Satish; Thank you for the masterful demonstration.
One of the alternatives caught my eye: —with-cxx=0 (I remember I had to do that ages ago on my macOS Darwin machine. I cleared *FLAGS and successfully completed make && make check as suggested; #======================================================================= It may be moot now. Here is the requested OS, compiler information: cat /etc/os-release NAME="Red Hat Enterprise Linux" VERSION="8.8 (Ootpa)" ID="rhel" ID_LIKE="fedora" VERSION_ID="8.8" PLATFORM_ID="platform:el8" PRETTY_NAME="Red Hat Enterprise Linux 8.8 (Ootpa)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:redhat:enterprise_linux:8::baseos" HOME_URL="https://urldefense.us/v3/__https://www.redhat.com/__;!!G_uCfscf7eWS!Z9OsinaKusqhhdPuDCNknHJq6f6UGZt17SofPYc-BvWQvrlqpeDbEEucEHNxioN04anLOPsjW0v_aCHG5RpV-0tjnQ$ " DOCUMENTATION_URL="https://urldefense.us/v3/__https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8__;!!G_uCfscf7eWS!Z9OsinaKusqhhdPuDCNknHJq6f6UGZt17SofPYc-BvWQvrlqpeDbEEucEHNxioN04anLOPsjW0v_aCHG5Roh1jkm1w$ " BUG_REPORT_URL="https://urldefense.us/v3/__https://bugzilla.redhat.com/__;!!G_uCfscf7eWS!Z9OsinaKusqhhdPuDCNknHJq6f6UGZt17SofPYc-BvWQvrlqpeDbEEucEHNxioN04anLOPsjW0v_aCHG5RpG5qdUaQ$ " REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 8" REDHAT_BUGZILLA_PRODUCT_VERSION=8.8 REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux" REDHAT_SUPPORT_PRODUCT_VERSION="8.8" clang version 20.0.0git (https://urldefense.us/v3/__https://github.com/llvm/llvm-project.git__;!!G_uCfscf7eWS!Z9OsinaKusqhhdPuDCNknHJq6f6UGZt17SofPYc-BvWQvrlqpeDbEEucEHNxioN04anLOPsjW0v_aCHG5RoxqM2a5g$ 48d0ef1a07993139e1acf65910704255443103a5) Target: x86_64-unknown-linux-gnu Thread model: posix InstalledDir: /tmp/build_release/bin Clang version: 20.0.0git LLVM version: LLVM version 20.0.0git (48d0ef1a07993139e1acf65910704255443103a5<unknown encoding> C++ standard: Host target: x86_64-unknown-linux-gnu Supported targets: Registered Targets: x86 - 32-bit X86: Pentium-Pro and above x86-64 - 64-bit X86: EM64T and AMD64 flang version 20.0.0git (https://urldefense.us/v3/__https://github.com/llvm/llvm-project.git__;!!G_uCfscf7eWS!Z9OsinaKusqhhdPuDCNknHJq6f6UGZt17SofPYc-BvWQvrlqpeDbEEucEHNxioN04anLOPsjW0v_aCHG5RoxqM2a5g$ 48d0ef1a07993139e1acf65910704255443103a5) Target: x86_64-unknown-linux-gnu Thread model: posix InstalledDir: /tmp/build_release/bin Flang version: 20.0.0git Host target: x86_64-unknown-linux-gnu Fortran compiler: GNU Fortran (GCC) 8.5.0 20210514 (Red Hat 8.5.0-4) Compiler path: /usr/bin/gfortran Version: -std=<standard> Assume that the input sources are for <standard>. Default flags: No default flags information available Target: x86_64-redhat-linux #======================================================================= Thank you again. > On Feb 20, 2025, at 2:44 PM, Satish Balay <balay....@fastmail.org> wrote: > > A couple of alternates (if mixing compiler versions can't be avoided): > > - don't need to use petsc from fortran: > [balay@frog petsc]$ ./configure --with-cc=clang --with-cxx=clang++ > --with-fc=0 --with-mpi=0 --download-f2cblaslapack && make && make check > > - don't use c++: > [balay@frog petsc]$ ./configure --with-cc=clang --with-cxx=0 > --with-fc=gfortran --with-mpi=0 && make && make check > > - add in v14 -lstdc++ location ahead in the search path - so that even when > -lgfortran is found in v11, v14 -lstdc++ gets picked up correctly. > [balay@frog petsc]$ ./configure > LDFLAGS=-L/opt/rh/gcc-toolset-14/root/usr/lib/gcc/x86_64-redhat-linux/14/ > --with-cc=clang --with-cxx=clang++ --with-fc=gfortran --with-mpi=0 && make && > make check > > Satish > > On Thu, 20 Feb 2025, Satish Balay wrote: > >> 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 >>>>> >>>>> >>>>> >>>>
