Compiling GraphBLAS fails with `C11 atomics: failed`

[e-eight]

Describe the bug I am trying to compile SuiteSparse-7.7.0. Running cmake .. from the build directory fails at the Building SuiteSparse:GraphBLAS version: v9.1.0, date: Mar 22, 2024 step with the following error:

-- Performing Test TEST_FOR_STDATOMIC
-- Performing Test TEST_FOR_STDATOMIC - Failed
-- Performing Test TEST_FOR_STDATOMIC_WITH_LIBATOMIC
-- Performing Test TEST_FOR_STDATOMIC_WITH_LIBATOMIC - Failed
CMake Error at GraphBLAS/cmake_modules/SuiteSparseAtomic.cmake:53 (message):
  C11 atomics: failed
Call Stack (most recent call first):
  GraphBLAS/CMakeLists.txt:426 (include)

To Reproduce Run cmake .. from the build directory.

Expected behavior Expected the GraphBLAS module to compile

Screenshots

Desktop (please complete the following information):

• OS: CentOS 7
• compiler: gcc 8.3
• BLAS and LAPACK library, if applicable: OpenBLAS
• Version 7.7.0

Additional context Trying to install this on a cluster.

[mmuetzel]

Could you please run cmake --fresh .. | tee cmake_config.log and upload that .log file here?

[e-eight]

Here is the log file. cmake_config.log

[DrTimothyAldenDavis]

Is there any way to get the output of the tests? It is in the GraphBLAS/cmake_modules/SuiteSparseAtomic.cmake file. GraphBLAS requires ANSI C11 support for atomic operations.

Try compiling this outside of the build system, with the compiler you used:

    // gcc, clang, icx, xlc, etc: see if -latomic is required
    #include <stdatomic.h>
    #include <stdint.h>
    int main (void)
    {
        _Atomic uint8_t t8 = 0 ;
        uint8_t e8 = 0, d8 = 0 ;
        atomic_compare_exchange_weak (&t8, &e8, d8) ;
        _Atomic uint16_t t16 = 0 ;
        uint16_t e16 = 0, d16 = 0 ;
        atomic_compare_exchange_weak (&t16, &e16, d16) ;
        _Atomic uint32_t t32 = 0 ;
        uint32_t e32 = 0, d32 = 0 ;
        atomic_compare_exchange_weak (&t32, &e32, d32) ;
        _Atomic uint64_t t64 = 0 ;
        uint64_t e64 = 0, d64 = 0 ;
        atomic_compare_exchange_weak (&t64, &e64, d64) ;
        return (0) ;
    }

Then try it with just gcc and then with gcc -latomic.

[DrTimothyAldenDavis]

gcc 8.3 is pretty old. That might be the problem.

[mmuetzel]

Thank you for the log.

It looks like you are building SuiteSparse with NVidia HPC (not with GCC).

Do you have the GCC Development Tools installed? See, e.g., https://forums.developer.nvidia.com/t/error-while-loading-shared-libraries-libatomic-so-1/213810

[DrTimothyAldenDavis]

It looks like you are building SuiteSparse with NVidia HPC (not with GCC).

Good catch -- I didn't notice that. I've never tried that compiler. It may also affect GraphBLAS later on.

GraphBLAS has an internal JIT that (by default) uses the same compiler used to compile GraphBLAS. It should configure itself properly once GraphBLAS is compiled correctly (see the SuiteSparse/GraphBLAS/Config/GB_config.h file), but you're in uncharted waters with that compiler. It's possible that could fail as well. Once you are able to compile GraphBLAS, try the demos and look at their raw output (build/gauss_demo.out and build/wildtype.out). If you run wildtype_demo again with

./build/wildtype_demo

the output should say "jit: cpu load" about 6 times. That would indicate that the first run of ./build/wild_type successfully compiled 6 JIT kernels and placed them in your ~/.SuiteSparse/GrB* folder, and then was able to simply load them the 2nd time you ran the demo.

[e-eight]

Thanks for the suggestions. Figured out what the problem was. I had some CUDA modules loaded, which automatically set CC, CXX, and FC to point to the NVidia compilers. After I disabled those, it still didn't build, because CMake then picked up an even older compiler, GCC 4.8.5.

Setting the CC, CXX, and FC variables to point to the GCC 8.3.0 compilers did the trick. Also had to add the path to the NVidia compilers to PATH so that CMake detects a CUDA compiler. The CMake part of the process works now.

[DrTimothyAldenDavis]

So can we close this issue now?

[e-eight]

Yes, please. Thanks again for all the help.