_M’?

     12 |     printf("SGEMM_UNROLL_M=%d\n", SGEMM_DEFAULT_UNROLL_M);
        |                                   ^~~~~~~~~~~~~~~~~~~~~~
        |                                   XGEMM_DEFAULT_UNROLL_M

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:12:35: note:
  each undeclared identifier is reported only once for each function it
  appears in

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:13:35: error:
  ‘SGEMM_DEFAULT_UNROLL_N’ undeclared (first use in this function); did
  you mean ‘QGEMM_DEFAULT_UNROLL_N’?

     13 |     printf("SGEMM_UNROLL_N=%d\n", SGEMM_DEFAULT_UNROLL_N);
        |                                   ^~~~~~~~~~~~~~~~~~~~~~
        |                                   QGEMM_DEFAULT_UNROLL_N

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:14:35: error:
  ‘DGEMM_DEFAULT_UNROLL_M’ undeclared (first use in this function); did
  you mean ‘XGEMM_DEFAULT_UNROLL_M’?

     14 |     printf("DGEMM_UNROLL_M=%d\n", DGEMM_DEFAULT_UNROLL_M);
        |                                   ^~~~~~~~~~~~~~~~~~~~~~
        |                                   XGEMM_DEFAULT_UNROLL_M

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:15:35: error:
  ‘DGEMM_DEFAULT_UNROLL_N’ undeclared (first use in this function); did
  you mean ‘QGEMM_DEFAULT_UNROLL_N’?

     15 |     printf("DGEMM_UNROLL_N=%d\n", DGEMM_DEFAULT_UNROLL_N);
        |                                   ^~~~~~~~~~~~~~~~~~~~~~
        |                                   QGEMM_DEFAULT_UNROLL_N

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:19:35: error:
  ‘CGEMM_DEFAULT_UNROLL_M’ undeclared (first use in this function); did
  you mean ‘XGEMM_DEFAULT_UNROLL_M’?

     19 |     printf("CGEMM_UNROLL_M=%d\n", CGEMM_DEFAULT_UNROLL_M);
        |                                   ^~~~~~~~~~~~~~~~~~~~~~
        |                                   XGEMM_DEFAULT_UNROLL_M

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:20:35: error:
  ‘CGEMM_DEFAULT_UNROLL_N’ undeclared (first use in this function); did
  you mean ‘QGEMM_DEFAULT_UNROLL_N’?

     20 |     printf("CGEMM_UNROLL_N=%d\n", CGEMM_DEFAULT_UNROLL_N);
        |                                   ^~~~~~~~~~~~~~~~~~~~~~
        |                                   QGEMM_DEFAULT_UNROLL_N

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:21:35: error:
  ‘ZGEMM_DEFAULT_UNROLL_M’ undeclared (first use in this function); did
  you mean ‘XGEMM_DEFAULT_UNROLL_M’?

     21 |     printf("ZGEMM_UNROLL_M=%d\n", ZGEMM_DEFAULT_UNROLL_M);
        |                                   ^~~~~~~~~~~~~~~~~~~~~~
        |                                   XGEMM_DEFAULT_UNROLL_M

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:22:35: error:
  ‘ZGEMM_DEFAULT_UNROLL_N’ undeclared (first use in this function); did
  you mean ‘QGEMM_DEFAULT_UNROLL_N’?

     22 |     printf("ZGEMM_UNROLL_N=%d\n", ZGEMM_DEFAULT_UNROLL_N);
        |                                   ^~~~~~~~~~~~~~~~~~~~~~
        |                                   QGEMM_DEFAULT_UNROLL_N

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:69:50: error:
  ‘SGEMM_DEFAULT_Q’ undeclared (first use in this function)

     69 |     printf("#define SLOCAL_BUFFER_SIZE\t%ld\n", (SGEMM_DEFAULT_Q * SGEMM_DEFAULT_UNROLL_N * 4 * 1 *  sizeof(float)));
        |                                                  ^~~~~~~~~~~~~~~

