Ok - I see this issue on CentOS [Stream/9].
What I have is:
>>>
[balay@frog petsc]$ clang --version
clang version 19.1.7 (CentOS 19.1.7-1.el9)
Target: x86_64-redhat-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
Configuration file: /etc/clang/x86_64-redhat-linux-gnu-clang.cfg
[balay@frog petsc]$ gfortran --version
GNU Fortran (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
<<<<
Now I build:
>>>
[balay@frog petsc]$ ./configure --with-cc=clang --with-cxx=clang++
--with-fc=gfortran --with-mpi=0 && make && make check
<snip>
*********************************************************************************
clang -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wconversion
-Wno-sign-conversion -Wno-float-conversion -Wno-implicit-float-conversion
-fstack-protector -Qunused-arguments -fvisibility=hidden -Wall -Wwrite-strings
-Wno-unknown-pragmas -Wconversion -Wno-sign-conversion -Wno-float-conversion
-Wno-implicit-float-conversion -fstack-protector -Qunused-arguments
-fvisibility=hidden -g3 -O0 -I/home/balay/petsc/include
-I/home/balay/petsc/arch-linux-c-debug/include -Wl,-export-dynamic ex19.c
-Wl,-rpath,/home/balay/petsc/arch-linux-c-debug/lib
-L/home/balay/petsc/arch-linux-c-debug/lib
-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/11
-L/usr/lib/gcc/x86_64-redhat-linux/11 -lpetsc -llapack -lblas -lm -lX11
-lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -o ex19
/opt/rh/gcc-toolset-14/root//usr/lib/gcc/x86_64-redhat-linux/14/../../../../bin/ld:
/home/balay/petsc/arch-linux-c-debug/lib/libpetsc.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::_M_replace_cold(char*, unsigned long, char const*, unsigned long, unsigned
long)'
<snip>
<<<<
Ok some v11 compiler libraries are getting mixed up (likely from -lgfortran)
causing grief.
>>>>>>>>
[root@frog ~]# yum remove gcc-toolset-14-runtime
Dependencies resolved.
================================================================================
Package Arch Version Repository Size
================================================================================
Removing:
gcc-toolset-14-runtime x86_64 14.0-1.el9 @appstream 11 k
Removing dependent packages:
clang x86_64 19.1.7-1.el9 @appstream 181 k
clang-tools-extra x86_64 19.1.7-1.el9 @appstream 69 M
gcc-toolset-14-binutils x86_64 2.41-3.el9 @appstream 27 M
Removing unused dependencies:
clang-libs x86_64 19.1.7-1.el9 @appstream 413 M
clang-resource-filesystem x86_64 19.1.7-1.el9 @appstream 15 k
compiler-rt x86_64 19.1.7-1.el9 @appstream 37 M
gcc-toolset-14-gcc x86_64 14.2.1-7.1.el9 @appstream 122 M
gcc-toolset-14-gcc-c++ x86_64 14.2.1-7.1.el9 @appstream 39 M
gcc-toolset-14-libstdc++-devel x86_64 14.2.1-7.1.el9 @appstream 22 M
libomp x86_64 19.1.7-1.el9 @appstream 1.9 M
libomp-devel x86_64 19.1.7-1.el9 @appstream 31 M
Transaction Summary
================================================================================
Remove 12 Packages
Freed space: 763 M
Is this ok [y/N]:
<<<<<
So this install of clang depends-on/requires gcc-toolset-14-gcc. Also
gfortran-14 is missing. Try installing it.
>>>>
[root@frog ~]# yum install gcc-toolset-14-gcc-gfortran
<<<<
Now retry build:
>>>
[balay@frog petsc]$ ./configure --with-cc=clang --with-cxx=clang++
--with-fc=gfortran --with-mpi=0 && make && make check
<snip>
Running PETSc check examples to verify correct installation
Using PETSC_DIR=/home/balay/petsc and PETSC_ARCH=arch-linux-c-debug
C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
Completed PETSc check examples
[balay@frog petsc]$
<<<<
Hm - Using gfortran-11 here [with gfortran-14 installed] somehow worked! But
perhaps its better to use gfortran-14 [as this install of clang requires g++-14]
>>>>
[balay@frog petsc]$ export PATH=/opt/rh/gcc-toolset-14/root/usr/bin:$PATH
[balay@frog petsc]$ gfortran --version
GNU Fortran (GCC) 14.2.1 20250110 (Red Hat 14.2.1-7)
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[balay@frog petsc]$ ./configure --with-cc=clang --with-cxx=clang++
--with-fc=gfortran --with-mpi=0 && make && make check
<snip>
CLINKER arch-linux-c-debug/lib/libpetsc.so.3.22.3
=========================================
Now to check if the libraries are working do:
make PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-linux-c-debug check
=========================================
Running PETSc check examples to verify correct installation
Using PETSC_DIR=/home/balay/petsc and PETSC_ARCH=arch-linux-c-debug
C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
Completed PETSc check examples
[balay@frog petsc]$
<<<<
So that worked!
Satish
On Thu, 20 Feb 2025, Satish Balay wrote:
> Actually, simpler:
>
> ./configure --with-cc=clang --with-cxx=clang++ --with-fc=gfortran
> --with-mpi=0
> --download-fblaslapack="$(DIR_SRC)/fblaslapack-$(FBLASLAPACK_VERSION).tar.gz"
> && make && make check
>
> > /opt/rh/gcc-toolset-12/root/usr/lib/gcc/x86_64-redhat-linux/12/../../../../bin/ld
>
> Hm - there was in issue with some (clang versions?) incompatibilities with
> gcc-12 - I think using gcc-11 (system default in that use case) worked. I'm
> not sure if you are seeing the same issue here.
>
> Satish
>
> On Thu, 20 Feb 2025, Satish Balay wrote:
>
> >
> > Any particular reason to use these flags? What clang version? OS?
> >
> > Best if you can send build logs [perhaps to petsc-maint]
> >
> > Can you try a simpler build and see if it works:
> >
> > ./configure --with-mpi-dir=/PATH_TO/models/src/v2021.03-2.0.3-llvm
> > --download-fblaslapack="$(DIR_SRC)/fblaslapack-$(FBLASLAPACK_VERSION).tar.gz"
> > && make && make check
> > or:
> > ./configure --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"
> > && make && make check
> >
> > Satish
> >
> > On Thu, 20 Feb 2025, Michael Schaferkotter wrote:
> >
> > > 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
> > >
> > >
> > >
> >
>
