April 2018 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Install location for MPIUNI mpi.h
by Satish Balay 25 Apr '18

25 Apr '18

On Wed, 25 Apr 2018, Jed Brown wrote: > Satish Balay <balay(a)mcs.anl.gov> writes: > > > On Wed, 25 Apr 2018, Jed Brown wrote: > > > >> It is currently installed to include/petsc/mpiuni/mpi.h and petscsys.h > >> includes it as <mpi.h>, which means that users of MPIUNI need to put > >> -I/prefix/include/petsc/mpiuni in their command lines. Matt and I agree > >> that this is bad. We disagree on the solution. > > > > Well in this context MPIUNI behaves like any other externalpackage. > > > >> He wants to install it to /prefix/include/mpi.h as though the user had > >> written --download-mpich. This would conflict if a user later installs > >> a real MPI to that location. > > > > We already have this conflict when switching between mpich and openmpi [so this issue would extend to mpiuni] > > You mean if someone --download-mpich and then manually installs Open MPI > to the same prefix, overwiting the MPICH header? Yes [and more generally with non-prefix install] > > Note that the option isn't --download-mpiuni, it's --with-mpi=0. Yes - and configure deals with it like externalpackage [wrt other dependencies] > > >> I would rather that petscsys.h include <petsc/mpiuni/mpi.h> because it > >> can't be used without PETSc and nobody who ever wrote #include <mpi.h> > >> in their own code will be happy if they get MPIUNI. > > > > The reason for using supporting '#include <mpi.h>' - is so that user > > codes that might use '#include <mpi.h>' would also work with mpiuni > > build of petsc. > > If a user does this and doesn't link PETSc, it literally won't work. I > conjecture that nobody that writes #include <mpi.h> in their code will > be happy if they get MPIUNI. I'm not sure how many externalpackages work with mpiuni with '#include <mpi.h>' > > Yeah - tradeoffs for each choice - so we settled on the current one - > > with petsc-makefile usage as the primary supported mode for users. > > > > This issue does not come up for such users. And non-petsc-makefile > > users were to grab all the flags from petsc makefiles and use them > > anyway. > > > > This issue is primarily comes up for users who expect the following to > > work [which never worked portably] > > > > gcc -Ipath_to_petsc_include -Lpath_to_petsc_lib -lpetsc > > It works now (as long as you use shared libraries), modulo MPI. i.e its a small subset of all use cases [prefix install + shared libraires + all externalpackages are also shared] Note: for regular non-prefix install - there is the extra -I$PETSC_DIR/$PETSC_ARCH/include [or you could say I$PETSC_DIR/include is the extra one that would have to be explicitly listed] Satish

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Re: [petsc-dev] Install location for MPIUNI mpi.h
by Jed Brown 25 Apr '18

25 Apr '18

Satish Balay <balay(a)mcs.anl.gov> writes: > On Wed, 25 Apr 2018, Jed Brown wrote: > >> It is currently installed to include/petsc/mpiuni/mpi.h and petscsys.h >> includes it as <mpi.h>, which means that users of MPIUNI need to put >> -I/prefix/include/petsc/mpiuni in their command lines. Matt and I agree >> that this is bad. We disagree on the solution. > > Well in this context MPIUNI behaves like any other externalpackage. > >> He wants to install it to /prefix/include/mpi.h as though the user had >> written --download-mpich. This would conflict if a user later installs >> a real MPI to that location. > > We already have this conflict when switching between mpich and openmpi [so this issue would extend to mpiuni] You mean if someone --download-mpich and then manually installs Open MPI to the same prefix, overwiting the MPICH header? Note that the option isn't --download-mpiuni, it's --with-mpi=0. >> I would rather that petscsys.h include <petsc/mpiuni/mpi.h> because it >> can't be used without PETSc and nobody who ever wrote #include <mpi.h> >> in their own code will be happy if they get MPIUNI. > > The reason for using supporting '#include <mpi.h>' - is so that user > codes that might use '#include <mpi.h>' would also work with mpiuni > build of petsc. If a user does this and doesn't link PETSc, it literally won't work. I conjecture that nobody that writes #include <mpi.h> in their code will be happy if they get MPIUNI. > Yeah - tradeoffs for each choice - so we settled on the current one - > with petsc-makefile usage as the primary supported mode for users. > > This issue does not come up for such users. And non-petsc-makefile > users were to grab all the flags from petsc makefiles and use them > anyway. > > This issue is primarily comes up for users who expect the following to > work [which never worked portably] > > gcc -Ipath_to_petsc_include -Lpath_to_petsc_lib -lpetsc It works now (as long as you use shared libraries), modulo MPI.