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:70:50: error:
  ‘DGEMM_DEFAULT_Q’ undeclared (first use in this function)

     70 |     printf("#define DLOCAL_BUFFER_SIZE\t%ld\n", (DGEMM_DEFAULT_Q * DGEMM_DEFAULT_UNROLL_N * 2 * 1 *  sizeof(double)));
        |                                                  ^~~~~~~~~~~~~~~

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:71:50: error:
  ‘CGEMM_DEFAULT_Q’ undeclared (first use in this function)

     71 |     printf("#define CLOCAL_BUFFER_SIZE\t%ld\n", (CGEMM_DEFAULT_Q * CGEMM_DEFAULT_UNROLL_N * 4 * 2 *  sizeof(float)));
        |                                                  ^~~~~~~~~~~~~~~

  /opt/minc_source/minc-toolkit-v2/build/OpenBLAS/getarch_2nd.c:72:50: error:
  ‘ZGEMM_DEFAULT_Q’ undeclared (first use in this function)

     72 |     printf("#define ZLOCAL_BUFFER_SIZE\t%ld\n", (ZGEMM_DEFAULT_Q * ZGEMM_DEFAULT_UNROLL_N * 2 * 2 *  sizeof(double)));
        |                                                  ^~~~~~~~~~~~~~~

  gmake[4]: *** [CMakeFiles/cmTC_92781.dir/build.make:78:
  CMakeFiles/cmTC_92781.dir/getarch_2nd.c.o] Error 1

  gmake[4]: Leaving directory
  '/opt/minc_source/minc-toolkit-v2/build/OpenBLAS-build/getarch2_build/CMakeFiles/CMakeTmp'


  gmake[3]: *** [Makefile:127: cmTC_92781/fast] Error 2

  gmake[3]: Leaving directory
  '/opt/minc_source/minc-toolkit-v2/build/OpenBLAS-build/getarch2_build/CMakeFiles/CMakeTmp'




Call Stack (most recent call first):
  cmake/system.cmake:157 (include)
  CMakeLists.txt:67 (include)


-- Configuring incomplete, errors occurred!
make[2]: *** [CMakeFiles/OpenBLAS.dir/build.make:92: OpenBLAS-prefix/src/OpenBLAS-stamp/OpenBLAS-configure] Error 1
make[1]: *** [CMakeFiles/Makefile2:3094: CMakeFiles/OpenBLAS.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

Seems similar to #168

[gdevenyi]

Can you please provide the complete reproducible set of steps you did to reach this error.

[alicelema]

Hello, I have the same problem on a fresh WSL Ubuntu 24.04.2 LTS.
Here are the steps I have followed

sudo apt-get install \
 build-essential g++ bc \
 cmake \
 bison flex \
 libx11-dev x11proto-core-dev \
 libxi6 libxi-dev \
 libxmu6 libxmu-dev libxmu-headers \
 libgl1-mesa-dev libglu1-mesa-dev \
 libjpeg-dev

git clone --recursive --branch release-1.9.18 https://github.com/BIC-MNI/minc-toolkit-v2.git minc-toolkit-v2

cd minc-toolkit-v2

mkdir build && cd build

sudo apt install gfortran # Had a message error during the cmake first time, adding the 
fortran compiler worked

cmake ..

make

And the build breaks here with the same error posted by @Markus92 .

I'm new to MRI and C compiling, In the documentation I did not understand if I had to do the second cmake command as it seemed redundant, but I may be mistaken :

