Arch Linux User Repository

@jrohwer

When building PETSc (more specifically, petsc4py), one test (ex100 from ksp) will fail if a previous (major) version is installed. I could not figure out why this happens. The solution would be to build in a clean root (which is a little bit complicated due to dependency on other AUR packages) or simply uninstall the old version before.

Any help to solve this issue is welcomed.

The location of scotch headers changed and this needs to be updated in the PKGBUILD for petsc: --with-ptscotch-include=/usr/include/scotch

% python
Python 3.13.11 (main, Dec  7 2025, 13:01:45) [GCC 15.2.1 20251112] on linux
>>> from petsc4py import PETSc
[...]
ImportError: /opt/petsc/linux-c-opt/lib/libpetsc.so.3.24: undefined symbol: _ZTVN10__cxxabiv117__class_type_infoE

As described by https://aur.archlinux.org/packages/petsc?O=20#comment-1005041, linking against libstdc++ fixes this. Patch:

diff --git a/PKGBUILD b/PKGBUILD
index 47a09b7..9095977 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -59,6 +59,9 @@ build() {
             --with-zfp=1 \
             $(sh ${srcdir}/test_optdepends.sh)"

+  # Link against libstdc++. Fixes python import error undefined symbol: _ZTVN10__cxxabiv117__class_type_infoE.
+  LDFLAGS="$LDFLAGS -lstdc++"
+
   echo './configure' ${CONFOPTS}
   echo 'CFLAGS='${CFLAGS}
   echo 'CXXFLAGS='${CXXFLAGS}

@carlosal1015: According to the PKGBUILD, scotch-metis does not provide METIS because it's not 100% compatible. So it will probably not work.

I don't know what libesmumps.so from scotch does. Scotch is a dependency for MUMPS, so the current situation looks reasonable to me.

I do not know if libptscotchparmetisv3.so.7.0 could or should works as replacement for /usr/lib/libparmetis.so from parmetis-git. If this is correct, should be nice.

Edited: Since libesmumps.so is provided by scotch. From now parmetis and mumps optional dependencies, it make sense since scotch is already a dependency?

@MartinDiehl superlu_dist is also in extra ;)

I had to do this to build petsc with ptscotch and kokkos:

diff --git a/test_optdepends.sh b/test_optdepends.sh
index 8f9090b..5b21607 100644
--- a/test_optdepends.sh
+++ b/test_optdepends.sh
@@ -11,7 +11,7 @@ CONFOPTS=""

 # Kokkos
 if [ -f "/usr/lib/libkokkoscore.so" ]; then
-  CONFOPTS="${CONFOPTS} --with-kokkos=1"
+  CONFOPTS="${CONFOPTS} --with-kokkos=1 --with-kokkos-lib=libkokkoscore.so --with-kokkos-include=/usr/include/kokkos"
 fi

 # HYPRE
@@ -38,15 +38,15 @@ if [ -f "/usr/lib/pkgconfig/scalapack.pc" ]; then
 fi

 # Scotch
-#if [ -f /usr/include/scotch.h ]; then
-#  SCOTCH_LIBS="libesmumps.so,libptscotch.so,libptscotcherr.so,libscotch.so,libscotcherr.so"
-#  # Include bzip2 if scotch was build with bzip2 support
-#  if [ -f /usr/include/bzlib.h ];then
-#    SCOTCH_LIBS="${SCOTCH_LIBS},libbz2.so"
-#  fi
-#  SCOTCH_LIBS="[${SCOTCH_LIBS}]"
-#  CONFOPTS="${CONFOPTS} --with-ptscotch=1 --with-bison=1"
-#fi
+if [ -f /usr/include/scotch.h ]; then
+  SCOTCH_LIBS="libesmumps.so,libptscotch.so,libptscotcherr.so,libscotch.so,libscotcherr.so"
+  # Include bzip2 if scotch was build with bzip2 support
+  if [ -f /usr/include/bzlib.h ];then
+    SCOTCH_LIBS="${SCOTCH_LIBS},libbz2.so"
+  fi
+  SCOTCH_LIBS="[${SCOTCH_LIBS}]"
+  CONFOPTS="${CONFOPTS} --with-ptscotch=1 --with-bison=1 --with-ptscotch-lib=$SCOTCH_LIBS --with-ptscotch-include=/usr/include"
+fi

 # SuperLU_DIST
 if [ -f "/usr/lib/pkgconfig/superlu_dist.pc" ]; then

Now scotch, scotch-metis and pastix are now in [extra].

@Alad: Thanks. I can certainly fix the permissions. Did you try using the Kokkos package instead of Trilinos? It seems that file locations differ, so Trilinos is not a direct replacement for Kokkos

The linking error mentioned by @carlosal1015 also stops slepc from building:

Checking PETSc installation...
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Checking link with code:

#include "petscsnes.h"
int main() {
PetscErrorCode ierr; Vec v; Mat m; KSP k;
ierr = PetscInitializeNoArguments();
ierr = VecCreate(PETSC_COMM_WORLD,&v);
ierr = MatCreate(PETSC_COMM_WORLD,&m);
ierr = KSPCreate(PETSC_COMM_WORLD,&k);
(void)ierr;
return 0;
}

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Running command:
cd /tmp/slepc-_acdm5dt;/usr/bin/make checklink LINKFLAGS=""
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Output:
/usr/bin/mpicxx -o checklink.o -c -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection         -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/home/custompkgs/hpc/petsc/src=/usr/src/debug/petsc  -std=gnu++17 -fPIC  -I/opt/petsc/linux-c-opt/include -I/usr/include/hypre -I/usr/include/suitesparse -I/usr/include -I/usr/include/superlu_dist -I/usr/include/superlu -I/usr/include/kokkos    checklink.c
/usr/bin/mpicxx -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now          -Wl,-z,pack-relative-relocs  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection         -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/home/custompkgs/hpc/petsc/src=/usr/src/debug/petsc  -o checklink checklink.o  -Wl,-rpath,/opt/petsc/linux-c-opt/lib -L/opt/petsc/linux-c-opt/lib -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/15.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/15.1.1 -lpetsc /usr/lib/libHYPRE.so -lspqr -lumfpack -lklu -lcholmod -lamd -lsuperlu_dist -ldmumps -lmumps_common -lpord -lpthread -lscalapack -lsuperlu -lfftw3_mpi -lfftw3 /usr/lib/libkokkoscore.so -llapack -lblas -lzfp -lzoltan -lptesmumps -lptscotchparmetisv3 -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -lnetcdf -lhdf5_hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -ltriangle -lgsl -lgslcblas -lm -lz -ljpeg -lyaml -lX11 -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `triangulate(char*, triangulateio*, triangulateio*, triangulateio*)'
collect2: error: ld returned 1 exit status
make: *** [makefile:2: checklink] Error 1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

ERROR: Unable to link with PETSc

Also the permissions on /etc/profile.d/petsc.sh are wrong on my machine:

% ls -ahl /etc/profile.d/petsc.sh
-rwxrwx--x 1 root root 99 28. Aug 00:45 /etc/profile.d/petsc.sh

Using chmod 644 instead of chmod +x avoids this issue -- any files in /etc/profile.d are sourced, not executed directly.