Build Failure with intel-oneapi-compilers using spack

[vijaymocherla]

Hi,

I encountered a build error while attempting to build SIRIUS using Spack on Ubuntu 22.04 with the oneapi. The error seems related to the splindex_iterator_t class, where the member idx is not recognized, and it suggests idx_ instead. Notably, this issue does not occur when using GCC or other compilers. It appears to be specific to the Intel compilers.

90     In file included from /tmp/vijay/spack-stage/spack-stage-sirius-develop-aipxlrstv3lm6oamzjk5ptdlzd2lagkq/spack-src/src/hamiltonian/local_operator.cpp:14:
     91     In file included from /tmp/vijay/spack-stage/spack-stage-sirius-develop-aipxlrstv3lm6oamzjk5ptdlzd2lagkq/spack-src/src/hamiltonian/local_operator.hpp:18:
     92     In file included from /tmp/vijay/spack-stage/spack-stage-sirius-develop-aipxlrstv3lm6oamzjk5ptdlzd2lagkq/spack-src/src/core/fft/fft.hpp:18:
  >> 93     /tmp/vijay/spack-stage/spack-stage-sirius-develop-aipxlrstv3lm6oamzjk5ptdlzd2lagkq/spack-src/src/core/splindex.hpp:268:48: error: no member named 'idx' in '
            splindex_iterator_t<Index_t>'; did you mean 'idx_'?
     94       268 |         splindex_iterator_t<Index_t> tmp(this->idx());
     95           |                                                ^~~
     96           |                                                idx_

To reproduce the error use:

spack install --add sirius%oneapi@2025.0.4 ^intel-oneapi-mkl ^eigen ^libvdwxc ^libxc@7.0.0 ^wannier90

Error output:

error.txt

[toxa81]

Dear @vijaymocherla
you are hitting an interesting bug that was never captured by our CI/CD. Which compiler are you using? It generates a call to a code that other compilers avoid.

[toxa81]

this compiles for me #1046

[vijaymocherla]

@toxa81 I'm using the newer clang based intel oneapi compilers icx,icpx and ifx.

If am not wrong intel has mostly stopped supporting the older classic compilers icc, icpc and ifort.

[toxa81]

@vijaymocherla can you test the fixed version? For that, you need to create a directory with spack.yaml environment file

spack:
  specs:
    - sirius@develop %oneapi@2025.0.4 ^intel-oneapi-mkl ^eigen ^libvdwxc ^libxc@7.0.0 ^wannier90
  view: true
  concretizer:
    unify: true
    reuse: true
  develop:
    sirius:
      spec: sirius@develop
      path: /path/to/SIRIUS

checkout SIRIUS cod, switch to fix/splindex_iterator branch, and then run the following commands in the directory with spack.yaml file: spack -e . concretize -f, spack -e . install

[mkrack]

A build of the CP2K toolchain with SIRIUS included using Intel oneAPI 2025 instead of 2024 fails because of the issue described above. After applying the fix fix/splindex_interator a new build error appears

