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BlueBrain
Issues while compiling with XL compiler
Here is summary of issues I see while building coreneuron+nmodl with XL compiler:
System details : Marconi100
Modules:
$ module list
Currently Loaded Modulefiles:
1) profile/base 2) python/3.8.2 3) xl/16.1.1--binary 4) cuda/11.2 5) cmake/3.20.0 6) git/2.27.0
Building as:
(venv) [pkumbhar@login01 build]$ cmake -DCMAKE_CXX_COMPILER=xlc++_r ..
-- The CXX compiler identification is XLClang 16.1.1.9
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /cineca/prod/opt/compilers/xl/16.1.1_sp4.1/binary/xlC/16.1.1/bin/xlc++_r - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- CHECKING FOR FLEX/BISON
-- Found FLEX: /usr/bin/flex (found suitable version "2.6.1", minimum required is "2.6")
-- Found BISON: /usr/bin/bison (found suitable version "3.0.4", minimum required is "3.0")
-- Found Git: /cineca/prod/opt/tools/git/2.27.0/gnu--8.4.0/bin/git (found version "2.27.0")
-- Sub-project : using fmt from "/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/ext/fmt"
-- Sub-project : using spdlog from "/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/ext/spdlog"
-- Sub-project : using pybind11 from "/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/ext/pybind11"
-- pybind11 v2.6.1
-- Found PythonInterp: /m100/home/userexternal/pkumbhar/venv/bin/python (found version "3.8.2")
-- Found PythonLibs: /cineca/prod/opt/compilers/python/3.8.2/none/lib/libpython3.8.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Failed
-- Performing Test HAS_FLTO_THIN
-- Performing Test HAS_FLTO_THIN - Failed
-- Sub-project : using cli11 from "/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/ext/cli11"
-- Sub-project : using eigen from "/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/ext/eigen"
-- Version: 6.2.0
-- Build type:
-- CXX_STANDARD: 14
-- Performing Test has_std_14_flag
-- Performing Test has_std_14_flag - Success
-- Performing Test has_std_1y_flag
-- Performing Test has_std_1y_flag - Success
-- Performing Test SUPPORTS_USER_DEFINED_LITERALS
-- Performing Test SUPPORTS_USER_DEFINED_LITERALS - Success
-- Performing Test FMT_HAS_VARIANT
-- Performing Test FMT_HAS_VARIANT - Success
-- Required features: cxx_variadic_templates
-- Looking for strtod_l
-- Looking for strtod_l - found
-- Sub-module : missing /m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/cmake/hpc-coding-conventions: running git submodule update --init
-- NMODL_FORMATTING: OFF
-- NMODL_FORMATTING_ON: all
-- NMODL_FORMATTING_CPP_CHANGES_ONLY: OFF
-- NMODL_TEST_FORMATTING: OFF
-- NMODL_FORMATTING_NO_SUBMODULES: ON
-- NMODL_CLANG_FORMAT: OFF
-- NMODL_CMAKE_FORMAT: OFF
-- NMODL_GIT_HOOKS: OFF
-- NMODL_GIT_COMMIT_HOOKS:
-- NMODL_GIT_PUSH_HOOKS: courtesy-msg
-- NMODL_STATIC_ANALYSIS: OFF
-- NMODL_TEST_STATIC_ANALYSIS: OFF
-- Could NOT find ClangFormat (missing: ClangFormat_EXECUTABLE)
-- CHECKING FOR PYTHON
-- Found PythonInterp: /m100/home/userexternal/pkumbhar/venv/bin/python (found suitable version "3.8.2", minimum required is "3.6")
--
-- Configured NMODL 0.3 (3e960d7d 2021-12-23 15:47:17 +0100)
--
-- You can now build NMODL using:
-- cmake --build . --parallel 8 [--target TARGET]
-- You might want to adjust the number of parallel build jobs for your system.
