JIT error on use of fabs with Serial/OpenMP thread models

[inducer]

Hi all,

I'm trying to run https://github.com/paranumal/libparanumal/ (for comparison purposes), and I'm not having a lot of luck. I updated the occa submodule in that repository, which got things building, but then if I run cnsMain (with the OpenMP and Serial thread models) in that repository, JIT compilation fails with a message like this:

terminate called after throwing an instance of 'occa::exception'
  what():
---[ Error ]--------------------------------------------------------------------
    File     : /home/andreas/pack/libparanumal/occa/src/occa/internal/modes/serial/device.cpp
    Line     : 378
    Function : operator()
    Message  : Error compiling [dopri5RkUpdate], Command: [g++ -O3 -g -std=c++11 -fPIC -shared /home/andreas/pack/libparanumal/.occa/cache/8e85837b18a49ef3/timeStepperDOPRI5.source.cpp -o /home/andreas/pack/libparanumal/.occa/cache/8e85837b18a49ef3/30c66ce7502e401b.binary  2>&1]
               Output:

               /home/andreas/pack/libparanumal/.occa/cache/8e85837b18a49ef3/timeStepperDOPRI5.source.cpp: In function ‘void dopri5ErrorEstimate(const int&, const double&, const double&, const double*, const double*, const double*, double*)’:
               /home/andreas/pack/libparanumal/.occa/cache/8e85837b18a49ef3/timeStepperDOPRI5.source.cpp:120:27: error: ‘fabs’ was not declared in this scope
                 120 |         const double qn = fabs(q[id]);
                     |                           ^~~~

    Stack
      15 occa::error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
      14 /home/andreas/pack/libparanumal/occa/lib/libocca.so(+0x2955fd)
      13 /home/andreas/pack/libparanumal/occa/lib/libocca.so(+0x295b0c)
      12 occa::io::stageFiles(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool, std::function<bool (std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)>)
      11 occa::io::stageFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::function<bool (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)>)
      10 occa::serial::device::buildKernel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, occa::hash_t, occa::json const&, bool)
       9 occa::serial::device::buildKernel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, occa::hash_t, occa::json const&)
       8 occa::device::buildKernel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, occa::json const&) const
       7 ./cnsMain(+0x290bab)
       6 ./cnsMain(+0x6971d)
       5 ./cnsMain(+0x5966e)
       4 ./cnsMain(+0x392f1)
       3 /lib/x86_64-linux-gnu/libc.so.6(+0x29ca8)
       2 /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85)
       1 ./cnsMain(+0x39e01)
================================================================================

I found #577 which seems related, but I couldn't quite figure out either why this was failing or what to do next. Here's my compiler info in case it's relevant:

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-19)

[noelchalmers]

I think the main branch of libParanumal uses an older occa submodule, and updating to the later release breaks some things because of some occa changes (in your case the missing fabs is because the cmath headers arent included by default anymore).

Give this branch a shot: https://github.com/paranumal/libparanumal/tree/development
Probably should just merge that into main and tag a new release.

[inducer]

Thanks! The development branch worked.

Probably should just merge that into main and tag a new release.

I realize I have zero say in this, but that sounds like a good idea. 🙂

[kris-rowe]

In v1.6 a flag was added for including C headers that were automatically added previously when using Serial mode (OpenMP inherits from this at the moment).

Apologies as I don't think this was well documented in the release notes.