Stack dump:
0.	Program arguments: /opt/intel/oneapi/compiler/2025.0/bin/compiler/clang++ @/tmp/icpx0985981021bDu3Qx/icpxargLlq1tw
1.	<eof> parser at end of file
2.	Optimizer
3.	Running pass "require<globals-aa>,function(invalidate<aa>),require<profile-summary>,cgscc(inline,function(tbaa-prop)),cgscc()" on module "/home/krack/github/mkrack/intel/cp2k/tools/toolchain/build/SIRIUS-7.6.1/src/hamiltonian/local_operator.cpp"
4.	Running pass "cgscc(inline,function(tbaa-prop))" on module "/home/krack/github/mkrack/intel/cp2k/tools/toolchain/build/SIRIUS-7.6.1/src/hamiltonian/local_operator.cpp"
 #0 0x000055b2a029ae37 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x606ee37)
 #1 0x000055b2a0299b94 llvm::sys::RunSignalHandlers() (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x606db94)
 #2 0x000055b2a0246865 (anonymous namespace)::CrashRecoveryContextImpl::HandleCrash(int, unsigned long) CrashRecoveryContext.cpp:0:0
 #3 0x000055b2a0246a7d CrashRecoverySignalHandler(int) CrashRecoveryContext.cpp:0:0
 #4 0x00001506664b6910 __restore_rt (/lib64/libpthread.so.0+0x16910)
 #5 0x000055b29f530fb0 llvm::vpo::VPOUtils::enclosingBeginDirective(llvm::Instruction*, llvm::DominatorTree*) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x5304fb0)
 #6 0x000055b2a0322213 hoistCalleeEntryBlockAllocas(llvm::BasicBlock*)::$_0::operator()(llvm::AllocaInst*, llvm::DominatorTree*) const InlineFunction.cpp:0:0
 #7 0x000055b29f4a44c3 hoistCalleeEntryBlockAllocas(llvm::BasicBlock*) InlineFunction.cpp:0:0
 #8 0x000055b29e477f5d llvm::InlineFunction(llvm::CallBase&, llvm::InlineFunctionInfo&, llvm::InlineReport*, llvm::InlineReportBuilder*, bool, llvm::AAResults*, bool, llvm::Function*) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x424bf5d)
 #9 0x000055b29e649ce9 llvm::InlinerPass::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager<llvm::LazyCallGraph::SCC, llvm::LazyCallGraph&>&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x441dce9)
#10 0x000055b29e649151 llvm::detail::PassModel<llvm::LazyCallGraph::SCC, llvm::InlinerPass, llvm::AnalysisManager<llvm::LazyCallGraph::SCC, llvm::LazyCallGraph&>, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager<llvm::LazyCallGraph::SCC, llvm::LazyCallGraph&>&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) PassBuilder.cpp:0:0
#11 0x000055b29eada4bc llvm::PassManager<llvm::LazyCallGraph::SCC, llvm::AnalysisManager<llvm::LazyCallGraph::SCC, llvm::LazyCallGraph&>, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager<llvm::LazyCallGraph::SCC, llvm::LazyCallGraph&>&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x48ae4bc)
#12 0x000055b29eada051 llvm::detail::PassModel<llvm::LazyCallGraph::SCC, llvm::PassManager<llvm::LazyCallGraph::SCC, llvm::AnalysisManager<llvm::LazyCallGraph::SCC, llvm::LazyCallGraph&>, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>, llvm::AnalysisManager<llvm::LazyCallGraph::SCC, llvm::LazyCallGraph&>, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager<llvm::LazyCallGraph::SCC, llvm::LazyCallGraph&>&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) PassBuilder.cpp:0:0
#13 0x000055b29ead8b03 llvm::ModuleToPostOrderCGSCCPassAdaptor::run(llvm::Module&, llvm::AnalysisManager<llvm::Module>&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x48acb03)
#14 0x000055b29ead7eb1 llvm::detail::PassModel<llvm::Module, llvm::ModuleToPostOrderCGSCCPassAdaptor, llvm::AnalysisManager<llvm::Module>>::run(llvm::Module&, llvm::AnalysisManager<llvm::Module>&) PassBuilder.cpp:0:0
#15 0x000055b29e6bec99 llvm::PassManager<llvm::Module, llvm::AnalysisManager<llvm::Module>>::run(llvm::Module&, llvm::AnalysisManager<llvm::Module>&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4492c99)
#16 0x000055b29e8f9faf llvm::ModuleInlinerWrapperPass::run(llvm::Module&, llvm::AnalysisManager<llvm::Module>&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x46cdfaf)