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Re: [petsc-dev] Install location for MPIUNI mpi.h
by Satish Balay 25 Apr '18

25 Apr '18

On Wed, 25 Apr 2018, Jed Brown wrote: > It is currently installed to include/petsc/mpiuni/mpi.h and petscsys.h > includes it as <mpi.h>, which means that users of MPIUNI need to put > -I/prefix/include/petsc/mpiuni in their command lines. Matt and I agree > that this is bad. We disagree on the solution. Well in this context MPIUNI behaves like any other externalpackage. > He wants to install it to /prefix/include/mpi.h as though the user had > written --download-mpich. This would conflict if a user later installs > a real MPI to that location. We already have this conflict when switching between mpich and openmpi [so this issue would extend to mpiuni] > > I would rather that petscsys.h include <petsc/mpiuni/mpi.h> because it > can't be used without PETSc and nobody who ever wrote #include <mpi.h> > in their own code will be happy if they get MPIUNI. The reason for using supporting '#include <mpi.h>' - is so that user codes that might use '#include <mpi.h>' would also work with mpiuni build of petsc. Yeah - tradeoffs for each choice - so we settled on the current one - with petsc-makefile usage as the primary supported mode for users. This issue does not come up for such users. And non-petsc-makefile users were to grab all the flags from petsc makefiles and use them anyway. This issue is primarily comes up for users who expect the following to work [which never worked portably] gcc -Ipath_to_petsc_include -Lpath_to_petsc_lib -lpetsc Satish

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Re: [petsc-dev] Install location for MPIUNI mpi.h
by Matthew Knepley 25 Apr '18

25 Apr '18

On Wed, Apr 25, 2018 at 2:36 PM, Jed Brown <jed(a)jedbrown.org> wrote: > It is currently installed to include/petsc/mpiuni/mpi.h and petscsys.h > includes it as <mpi.h>, which means that users of MPIUNI need to put > -I/prefix/include/petsc/mpiuni in their command lines. Matt and I agree > that this is bad. We disagree on the solution. > > He wants to install it to /prefix/include/mpi.h as though the user had > written --download-mpich. This would conflict if a user later installs > a real MPI to that location. > The idea should be that "installing" means that everyone is using compatible things from that location. If you allow an MPIUNI PETSc to be installed to a location that also has another MPI, what does mpiexec in ./bin do? There is just as much potential for confusion as there is when putting an MPICH PETSc in a location with OpenMPI installed. Matt > I would rather that petscsys.h include <petsc/mpiuni/mpi.h> because it > can't be used without PETSc and nobody who ever wrote #include <mpi.h> > in their own code will be happy if they get MPIUNI. > -- 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.caam.rice.edu/~mk51/>

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Install location for MPIUNI mpi.h
by Jed Brown 25 Apr '18

25 Apr '18

It is currently installed to include/petsc/mpiuni/mpi.h and petscsys.h includes it as <mpi.h>, which means that users of MPIUNI need to put -I/prefix/include/petsc/mpiuni in their command lines. Matt and I agree that this is bad. We disagree on the solution. He wants to install it to /prefix/include/mpi.h as though the user had written --download-mpich. This would conflict if a user later installs a real MPI to that location. I would rather that petscsys.h include <petsc/mpiuni/mpi.h> because it can't be used without PETSc and nobody who ever wrote #include <mpi.h> in their own code will be happy if they get MPIUNI.

