[petsc-users] Undefined reference in PETSc 3.13+ with old MPI version

Barry Smith bsmith at petsc.dev
Sat Apr 10 12:31:28 CDT 2021

  Depending on the network you can remove the ./configure options --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90  and use instead --with-cc=icc --with-cxx=icpc and--with-fc=ifort --download-openmpi 


> On Apr 10, 2021, at 12:18 PM, Danyang Su <danyang.su at gmail.com> wrote:
> Dear PETSc developers and users,
> I am trying to install the latest PETSc version on an ancient cluster. The OpenMPI version is 1.6.5 and Compiler is Intel 14.0, which are the newest on that cluster. I have no problem to install PETSc up to version 3.12.5. However, if I try to use PETSc 3.13+, there are three undefined reference errors in MPI_Win_allocate, MPI_Win_attach and MPI_Win_create_dynamic. I know these three functions are available from OpenMPI 2.0+. Because the cluster is not in technical support anymore, there is no way I can install new OpenMPI version or do some update. Is it possible to disable these three functions in PETSc 3.13+ version?
> The errors occur in ‘make check’ step:
> /home/dsu/soft/petsc/petsc-3.13.0/linux-intel-openmpi/lib/libpetsc.so: undefined reference to `MPI_Win_allocate'
> /home/dsu/soft/petsc/petsc-3.13.0/linux-intel-openmpi/lib/libpetsc.so: undefined reference to `MPI_Win_attach'
> /home/dsu/soft/petsc/petsc-3.13.0/linux-intel-openmpi/lib/libpetsc.so: undefined reference to `MPI_Win_create_dynamic'
> The configuration used is shown below:
> ./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-mumps --download-scalapack --download-parmetis --download-metis --download-fblaslapack --download-hypre --download-superlu --download-hdf5=yes --with-debugging=0 COPTFLAGS="-O3 -march=native -mtune=native" CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3 -march=native -mtune=nativels"
> Thanks,
> Danyang

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