#17 0x000055b29e8f9c11 llvm::detail::PassModel<llvm::Module, llvm::ModuleInlinerWrapperPass, llvm::AnalysisManager<llvm::Module>>::run(llvm::Module&, llvm::AnalysisManager<llvm::Module>&) PassBuilder.cpp:0:0
#18 0x000055b29e6bec99 llvm::PassManager<llvm::Module, llvm::AnalysisManager<llvm::Module>>::run(llvm::Module&, llvm::AnalysisManager<llvm::Module>&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4492c99)
#19 0x000055b29eea3b22 (anonymous namespace)::EmitAssemblyHelper::RunOptimizationPipeline(clang::BackendAction, std::__1::unique_ptr<llvm::raw_pwrite_stream, std::__1::default_delete<llvm::raw_pwrite_stream>>&, std::__1::unique_ptr<llvm::ToolOutputFile, std::__1::default_delete<llvm::ToolOutputFile>>&, clang::BackendConsumer*) BackendUtil.cpp:0:0
#20 0x000055b29eb20f03 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem>, std::__1::unique_ptr<llvm::raw_pwrite_stream, std::__1::default_delete<llvm::raw_pwrite_stream>>, clang::BackendConsumer*) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x48f4f03)
#21 0x000055b29e608a02 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x43dca02)
#22 0x000055b29e33326a clang::ParseAST(clang::Sema&, bool, bool) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x410726a)
#23 0x000055b29e689a7c clang::CodeGenAction::ExecuteAction() (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x445da7c)
#24 0x000055b29f05507e clang::FrontendAction::Execute() (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4e2907e)
#25 0x000055b29f054bc1 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4e28bc1)
#26 0x000055b29e806305 clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x45da305)
#27 0x000055b29ef93cab cc1_main(llvm::ArrayRef<char const*>, char const*, void*) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4d67cab)
#28 0x000055b29e89e8ac ExecuteCC1Tool(llvm::SmallVectorImpl<char const*>&, llvm::ToolContext const&) driver.cpp:0:0
#29 0x000055b2a0963bfd void llvm::function_ref<void ()>::callback_fn<clang::driver::CC1Command::Execute(llvm::ArrayRef<std::__1::optional<llvm::StringRef>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>*, bool*) const::$_0>(long) Job.cpp:0:0
#30 0x000055b29f1afd56 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref<void ()>) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4f83d56)
#31 0x000055b29f1afe7e clang::driver::CC1Command::Execute(llvm::ArrayRef<std::__1::optional<llvm::StringRef>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>*, bool*) const (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4f83e7e)
#32 0x000055b29f2116ad clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4fe56ad)
#33 0x000055b29f2112f7 clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*>>&, bool) const (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4fe52f7)
#34 0x000055b29f210670 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*>>&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4fe4670)
#35 0x000055b29ef96690 clang_main(int, char**, llvm::ToolContext const&) (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x4d6a690)
#36 0x000055b29eb1c049 main (/opt/intel/oneapi/compiler/2025.0/bin/compiler/clang+++0x48f0049)
#37 0x00001506662de24d __libc_start_main /usr/src/debug/glibc-2.31-150300.63.1.x86_64/csu/../csu/libc-start.c:342:0
#38 0x000055b29f6a837e _start /export/project/tools-build/toolchain-cross/src/glibc/csu/../sysdeps/x86_64/start.S:122:0
icpx: error: clang frontend command failed with exit code 139 (use -v to see invocation)
Intel(R) oneAPI DPC++/C++ Compiler 2025.0.4 (2025.0.4.20241205)
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /opt/intel/oneapi/compiler/2025.0/bin/compiler
Configuration file: /opt/intel/oneapi/compiler/2025.0/bin/compiler/../icpx.cfg
icpx: note: diagnostic msg: 
********************