-- Some non-default targets you might want to build:
-- --------------------+--------------------------------------------------------
-- Target | Description
-- --------------------+--------------------------------------------------------
-- test | Run unit tests
-- install | Will install NMODL to: /usr/local
-- --------------------+--------------------------------------------------------
-- Build option | Status
-- --------------------+--------------------------------------------------------
-- CXX COMPILER | /cineca/prod/opt/compilers/xl/16.1.1_sp4.1/binary/xlC/16.1.1/bin/xlc++_r
-- COMPILE FLAGS |
-- Build Type |
-- Legacy Units | OFF
-- Python Bindings | ON
-- Flex | /usr/bin/flex
-- Bison | /usr/bin/bison
-- Python | /m100/home/userexternal/pkumbhar/venv/bin/python
-- --------------+--------------------------------------------------------------
-- See documentation : https://github.com/BlueBrain/nmodl/
-- --------------+--------------------------------------------------------------
--
-- Configuring done
-- Generating done
-- Build files have been written to: /m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/build
Issues
- Link issue with test:
]$ make
[ 1%] Built target pyembed
[ 2%] Built target fmt
[ 4%] Built target test_util
[ 5%] Built target pyastgen
[ 21%] Built target lexer_obj
[ 22%] Built target lexer
[ 23%] Built target printer_obj
[ 24%] Built target printer
[ 25%] Built target symtab_obj
[ 26%] Built target symtab
[ 30%] Built target util_obj
[ 30%] Built target util
[ 31%] Built target pywrapper
[ 48%] Built target visitor_obj
[ 50%] Built target visitor
[ 50%] Linking CXX executable ../../bin/testvisitor
../../src/visitors/libvisitor.a(visitor_utils.cpp.o): In function `nmodl::statement_dependencies[abi:cxx11](std::shared_ptr<nmodl::ast::Expression> const&, std::shared_ptr<nmodl::ast::Expression> const&)':
/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/src/visitors/visitor_utils.cpp:(.text+0x7c8b0): undefined reference to `nmodl::visitor::MetaAstLookupVisitor<nmodl::visitor::Visitor>::MetaAstLookupVisitor()'
../../src/visitors/libvisitor.a(visitor_utils.cpp.o): In function `nmodl::collect_nodes(nmodl::ast::Ast const&, std::vector<nmodl::ast::AstNodeType, std::allocator<nmodl::ast::AstNodeType> > const&)':
/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/src/visitors/visitor_utils.cpp:(.text+0x7d648): undefined reference to `nmodl::visitor::MetaAstLookupVisitor<nmodl::visitor::ConstVisitor>::MetaAstLookupVisitor()'
../../src/visitors/libvisitor.a(visitor_utils.cpp.o): In function `nmodl::collect_nodes(nmodl::ast::Ast&, std::vector<nmodl::ast::AstNodeType, std::allocator<nmodl::ast::AstNodeType> > const&)':
/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/src/visitors/visitor_utils.cpp:(.text+0x7dbe0): undefined reference to `nmodl::visitor::MetaAstLookupVisitor<nmodl::visitor::Visitor>::MetaAstLookupVisitor()'
make[2]: *** [test/unit/CMakeFiles/testvisitor.dir/build.make:496: bin/testvisitor] Error 1
make[1]: *** [CMakeFiles/Makefile2:1235: test/unit/CMakeFiles/testvisitor.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
...
[100%] Linking CXX executable ../bin/nmodl
visitors/libvisitor.a(visitor_utils.cpp.o): In function `nmodl::statement_dependencies[abi:cxx11](std::shared_ptr<nmodl::ast::Expression> const&, std::shared_ptr<nmodl::ast::Expression> const&)':
/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/src/visitors/visitor_utils.cpp:(.text+0x7c8b0): undefined reference to `nmodl::visitor::MetaAstLookupVisitor<nmodl::visitor::Visitor>::MetaAstLookupVisitor()'
visitors/libvisitor.a(visitor_utils.cpp.o): In function `nmodl::collect_nodes(nmodl::ast::Ast const&, std::vector<nmodl::ast::AstNodeType, std::allocator<nmodl::ast::AstNodeType> > const&)':
/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/src/visitors/visitor_utils.cpp:(.text+0x7d648): undefined reference to `nmodl::visitor::MetaAstLookupVisitor<nmodl::visitor::ConstVisitor>::MetaAstLookupVisitor()'
visitors/libvisitor.a(visitor_utils.cpp.o): In function `nmodl::collect_nodes(nmodl::ast::Ast&, std::vector<nmodl::ast::AstNodeType, std::allocator<nmodl::ast::AstNodeType> > const&)':
/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/src/visitors/visitor_utils.cpp:(.text+0x7dbe0): undefined reference to `nmodl::visitor::MetaAstLookupVisitor<nmodl::visitor::Visitor>::MetaAstLookupVisitor()'
make[3]: *** [src/CMakeFiles/nmodl.dir/build.make:106: bin/nmodl] Error 1
make[2]: *** [CMakeFiles/Makefile2:1612: src/CMakeFiles/nmodl.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:1619: src/CMakeFiles/nmodl.dir/rule] Error 2
- Issue with Eigen based test compilation:
In file included from /m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/test/unit/newton/newton.cpp:14:
In file included from /m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/src/nmodl.hpp:19:
In file included from /m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/src/solver/newton/newton.hpp:22:
In file included from /m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/ext/eigen/Eigen/LU:11:
In file included from /m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/ext/eigen/Eigen/Core:210:
/m100/home/userexternal/pkumbhar/CoreNeuron/external/nmodl/ext/eigen/Eigen/src/Core/arch/AltiVec/PacketMath.h:830:117: error: no matching function for call to 'vec_madd'
template<> EIGEN_STRONG_INLINE Packet8us pmadd(const Packet8us& a, const Packet8us& b, const Packet8us& c) { return vec_madd(a,b,c); }
this requires add_definitions(-DEIGEN_DONT_VECTORIZE=1).
