[petsc-users] error with xlib
Satish Balay
balay at mcs.anl.gov
Mon Apr 13 12:19:47 CDT 2020
And here is a p4est build.
Satish
--------
balay at kpro petsc % ./configure --with-mpi-dir=$HOME/soft/mpich-3.3.2 --with-zlib=1 --download-p4est
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
=============================================================================== ***** WARNING: You have an older version of Gnu make, it will work, but may not support all the parallel testing options. You can install the latest Gnu make with your package manager, such as brew or macports, or use the --download-make option to get the latest Gnu make ***** =============================================================================== ======
========================================================================= Trying to download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING =============================================================================== =============================================================================== Running configure on SOWING; this may take several minutes =============================================================================== ===========
==================================================================== Running make on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make install on SOWING; this may take several minutes =============================================================================== ================
=============================================================== Trying to download git://https://github.com/tisaac/p4est for P4EST =============================================================================== =============================================================================== Trying to bootstrap p4est using autotools; this may take several minutes =============================================================================== =====================
========================================================== Running configure on P4EST; this may take several minutes =============================================================================== =============================================================================== Running make on P4EST; this may take several minutes =============================================================================== ==========================
===================================================== Running make install on P4EST; this may take several minutes =============================================================================== Compilers:
C Compiler: /Users/balay/soft/mpich-3.3.2/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3
Version: Apple clang version 11.0.0 (clang-1100.0.33.8)
C++ Compiler: /Users/balay/soft/mpich-3.3.2/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -fvisibility=hidden -g
Version: Apple clang version 11.0.0 (clang-1100.0.33.8)
Fortran Compiler: /Users/balay/soft/mpich-3.3.2/bin/mpif90 -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g
Version: GNU Fortran (Homebrew GCC 9.3.0) 9.3.0
Linkers:
Shared linker: /Users/balay/soft/mpich-3.3.2/bin/mpicc -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3
Dynamic linker: /Users/balay/soft/mpich-3.3.2/bin/mpicc -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3
Libraries linked against: -lc++ -ldl
make:
Version: 3.81
/usr/bin/make
BlasLapack:
Library: -llapack -lblas
Unknown if this uses OpenMP (try export OMP_NUM_THREADS=<1-4> yourprogram -log_view)
uses 4 byte integers
MPI:
Version: 3
Includes: -I/Users/balay/soft/mpich-3.3.2/include
Mpiexec: /Users/balay/soft/mpich-3.3.2/bin/mpiexec
MPICH_NUMVERSION: 30302300
pthread:
X:
Includes: -I/opt/X11/include
Library: -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -lX11
zlib:
Library: -lz
cmake:
Version: 3.16.5
/usr/local/bin/cmake
regex:
p4est:
Includes: -I/Users/balay/petsc/arch-darwin-c-debug/include
Library: -Wl,-rpath,/Users/balay/petsc/arch-darwin-c-debug/lib -L/Users/balay/petsc/arch-darwin-c-debug/lib -lp4est -lsc
sowing:
Version: 1.1.25
/Users/balay/petsc/arch-darwin-c-debug/bin/bfort
Language used to compile PETSc: C
PETSc:
PETSC_ARCH: arch-darwin-c-debug
PETSC_DIR: /Users/balay/petsc
Scalar type: real
Precision: double
Integer size: 4 bytes
shared libraries: enabled
Memory alignment from malloc(): 16 bytes
xxx=========================================================================xxx
Configure stage complete. Now build PETSc libraries with:
make PETSC_DIR=/Users/balay/petsc PETSC_ARCH=arch-darwin-c-debug all
xxx=========================================================================xxx
balay at kpro petsc %
On Mon, 13 Apr 2020, Satish Balay via petsc-users wrote:
> you haven't sent any logs for this issue..
> [../arch-macosx-gnu-O-omp.py script or configure.log with the failure]
>
> Satish
>
> -------
> ipro:petsc balay$ ./configure --with-fortran-bindings=0 --with-mpi=0 --with-zlib=1
> ===============================================================================
> Configuring PETSc to compile on your system
> ===============================================================================
> =============================================================================== ***** WARNING: You have an older version of Gnu make, it will work, but may not support all the parallel testing options. You can install the latest Gnu make with your package manager, such as brew or macports, or use the --download-make option to get the latest Gnu make ***** =============================================================================== Comp
il
> ers:
> C Compiler: gcc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3
> Version: Apple clang version 11.0.3 (clang-1103.0.32.29)
> C++ Compiler: g++ -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -fvisibility=hidden -g -std=c++14
> Version: Apple clang version 11.0.3 (clang-1103.0.32.29)