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
icpx: note: diagnostic msg: /tmp/icpx-a4ea21354a/local_operator-a0b8bd.cpp
icpx: note: diagnostic msg: /tmp/icpx-a4ea21354a/local_operator-a0b8bd.sh
icpx: note: diagnostic msg: 

********************
make[2]: *** [src/CMakeFiles/sirius_cxx.dir/build.make:110: src/CMakeFiles/sirius_cxx.dir/hamiltonian/local_operator.cpp.o] Error 1
make[2]: Leaving directory '/home/krack/github/mkrack/intel/cp2k/tools/toolchain/build/SIRIUS-7.6.1/build'
make[1]: *** [CMakeFiles/Makefile2:250: src/CMakeFiles/sirius_cxx.dir/all] Error 2
make[1]: Leaving directory '/home/krack/github/mkrack/intel/cp2k/tools/toolchain/build/SIRIUS-7.6.1/build'
make: *** [Makefile:139: all] Error 2

[mtaillefumier]

my guess is that It is a compiler bug.

[mkrack]

my guess is that It is a compiler bug.

Well, yes, that's possible. That is why we still stick to Intel oneAPI 2024 with CP2K for the time being. If it is a compiler bug, it would make sense if that bug would be filed from the SIRIUS developer team.

[vijaymocherla]

@toxa81 The build still fails for me. But, now its due to the libvdwxc dependency.

Here's the error output:

==> Error: ProcessError: Command exited with status 2:
    '/apps/spack/opt/spack/linux-ubuntu24.04-skylake/gcc-13.3.0/gmake-4.4.1-oq5nw7wuwzvhrs2ceed6dxdlrtzm44vb/bin/make' '-j16' 'V=1'

4 errors found in build log:
     243    libtool: compile:  /tmp/sai/spack-stage/spack-stage-libvdwxc-0.4.0-3k5
            mksugf2e2tom3ndzfehkd6uupcusx/spack-src/config/wrappers/wrap-mpicc -DH
            AVE_CONFIG_H -I. -I.. -O2 -MT vdw_kernel.lo -MD -MP -MF .deps/vdw_kern
            el.Tpo -c vdw_kernel.c -o vdw_kernel.o >/dev/null 2>&1
     244    mv -f .deps/vdw_kernel.Tpo .deps/vdw_kernel.Plo
     245    /bin/bash ../libtool  --tag=CC   --mode=link /tmp/sai/spack-stage/spac
            k-stage-libvdwxc-0.4.0-3k5mksugf2e2tom3ndzfehkd6uupcusx/spack-src/conf
            ig/wrappers/wrap-mpicc  -O2   -o libvdwxc.la -rpath /apps/spack/opt/sp
            ack/linux-ubuntu24.04-skylake/oneapi-2025.0.4/libvdwxc-0.4.0-3k5mksugf
            2e2tom3ndzfehkd6uupcusx/lib vdw_kernel.lo vdw_core.lo vdw_q0.lo vdw_mp
            i.lo   -lfftw3_mpi -lfftw3 -lm
     246    libtool: link: /tmp/sai/spack-stage/spack-stage-libvdwxc-0.4.0-3k5mksu
            gf2e2tom3ndzfehkd6uupcusx/spack-src/config/wrappers/wrap-mpicc -shared
              -fPIC -DPIC  .libs/vdw_kernel.o .libs/vdw_core.o .libs/vdw_q0.o .lib
            s/vdw_mpi.o   -lfftw3_mpi -lfftw3 -lm  -O2   -Wl,-soname -Wl,libvdwxc.
            so.0 -o .libs/libvdwxc.so.0.0.0
     247    /usr/bin/ld: /usr/local/lib/libfftw3_mpi.a(api.o): relocation R_X86_64
            _32S against `.text' can not be used when making a shared object; reco
            mpile with -fPIC
     248    /usr/bin/ld: failed to set dynamic section sizes: bad value
  >> 249    icx: error: linker command failed with exit code 1 (use -v to see invo
            cation)
  >> 250    make[2]: *** [Makefile:526: libvdwxc.la] Error 1
     251    make[2]: Leaving directory '/tmp/sai/spack-stage/spack-stage-libvdwxc-
            0.4.0-3k5mksugf2e2tom3ndzfehkd6uupcusx/spack-src/src'
  >> 252    make[1]: *** [Makefile:545: all-recursive] Error 1
     253    make[1]: Leaving directory '/tmp/sai/spack-stage/spack-stage-libvdwxc-
            0.4.0-3k5mksugf2e2tom3ndzfehkd6uupcusx/spack-src'
  >> 254    make: *** [Makefile:452: all] Error 2

[vijaymocherla]

@toxa81 Please ignore the previous comment, that was an error due to issue with ld path on my machine. I get the same error as @mkrack.

