Opened 7 years ago

Closed 6 years ago

#54119 closed defect (fixed)

petsc configure python bug

Reported by: jjstickel (Jonathan Stickel) Owned by: seanfarley (Sean Farley)
Priority: Normal Milestone:
Component: ports Version:
Keywords: Cc:
Port: petsc

Description

I received a configure error when installing petsc while having python35 set by "port select". From the log: 

:info:configure Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_sea.us.rsync.macports.org_release_tarballs_ports_math_petsc/petsc/work/v3.7.4" && ./configure --prefix=/opt/local --prefix=/opt/local/lib/petsc --with-valgrind=0 --with-shared-libraries --with-debugging=0 --with-c2html-dir=/opt/local --without-x --with-blas-lapack-lib=/System/Library/Frameworks/Accelerate.framework/Versions/Current/Accelerate --with-hwloc-dir=/opt/local --with-suitesparse-dir=/opt/local --with-metis-dir=/opt/local --with-parmetis-dir=/opt/local --with-hdf5-dir=/opt/local CC="/opt/local/bin/mpicc-openmpi-mp" CXX="/opt/local/bin/mpicxx-openmpi-mp" FC="/opt/local/bin/mpif90-openmpi-mp" F77="/opt/local/bin/mpif90-openmpi-mp" F90="/opt/local/bin/mpif90-openmpi-mp" COPTFLAGS="-Os" CXXOPTFLAGS="-Os" FOPTFLAGS="-Os" LDFLAGS="-L/opt/local/lib -Wl,-headerpad_max_install_names" CPPFLAGS="-I/opt/local/include" CFLAGS="-Os -arch x86_64" CXXFLAGS="-Os" FFLAGS="-Os" FCFLAGS="-Os" F90FLAGS="-Os" PETSC_ARCH="arch-macports" --with-mpiexec=mpiexec-openmpi-mp 
:debug:configure system:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_sea.us.rsync.macports.org_release_tarballs_ports_math_petsc/petsc/work/v3.7.4" && ./configure --prefix=/opt/local --prefix=/opt/local/lib/petsc --with-valgrind=0 --with-shared-libraries --with-debugging=0 --with-c2html-dir=/opt/local --without-x --with-blas-lapack-lib=/System/Library/Frameworks/Accelerate.framework/Versions/Current/Accelerate --with-hwloc-dir=/opt/local --with-suitesparse-dir=/opt/local --with-metis-dir=/opt/local --with-parmetis-dir=/opt/local --with-hdf5-dir=/opt/local CC="/opt/local/bin/mpicc-openmpi-mp" CXX="/opt/local/bin/mpicxx-openmpi-mp" FC="/opt/local/bin/mpif90-openmpi-mp" F77="/opt/local/bin/mpif90-openmpi-mp" F90="/opt/local/bin/mpif90-openmpi-mp" COPTFLAGS="-Os" CXXOPTFLAGS="-Os" FOPTFLAGS="-Os" LDFLAGS="-L/opt/local/lib -Wl,-headerpad_max_install_names" CPPFLAGS="-I/opt/local/include" CFLAGS="-Os -arch x86_64" CXXFLAGS="-Os" FFLAGS="-Os" FCFLAGS="-Os" F90FLAGS="-Os" PETSC_ARCH="arch-macports" --with-mpiexec=mpiexec-openmpi-mp 
:info:configure Configure does not support Python 3 yet, please run as
:info:configure   python2 './configure' '--prefix=/opt/local' '--prefix=/opt/local/lib/petsc' '--with-valgrind=0' '--with-shared-libraries' '--with-debugging=0' '--with-c2html-dir=/opt/local' '--without-x' '--with-blas-lapack-lib=/System/Library/Frameworks/Accelerate.framework/Versions/Current/Accelerate' '--with-hwloc-dir=/opt/local' '--with-suitesparse-dir=/opt/local' '--with-metis-dir=/opt/local' '--with-parmetis-dir=/opt/local' '--with-hdf5-dir=/opt/local' 'CC=/opt/local/bin/mpicc-openmpi-mp' 'CXX=/opt/local/bin/mpicxx-openmpi-mp' 'FC=/opt/local/bin/mpif90-openmpi-mp' 'F77=/opt/local/bin/mpif90-openmpi-mp' 'F90=/opt/local/bin/mpif90-openmpi-mp' 'COPTFLAGS=-Os' 'CXXOPTFLAGS=-Os' 'FOPTFLAGS=-Os' 'LDFLAGS=-L/opt/local/lib -Wl,-headerpad_max_install_names' 'CPPFLAGS=-I/opt/local/include' 'CFLAGS=-Os -arch x86_64' 'CXXFLAGS=-Os' 'FFLAGS=-Os' 'FCFLAGS=-Os' 'F90FLAGS=-Os' 'PETSC_ARCH=arch-macports' '--with-mpiexec=mpiexec-openmpi-mp'
:info:configure Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_sea.us.rsync.macports.org_release_tarballs_ports_math_petsc/petsc/work/v3.7.4" && ./configure --prefix=/opt/local --prefix=/opt/local/lib/petsc --with-valgrind=0 --with-shared-libraries --with-debugging=0 --with-c2html-dir=/opt/local --without-x --with-blas-lapack-lib=/System/Library/Frameworks/Accelerate.framework/Versions/Current/Accelerate --with-hwloc-dir=/opt/local --with-suitesparse-dir=/opt/local --with-metis-dir=/opt/local --with-parmetis-dir=/opt/local --with-hdf5-dir=/opt/local CC="/opt/local/bin/mpicc-openmpi-mp" CXX="/opt/local/bin/mpicxx-openmpi-mp" FC="/opt/local/bin/mpif90-openmpi-mp" F77="/opt/local/bin/mpif90-openmpi-mp" F90="/opt/local/bin/mpif90-openmpi-mp" COPTFLAGS="-Os" CXXOPTFLAGS="-Os" FOPTFLAGS="-Os" LDFLAGS="-L/opt/local/lib -Wl,-headerpad_max_install_names" CPPFLAGS="-I/opt/local/include" CFLAGS="-Os -arch x86_64" CXXFLAGS="-Os" FFLAGS="-Os" FCFLAGS="-Os" F90FLAGS="-Os" PETSC_ARCH="arch-macports" --with-mpiexec=mpiexec-openmpi-mp

I was able to install petsc successfully after selecting python27 instead. In case it matters, my variant set is: 

  petsc @3.7.4_0+accelerate+gfortran+hdf5+hwloc+openmpi+parmetis+suitesparse (active)

I also found that the dependency lbzip2 is missing from the Portfile for petsc, again failing at the configure phase. Installing lbzip2 resolved this second issue.

Change History (3)

comment:1 Changed 7 years ago by seanfarley (Sean Farley)

Owner: set to seanfarley
Status: new → accepted

Ah, good catch. Thanks for the report. I'll try to fix this soon.

comment:2 Changed 6 years ago by mf2k (Frank Schima)

Cc: sean@… removed

comment:3 Changed 6 years ago by seanfarley (Sean Farley)

Resolution: → fixed
Status: accepted → closed

In 221d10e025ae0948c292e178850d9117d57d0289/macports-ports:

petsc: update to 3.8.3

This patch corrects the sundials dependency, patches configure to use MacPorts
python, and correct the petsc.pc pkgconfig file.

Fixes: #54119
Fixes: #55877
Fixes: #55889

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