[petsc-users] error with xlib

Satish Balay balay at mcs.anl.gov
Mon Apr 13 12:08:05 CDT 2020 

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 *****                                                                                                   ===============================================================================                                                                                     Compil
 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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