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Re: [petsc-dev] Error with --download-strumpack
by Satish Balay 24 Apr '18

24 Apr '18

I have this change at: https://bitbucket.org/petsc/petsc/pull-requests/945/strumpack-update-to-ver… Satish On Tue, 24 Apr 2018, Satish Balay wrote: > If upgrading petsc to strumpack-2.2.0 - you can do: > > diff --git a/config/BuildSystem/config/packages/strumpack.py b/config/BuildSystem/config/packages/strumpack.py > index e3d32666f0..62054b4fb5 100644 > --- a/config/BuildSystem/config/packages/strumpack.py > +++ b/config/BuildSystem/config/packages/strumpack.py > @@ -4,8 +4,9 @@ import os > class Configure(config.package.CMakePackage): > def __init__(self, framework): > config.package.CMakePackage.__init__(self, framework) > - self.gitcommit = 'v2.1.0' > - self.download = ['git://https://github.com/pghysels/STRUMPACK','http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz'] > + self.gitcommit = 'v2.2.0' > + self.download = ['git://https://github.com/pghysels/STRUMPACK','https://github.com/pghysels/STRUMPACK/archive/'+self.gitcommit+'.tar.gz'] > + self.downloaddirnames = ['STRUMPACK','strumpack'] > self.functions = ['STRUMPACK_init'] > self.includes = ['StrumpackSparseSolver.h'] > self.liblist = [['libstrumpack.a']] > > > Satish > > On Tue, 24 Apr 2018, Junchao Zhang wrote: > > > Great, thanks. > > > > --Junchao Zhang > > > > On Tue, Apr 24, 2018 at 11:54 AM, Balay, Satish <balay(a)mcs.anl.gov> wrote: > > > > > Ok - for https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz to > > > work - you need: > > > > > > > > > diff --git a/config/BuildSystem/config/packages/strumpack.py > > > b/config/BuildSystem/config/packages/strumpack.py > > > index e3d32666f0..0edd9c19e0 100644 > > > --- a/config/BuildSystem/config/packages/strumpack.py > > > +++ b/config/BuildSystem/config/packages/strumpack.py > > > @@ -6,6 +6,7 @@ class Configure(config.package.CMakePackage): > > > config.package.CMakePackage.__init__(self, framework) > > > self.gitcommit = 'v2.1.0' > > > self.download = ['git://https://github.com/pghysels/STRUMPACK > > > ','http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz > > > '] > > > + self.downloaddirnames = ['STRUMPACK','strumpack'] > > > self.functions = ['STRUMPACK_init'] > > > self.includes = ['StrumpackSparseSolver.h'] > > > self.liblist = [['libstrumpack.a']] > > > > > > Are you updating petsc-master to use v2.2.0 of strumpack? > > > > > > Satish > > > > > > On Tue, 24 Apr 2018, Satish Balay wrote: > > > > > > > You can use: > > > > > > > > --download-strumpack=1 --download-strumpack-commit=v2.2.0 > > > > > > > > Currently the tarball URL used is > > > > http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz > > > > - and it uses the notation: > > > > > > > > strumpack-2.1.0/ > > > > > > > > But https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz would > > > > be using a different notation for 'dirname' - so configure can't find > > > > it. > > > > > > > > Satish > > > > > > > > On Tue, 24 Apr 2018, Junchao Zhang wrote: > > > > > > > > > Hi, Satish, > > > > > This configure option --download-strumpack= > > > > > https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz does not > > > work. It > > > > > looks it is because the package uses upper case for its name. > > > > > > > > > > ************************************************************ > > > ******************* > > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > > > for > > > > > details): > > > > > ------------------------------------------------------------ > > > ------------------- > > > > > Error during download/extract/detection of STRUMPACK: > > > > > > > > > > Looking for STRUMPACK at git.strumpack, hg.strumpack or a directory > > > > > starting with ['strumpack'] > > > > > > > > > > --Junchao Zhang > > > > > > > > > > > > > > > > > > > > > > >

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Re: [petsc-dev] Error with --download-strumpack
by Satish Balay 24 Apr '18

