[petsc-users] Info; build petsc-3.20.2 with llvm check fails

[Michael Schaferkotter]

build petsc-3.20.3 with llvm, clang, clang++, gfortran 

CFLAGS='-std=c++11'
CXXFLAGS='-std=c++11 -D_GLIBCXX_USE_CXX11_ABI=1'
LDLIBS += -lstdc++

$PETSC_ARCH     arch-linux-c-opt
MPIF90  = ./models/src/v2021.03-2.0.3-llvm/bin/mpif90
MPICC   = ./models/src/v2021.03-2.0.3-llvm/bin/mpicc
CLANG   = clang
FC   = gfortran


Petsc libraries are built;
/models/src/v2021.03-2.0.3-llvm/lib/libpetsc.so@
/models/src/v2021.03-2.0.3-llvm/lib/libpetsc.so.3.020@
/models/src/v2021.03-2.0.3-llvm/lib/libpetsc.so.3.020.3*


The configure is this:
        cd $(PETSC_SRC) && unset CXX CC FC F77 && $(PYTHON2) ./configure 
--prefix=$(PREFIX) \
  --with-cc=clang \
  --with-cxx=clang++ \
  --with-fc=gfortran \
  --download-mpich="$(DIR_SRC)/mpich-$(MPICH_VERSION).tar.gz" \
  --download-fblaslapack="$(DIR_SRC)/fblaslapack-$(FBLASLAPACK_VERSION).tar.gz" 
\
  --download-sowing \
  --with-debugging=$(PETSC_DBG) \
  --with-shared-libraries=1 \
 CFLAGS='-std=c11' \
  CXXFLAGS='-std=c++11 -D_GLIBCXX_USE_CXX11_ABI=1' \
  CPPFLAGS='-D_GLIBCXX_USE_CXX11_ABI=1' \
  LDFLAGS='-L$(LLVM_LIB)' \
  LIBS='-lstdc++’ \
  --COPTFLAGS=$(COPTFLAGS) --CXXOPTFLAGS=$(CXXOPTFLAGS) --FOPTFLAGS=$(FOPTFLAGS)


Here is the make:

        $(MAKE) -C $(PETSC_SRC) PETSC_DIR=$(PETSC_SRC) PETSC_ARCH=$(PETSC_ARCH) 
all


Check-petsc is:

        $(MAKE) -C $(PETSC_SRC) PETSC_DIR=$(PETSC_SRC) PETSC_ARCH=$(PETSC_ARCH) 
test

Here is the log file for test:

make[1]: Entering directory 
'/models/src/v2021.03-2.0.3-llvm/build/petsc/petsc-3.20.3'
/usr/bin/python3 
/models/src/v2021.03-2.0.3-llvm/build/petsc/petsc-3.20.3/config/gmakegentest.py 
--petsc-dir=/models/src/v2021.03-2.0.3-llvm/build/petsc/petsc-3.20.3 
--petsc-arch=arch-linux-c-opt --testdir=./arch-linux-c-opt/tests --srcdir 
/models/src/v2021.03-2.0.3-llvm/build/petsc/petsc-3.20.3/src --pkg-pkgs "sys 
vec mat dm ksp snes ts tao"
Using MAKEFLAGS: iw -- PETSC_ARCH=arch-linux-c-opt 
PETSC_DIR=/models/src/v2021.03-2.0.3-llvm/build/petsc/petsc-3.20.3
         CC arch-linux-c-opt/tests/sys/classes/draw/tests/ex1.o
    CLINKER arch-linux-c-opt/tests/sys/classes/draw/tests/ex1
/opt/rh/gcc-toolset-12/root/usr/lib/gcc/x86_64-redhat-linux/12/../../../../bin/ld:
 arch-linux-c-opt/lib/libpetsc.so: undefined reference to 
`std::__cxx11::basic_ostringstream<char, std::char_traits<char>, 
std::allocator<char> >::basic_ostringstream()'
/opt/rh/gcc-toolset-12/root/usr/lib/gcc/x86_64-redhat-linux/12/../../../../bin/ld:
 arch-linux-c-opt/lib/libpetsc.so: undefined reference to 
`std::__throw_bad_array_new_length()'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: [gmakefile.test:273: 
arch-linux-c-opt/tests/sys/classes/draw/tests/ex1] Error 1 (ignored)


There are many errors of the ilk: 

std::__cxx11::basic_ostringstream<char, std::char_traits<char>, 
std::allocator<char> >::basic_ostringstream()

[lib]$ nm -A libpetsc.so | grep basic_ostringstream
libpetsc.so:                 U 
_ZNKSt7__cxx1119basic_ostringstreamIcSt11char_traitsIcESaIcEE3strEv@GLIBCXX_3.4.21
libpetsc.so:                 U 
_ZNSt7__cxx1119basic_ostringstreamIcSt11char_traitsIcESaIcEEC1Ev
libpetsc.so:                 U 
_ZNSt7__cxx1119basic_ostringstreamIcSt11char_traitsIcESaIcEED1Ev@GLIBCXX_3.4.21


I/m new to llvm and this is the first time to compile petsc.3.20.3 with llvm 
compilers.

Clearly something is amiss.

Any ideas appreciated.

Michael