> Fortran Compiler: gfortran -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g
> Version: GNU Fortran (Homebrew GCC 9.3.0) 9.3.0
> Linkers:
> Shared linker: gcc -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3
> Dynamic linker: gcc -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3
> Libraries linked against: -lc++ -ldl
> make:
> Version: 3.81
> /usr/bin/make
> BlasLapack:
> Library: -llapack -lblas
> Unknown if this uses OpenMP (try export OMP_NUM_THREADS=<1-4> yourprogram -log_view)
> uses 4 byte integers
> pthread:
> zlib:
> Library: -lz
> cmake:
> Version: 3.16.5
> /usr/local/bin/cmake
> X:
> Includes: -I/opt/X11/include
> Library: -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -lX11
> regex:
> Language used to compile PETSc: C
> PETSc:
> PETSC_ARCH: arch-darwin-c-debug
> PETSC_DIR: /Users/balay/petsc
> Scalar type: real
> Precision: double
> Integer size: 4 bytes
> shared libraries: enabled
> Memory alignment from malloc(): 16 bytes
> xxx=========================================================================xxx
> Configure stage complete. Now build PETSc libraries with:
> make PETSC_DIR=/Users/balay/petsc PETSC_ARCH=arch-darwin-c-debug all
> xxx=========================================================================xxx
> ipro:petsc balay$
>
>
>
> On Mon, 13 Apr 2020, Mark Adams wrote:
>
> > On Mon, Apr 13, 2020 at 12:48 PM Satish Balay <balay at mcs.anl.gov> wrote:
> >
> > > This is very funky
> > >
> > > >>>
> > > Configure Options: --configModules=PETSc.Configure
> > > --optionsModule=config.compilerOptions
> > > --with-mpi-dir=/usr/local/Cellar/mpich/3.3.2 COPTFLAGS="-O2 -g
> > > -Xpreprocessor -fopenmp -I"$(brew --prefix libomp)/include" -L"$(brew
> > > --prefix libomp)/lib -lomp"" CXXOPTFLAGS="-O2 -g -Xpreprocessor -fopenmp
> > > -I"$(brew --prefix libomp)/include" -L"$(brew --prefix libomp)/lib -lomp""
> > > FOPTFLAGS="-O2 -g -Xpreprocessor -fopenmp -I"$(brew --prefix
> > > libomp)/include" -L"$(brew --prefix libomp)/lib -lomp""
> > > --download-parmetis=1 --download-metis=1 --download-hypre=1
> > > --download-triangle=1 --download-p4est=1 --download-zlib --with-x=0
> > > --download-ctetgen --with-debugging=0 --download-hdf5=1
> > > PETSC_ARCH=arch-macosx-gnu-O-omp --with-openmp=1 --with-log=0
> > > --with-threadsafety --download-chaco
> > > <<<
> > >
> > > -I"$(brew --prefix libomp)/include" type options to configure doesn't make
> > > sense. You are using bash syntax here - and expecting configure to resolve
> > > it. Its best for your bash shell to evaluate this before passing this info
> > > to configure
> > >
> > > Also --download-zlib isn't needed on OSX
> > >
> >
> > Hum, I get:
> >
> > 12:52 mark/feature-xgc-interface-rebase *= ~/Codes/petsc$
> > ../arch-macosx-gnu-O-omp.py
> > ===============================================================================
> > Configuring PETSc to compile on your system
> >
> > ===============================================================================
> > TESTING: configureExternalPackagesDir from
> > config.framework(config/BuildSystem/config/framework.py:911)
> >
> >
> > *******************************************************************************
> > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
> > details):
> > -------------------------------------------------------------------------------
> > Package p4est requested but dependency zlib not requested. Perhaps you want
> > --download-zlib
> > *******************************************************************************
> >
> >
> >
> > >
> > > Satish
> > >
> > >
> > > On Mon, 13 Apr 2020, Mark Adams wrote:
> > >
> > > > Now that I look at it, I see:
> > > >
> > > > CFLAGS="-fstack-protector -fno-stack-check -Qunused-arguments -O2 -g
> > > > -Xpreprocessor -fopenmp -I"$(brew --prefix libomp)/include" -L"$(brew
> > > > --prefix libomp)/lib -lomp""
> > > > prefix="/Users/markadams/Codes/petsc/arch-macosx-gnu-O-omp"
> > > >
> > > > Note the two ". That does not look right. I use
> > > >
> > > > 'COPTFLAGS=-O2 -g -Xpreprocessor -fopenmp -I"$(brew --prefix
> > > > libomp)/include" -L"$(brew --prefix libomp)/lib -lomp" ',
> > > >
> > > > I know how to do stuff like:
> > > >
> > > > '--with-blaslapack-lib=-L' + os.environ['OLCF_NETLIB_LAPACK_ROOT'] +
> > > > '/lib64 -lblas -llapack'
> > > >
> > > > Is there like and os.exec that I could use like this for my FLAGS?
> > > >
> > > >
> > > >
> > > > On Mon, Apr 13, 2020 at 11:46 AM Matthew Knepley <knepley at gmail.com>
> > > wrote:
> > > >
> > > > > On Mon, Apr 13, 2020 at 11:34 AM Mark Adams <mfadams at lbl.gov> wrote:
> > > > >
> > > > >> I get this error configuring zlib, osx, with OpenMP.
> > > > >> Any ideas?
> > > > >>
> > > > >
> > > > > This failed without output
> > > > >
> > > > > Executing: cd
> > > > >
> > > /Users/markadams/Codes/petsc/arch-macosx-gnu-O-omp/externalpackages/zlib-1.2.11
> > > > > && CC="/usr/local/Cellar/mpich/3.3.2/bin/mpicc"
> > > CFLAGS="-fstack-protector
> > > > > -fno-stack-check -Qunused-arguments -O2 -g -Xpreprocessor -fopenmp
> > > > > -I"$(brew --prefix libomp)/include" -L"$(brew --prefix libomp)/lib
> > > -lomp""
> > > > > prefix="/Users/markadams/Codes/petsc/arch-macosx-gnu-O-omp"
> > > ./configure &&
> > > > > /usr/bin/make -j7 -l12.0 && /usr/bin/make install
> > > > >
> > > > > So execute each step in turn and see what fails.
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Matt
> > > > >
> > > > >
> > > > >> Thanks,
> > > > >> Mark
> > > > >>
> > > > >
> > > > >
> > > > > --
> > > > > What most experimenters take for granted before they begin their
> > > > > experiments is infinitely more interesting than any results to which
> > > their
> > > > > experiments lead.
> > > > > -- Norbert Wiener
> > > > >
> > > > > https://www.cse.buffalo.edu/~knepley/
> > > > > <http://www.cse.buffalo.edu/~knepley/>
> > > > >
> > > >
> > >
> > >
> >
>
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