24 Apr '18

If upgrading petsc to strumpack-2.2.0 - you can do: diff --git a/config/BuildSystem/config/packages/strumpack.py b/config/BuildSystem/config/packages/strumpack.py index e3d32666f0..62054b4fb5 100644 --- a/config/BuildSystem/config/packages/strumpack.py +++ b/config/BuildSystem/config/packages/strumpack.py @@ -4,8 +4,9 @@ import os class Configure(config.package.CMakePackage): def __init__(self, framework): config.package.CMakePackage.__init__(self, framework) - self.gitcommit = 'v2.1.0' - self.download = ['git://https://github.com/pghysels/STRUMPACK','http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz'] + self.gitcommit = 'v2.2.0' + self.download = ['git://https://github.com/pghysels/STRUMPACK','https://github.com/pghysels/STRUMPACK/archive/'+self.gitcommit+'.tar.gz'] + self.downloaddirnames = ['STRUMPACK','strumpack'] self.functions = ['STRUMPACK_init'] self.includes = ['StrumpackSparseSolver.h'] self.liblist = [['libstrumpack.a']] Satish On Tue, 24 Apr 2018, Junchao Zhang wrote: > Great, thanks. > > --Junchao Zhang > > On Tue, Apr 24, 2018 at 11:54 AM, Balay, Satish <balay(a)mcs.anl.gov> wrote: > > > Ok - for https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz to > > work - you need: > > > > > > diff --git a/config/BuildSystem/config/packages/strumpack.py > > b/config/BuildSystem/config/packages/strumpack.py > > index e3d32666f0..0edd9c19e0 100644 > > --- a/config/BuildSystem/config/packages/strumpack.py > > +++ b/config/BuildSystem/config/packages/strumpack.py > > @@ -6,6 +6,7 @@ class Configure(config.package.CMakePackage): > > config.package.CMakePackage.__init__(self, framework) > > self.gitcommit = 'v2.1.0' > > self.download = ['git://https://github.com/pghysels/STRUMPACK > > ','http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz > > '] > > + self.downloaddirnames = ['STRUMPACK','strumpack'] > > self.functions = ['STRUMPACK_init'] > > self.includes = ['StrumpackSparseSolver.h'] > > self.liblist = [['libstrumpack.a']] > > > > Are you updating petsc-master to use v2.2.0 of strumpack? > > > > Satish > > > > On Tue, 24 Apr 2018, Satish Balay wrote: > > > > > You can use: > > > > > > --download-strumpack=1 --download-strumpack-commit=v2.2.0 > > > > > > Currently the tarball URL used is > > > http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz > > > - and it uses the notation: > > > > > > strumpack-2.1.0/ > > > > > > But https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz would > > > be using a different notation for 'dirname' - so configure can't find > > > it. > > > > > > Satish > > > > > > On Tue, 24 Apr 2018, Junchao Zhang wrote: > > > > > > > Hi, Satish, > > > > This configure option --download-strumpack= > > > > https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz does not > > work. It > > > > looks it is because the package uses upper case for its name. > > > > > > > > ************************************************************ > > ******************* > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > > for > > > > details): > > > > ------------------------------------------------------------ > > ------------------- > > > > Error during download/extract/detection of STRUMPACK: > > > > > > > > Looking for STRUMPACK at git.strumpack, hg.strumpack or a directory > > > > starting with ['strumpack'] > > > > > > > > --Junchao Zhang > > > > > > > > > > > > > > >

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Re: [petsc-dev] Error with --download-strumpack
by Junchao Zhang 24 Apr '18