Here's an additional snippet of output logfile:

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
icpx: note: diagnostic msg: /tmp/icpx-f0743d6316/hamiltonian_k-4adbf1.cpp
icpx: note: diagnostic msg: /tmp/icpx-f0743d6316/hamiltonian_k-4adbf1.sh
icpx: note: diagnostic msg: 

********************
make[2]: *** [src/CMakeFiles/sirius_cxx.dir/build.make:96: src/CMakeFiles/sirius_cxx.dir/hamiltonian/hamiltonian_k.cpp.o] Error 1
1 warning generated.
1 warning generated.
In file included from /apps/src/SIRIUS/src/mixer/mixer_functions.cpp:16:
In file included from /apps/src/SIRIUS/src/mixer/mixer_functions.hpp:17:
In file included from /apps/src/SIRIUS/src/function3d/periodic_function.hpp:17:
In file included from /apps/src/SIRIUS/src/context/simulation_context.hpp:22:
/apps/src/SIRIUS/src/core/fft/fft.hpp:102:60: warning: 'result_of<(lambda at /apps/src/SIRIUS/src/core/fft/fft.hpp:159:29) (int)>' is deprecated: use 'std::invoke_result' instead [-Wdeprecated-declarations]
  102 |         typename std::enable_if<std::is_same<typename std::result_of<F(Args...)>::type, T>::value, void>::type;
      |                                                            ^
/apps/src/SIRIUS/src/function3d/smooth_periodic_function.hpp:280:22: note: in instantiation of function template specialization 'sirius::fft::spfft_input<double>' requested here
  280 |                 fft::spfft_input(*spfft_, frg_ptr);
      |                      ^
/apps/src/SIRIUS/src/function3d/field4d.hpp:128:31: note: in instantiation of member function 'sirius::Smooth_periodic_function<double>::fft_transform' requested here
  128 |             component(i).rg().fft_transform(direction__);
      |                               ^
/usr/lib/gcc/x86_64-linux-gnu/13/../../../../include/c++/13/type_traits:2590:9: note: 'result_of<(lambda at /apps/src/SIRIUS/src/core/fft/fft.hpp:159:29) (int)>' has been explicitly marked deprecated here
 2590 |     { } _GLIBCXX17_DEPRECATED_SUGGEST("std::invoke_result");
      |         ^
/usr/lib/gcc/x86_64-linux-gnu/13/../../../../include/x86_64-linux-gnu/c++/13/bits/c++config.h:122:45: note: expanded from macro '_GLIBCXX17_DEPRECATED_SUGGEST'
  122 | # define _GLIBCXX17_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
      |                                             ^
/usr/lib/gcc/x86_64-linux-gnu/13/../../../../include/x86_64-linux-gnu/c++/13/bits/c++config.h:98:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
   98 |   __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
      |                   ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
make[2]: Leaving directory '/tmp/sai/spack-stage/spack-stage-sirius-develop-2vt5p2wyfe4b2u4nnwigacs3rhew3raw/spack-build-2vt5p2w'
make[1]: *** [CMakeFiles/Makefile2:1467: src/CMakeFiles/sirius_cxx.dir/all] Error 2
make[1]: Leaving directory '/tmp/sai/spack-stage/spack-stage-sirius-develop-2vt5p2wyfe4b2u4nnwigacs3rhew3raw/spack-build-2vt5p2w'
make: *** [Makefile:149: all] Error 2

[ningli-amd]

I could reproduce the same error @vijaymocherla reported initially with the LLVM clang 19 compiler too (OneAPI 2025 is based on clang 19).

Clang 19 has introduced new syntax checking as summarized in https://releases.llvm.org/19.1.0/tools/clang/docs/ReleaseNotes.html. Related to the present build error is: "Clang now looks up members of the current instantiation in the template definition context if the current instantiation has no dependent base classes". This change appears to affect many applications. Some SIRIUS header files need updates.

[lysea82]

rocky linux 9 with intel oneapi 2025, i ran into the same situation while compiling cp2k 2025 with the cp2k installation toolchain.