 cmake .. \
-DCMAKE_BUILD_TYPE:STRING=Release   \
-DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.18 \
-DMT_BUILD_ABC:BOOL=ON   \
-DMT_BUILD_ANTS:BOOL=ON   \
-DMT_BUILD_C3D:BOOL=ON   \
-DMT_BUILD_ELASTIX:BOOL=ON   \
-DMT_BUILD_IM:BOOL=OFF   \
-DMT_BUILD_ITK_TOOLS:BOOL=ON   \
-DMT_BUILD_LITE:BOOL=OFF   \
-DMT_BUILD_SHARED_LIBS:BOOL=ON   \
-DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
-DMT_USE_OPENMP:BOOL=ON   \
-DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
-DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
-DUSE_SYSTEM_GLUT:BOOL=OFF   \
-DUSE_SYSTEM_GSL:BOOL=OFF   \
-DUSE_SYSTEM_HDF5:BOOL=OFF   \
-DUSE_SYSTEM_ITK:BOOL=OFF   \
-DUSE_SYSTEM_NETCDF:BOOL=OFF   \
-DUSE_SYSTEM_NIFTI:BOOL=OFF   \
-DUSE_SYSTEM_PCRE:BOOL=OFF   \
-DUSE_SYSTEM_ZLIB:BOOL=OFF 

I then also tried with the above command, which gave me a different error (Which I will describe in another issue to not go out of the scope of this issue).

[gdevenyi]

As per the original thread #168 the packages from https://bic-mni.github.io/ or https://github.com/gdevenyi/NeuroAnsible are also options for installing things.

Based on the original thread, it looks like you probably have a "too new" CPU or "too new" compiler the current version of OpenBLAS doens't support for building against. We will need to investigate upgrading OpenBLAS when we have time.

[vfonov]

Temporary solution is to build without OpenBLAS support. It is not actually used in many programs. The version that I build for the conda is compiled without OpenBLAS.

[alicelema]

Thank you for the answers. I have managed to install MINC on a virtual machine (ubuntu 20.04) what seems to work instead of WSL.

[Markus92]

My solution was to link to system OpenBLAS and use Ubuntu 22.04. Following commands worked to generate a Singularity container.

Bootstrap: docker
From: ubuntu:22.04

%post
    export DEBIAN_FRONTEND=noninteractive
    apt-get update && apt-get install -y \
        build-essential g++ bc \
        cmake \
        bison flex \
        libx11-dev x11proto-core-dev \
        libxi6 libxi-dev \
        libxrandr-dev libxxf86vm-dev \
        libxmu6 libxmu-dev libxmu-headers \
        libgl1-mesa-dev libglu1-mesa-dev \
        libjpeg-dev \
        git gfortran \
        libopenblas-dev \
        liblapacke-dev \
        && rm -rf /var/lib/apt/lists/*

    mkdir -p /opt/minc_source
    cd /opt/minc_source
    git clone --recursive --branch release-1.9.18 https://github.com/BIC-MNI/minc-toolkit-v2.git minc-toolkit-v2
    cd minc-toolkit-v2
    mkdir build && cd build

    cmake .. \
    -DCMAKE_BUILD_TYPE:STRING=Release   \
    -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.18 \
    -DMT_BUILD_ABC:BOOL=ON   \
    -DMT_BUILD_ANTS:BOOL=ON   \
    -DMT_BUILD_C3D:BOOL=ON   \
    -DMT_BUILD_ELASTIX:BOOL=ON   \
    -DMT_BUILD_IM:BOOL=OFF   \
    -DMT_BUILD_ITK_TOOLS:BOOL=ON   \
    -DMT_BUILD_LITE:BOOL=OFF   \
    -DMT_BUILD_SHARED_LIBS:BOOL=ON   \
    -DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
    -DMT_BUILD_OPENBLAS:BOOL=OFF \
    -DMT_USE_OPENMP:BOOL=ON   \
    -DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
    -DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
    -DUSE_SYSTEM_GLUT:BOOL=OFF   \
    -DUSE_SYSTEM_GSL:BOOL=OFF   \
    -DUSE_SYSTEM_HDF5:BOOL=OFF   \
    -DUSE_SYSTEM_ITK:BOOL=OFF   \
    -DUSE_SYSTEM_NETCDF:BOOL=OFF   \
    -DUSE_SYSTEM_NIFTI:BOOL=OFF   \
    -DUSE_SYSTEM_PCRE:BOOL=OFF   \
    -DUSE_SYSTEM_ZLIB:BOOL=OFF

    make -j$(nproc) && make install