24 Apr '18

Great, thanks. --Junchao Zhang On Tue, Apr 24, 2018 at 11:54 AM, Balay, Satish <balay(a)mcs.anl.gov> wrote: > Ok - for https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz to > work - you need: > > > diff --git a/config/BuildSystem/config/packages/strumpack.py > b/config/BuildSystem/config/packages/strumpack.py > index e3d32666f0..0edd9c19e0 100644 > --- a/config/BuildSystem/config/packages/strumpack.py > +++ b/config/BuildSystem/config/packages/strumpack.py > @@ -6,6 +6,7 @@ class Configure(config.package.CMakePackage): > config.package.CMakePackage.__init__(self, framework) > self.gitcommit = 'v2.1.0' > self.download = ['git://https://github.com/pghysels/STRUMPACK > ','http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz > '] > + self.downloaddirnames = ['STRUMPACK','strumpack'] > self.functions = ['STRUMPACK_init'] > self.includes = ['StrumpackSparseSolver.h'] > self.liblist = [['libstrumpack.a']] > > Are you updating petsc-master to use v2.2.0 of strumpack? > > Satish > > On Tue, 24 Apr 2018, Satish Balay wrote: > > > You can use: > > > > --download-strumpack=1 --download-strumpack-commit=v2.2.0 > > > > Currently the tarball URL used is > > http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz > > - and it uses the notation: > > > > strumpack-2.1.0/ > > > > But https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz would > > be using a different notation for 'dirname' - so configure can't find > > it. > > > > Satish > > > > On Tue, 24 Apr 2018, Junchao Zhang wrote: > > > > > Hi, Satish, > > > This configure option --download-strumpack= > > > https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz does not > work. It > > > looks it is because the package uses upper case for its name. > > > > > > ************************************************************ > ******************* > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > for > > > details): > > > ------------------------------------------------------------ > ------------------- > > > Error during download/extract/detection of STRUMPACK: > > > > > > Looking for STRUMPACK at git.strumpack, hg.strumpack or a directory > > > starting with ['strumpack'] > > > > > > --Junchao Zhang > > > > > > > > >

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Re: [petsc-dev] Error with --download-strumpack
by Satish Balay 24 Apr '18

24 Apr '18

Ok - for https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz to work - you need: diff --git a/config/BuildSystem/config/packages/strumpack.py b/config/BuildSystem/config/packages/strumpack.py index e3d32666f0..0edd9c19e0 100644 --- a/config/BuildSystem/config/packages/strumpack.py +++ b/config/BuildSystem/config/packages/strumpack.py @@ -6,6 +6,7 @@ class Configure(config.package.CMakePackage): config.package.CMakePackage.__init__(self, framework) self.gitcommit = 'v2.1.0' self.download = ['git://https://github.com/pghysels/STRUMPACK','http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz'] + self.downloaddirnames = ['STRUMPACK','strumpack'] self.functions = ['STRUMPACK_init'] self.includes = ['StrumpackSparseSolver.h'] self.liblist = [['libstrumpack.a']] Are you updating petsc-master to use v2.2.0 of strumpack? Satish On Tue, 24 Apr 2018, Satish Balay wrote: > You can use: > > --download-strumpack=1 --download-strumpack-commit=v2.2.0 > > Currently the tarball URL used is > http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz > - and it uses the notation: > > strumpack-2.1.0/ > > But https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz would > be using a different notation for 'dirname' - so configure can't find > it. > > Satish > > On Tue, 24 Apr 2018, Junchao Zhang wrote: > > > Hi, Satish, > > This configure option --download-strumpack= > > https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz does not work. It > > looks it is because the package uses upper case for its name. > > > > ******************************************************************************* > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > details): > > ------------------------------------------------------------------------------- > > Error during download/extract/detection of STRUMPACK: > > > > Looking for STRUMPACK at git.strumpack, hg.strumpack or a directory > > starting with ['strumpack'] > > > > --Junchao Zhang > > > >

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Re: [petsc-dev] Error with --download-strumpack
by Satish Balay 24 Apr '18

24 Apr '18

You can use: --download-strumpack=1 --download-strumpack-commit=v2.2.0 Currently the tarball URL used is http://portal.nersc.gov/project/sparse/strumpack/strumpack-2.1.0.tar.gz - and it uses the notation: strumpack-2.1.0/ But https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz would be using a different notation for 'dirname' - so configure can't find it. Satish On Tue, 24 Apr 2018, Junchao Zhang wrote: > Hi, Satish, > This configure option --download-strumpack= > https://github.com/pghysels/STRUMPACK/archive/v2.2.0.tar.gz does not work. It > looks it is because the package uses upper case for its name. > > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > ------------------------------------------------------------------------------- > Error during download/extract/detection of STRUMPACK: > > Looking for STRUMPACK at git.strumpack, hg.strumpack or a directory > starting with ['strumpack'] > > --Junchao Zhang >

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