[petsc-users] PETSc on fedora 36

[Antonio T. sagitter]

Hi all.

On 23/08/22 16:33, Rafel Amer Ramon wrote:
> Hi,
> 
> the files rules and variables are in /usr/lib64/petsc/conf, so I have set
> 
> ~$ export PETSC_DIR=/usr
> 
> ~$ cat Makefile
> 
> e: e.o
>      ${CLINKER} -o e e.o ${PETSC_LIB}
> 
> include ${PETSC_DIR}/lib64/petsc/conf/variables
> include ${PETSC_DIR}/lib64/petsc/conf/rules
> 
> ~$
> 
> but, when I try to compile the program, I get the error
> 
> ~$ make e
> gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -fPIC -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3  -o e e.o -L/usr/lib64 -L/usr//lib -lpetsc -lsuperlu -lflexiblas -lcgns -lhdf5 -lhdf5_hl -lmetis -lm -lX11 -lquadmath -lstdc++ -ldl
> /usr/bin/ld: cannot open linker script file /builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld: El fitxer o directori no existeix
> collect2: error: ld returned 1 exit status
> make: *** [Makefile:2: e] Error 1
> 
> In the file /usr/lib64/petsc/conf/petscvariables, there are some 
> references to the inexistent file 
> /builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld:
> 
> ~$ grep /builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld /usr/lib64/petsc/conf/petscvariables
> CXX_LINKER_FLAGS = -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -fPIC  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3
> PCC_LINKER_FLAGS = -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -fPIC -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3
> FC_LINKER_FLAGS = -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -fPIC -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -lgfortran -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -O3 -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -O3
> CONFIGURE_OPTIONS = --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --with-dependency-tracking=0 --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-cc=gcc --with-cxx=g++ --with-fc=gfortran CFLAGS=\"-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -fPIC\" CXXFLAGS=\"-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -fPIC\" FFLAGS=\"-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -O3 -fPIC\" LDFLAGS=\"-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -fPIC\" COPTFLAGS=\"-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3\" CXXOPTFLAGS=\"-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3\" FOPTFLAGS=\"-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -O3\" FCFLAGS=\"-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -O3 -fPIC\" --CC_LINKER_FLAGS=\"-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld\" --FC_LINKER_FLAGS=\"-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -lgfortran\" --with-default-arch=0 --with-make=1 --with-cmake-exec=/usr/bin/cmake3 --with-ctest-exec=/usr/bin/ctest3 --with-single-library=1 --with-precision=double --with-petsc-arch=x86_64 --with-clanguage=C --with-shared-libraries=1 --with-fortran-interfaces=1 --with-windows-graphics=0 --CC=gcc --FC=gfortran --CXX=g++ --with-shared-ld=ld --with-pic=1 --with-clib-autodetect=0 --with-fortranlib-autodetect=0 --with-threadsafety=0 --with-log=1 --with-mkl_sparse=0 --with-mkl_sparse_optimize=0 --with-mkl_cpardiso=0 --with-mkl_pardiso=0 --with-python=0 --with-cxxlib-autodetect=1 --with-debugging=0 --with-mumps-serial=1 --with-mpi=0 --with-hdf5=1 --with-hdf5-include= --with-hdf5-lib=\"-lhdf5 -lhdf5_hl\" --with-cgns=1 --with-cgns-include= --with-cgns-lib=-lcgns --with-x=1 --with-openmp=0 --with-hwloc=0 --with-ssl=0 --with-pthread=1 --with-valgrind=1 --with-64-bit-indices=0 --with-blaslapack=1 --with-blaslapack-lib=-lflexiblas --with-blaslapack-include=/usr/include/flexiblas --with-metis=1 --with-superlu=1 --with-superlu-include=/usr/include/SuperLU --with-superlu-lib=-lsuperlu
> SL_LINKER_FUNCTION = -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -Wl,-soname,$(call SONAME_FUNCTION,$(notdir $(1)),$(2))
> ~$
> 
> 
> then, I get the error
> 
> /usr/bin/ld: cannot open linker script file /builddir/build/BUILD/petsc-3.16.4/.package_note-petsc-3.16.4-3.fc36.x86_64.ld: the file or folder doesn't exist
> 
> Best regards,
> 
> Rafel Amer
> 
> 
> 
> 

Links to unknown folders are generated by a new functionality of RPM 
packaging in Fedora 
(https://fedoraproject.org/wiki/Changes/Package_information_on_ELF_objects#Package_information_on_ELF_objects), 

the files rules and variables acquire these broken links during RPM 
building.

I'm disabling "package-note" links in the PETSc rpms in next build 
release. Please, let me know if they're still there by opening a 
bugzilla ticket (https://bugzilla.redhat.com/) if you still want to use 
PETSc from Fedora repositories.

-- 
---
Antonio Trande
Fedora Project
mailto: sagitter at fedoraproject.org
GPG key: 0xCC1CFEF30920C8AE
GPG key server: https://keyserver1.pgp.com/
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