[petsc-dev] --download and spack

Balay, Satish balay at mcs.anl.gov
Sun Oct 21 13:27:28 CDT 2018 

On Sun, 21 Oct 2018, Smith, Barry F. wrote:

> 
> 
> > On Oct 21, 2018, at 12:57 PM, Balay, Satish <balay at mcs.anl.gov> wrote:
> > 
> > Spack model is not to trust any system stuff - they are likely
> > incomaptible [esp when there are multiple compiler configs].
> 
>    I'd trust system blas over OpenBLAS.

sure - with the specific knowledge you have - - regarding Mac, and
petsc - this is obvious. But for spack - a general- purpose tool - its
not.  [and in some install situations - its unlikely to work - as
mentioned below]
> 
> > 
> > So one would have to explicitly list them in ~/.spack/package.py - if one wants it.
> 
>    It's the editing the damn file that is annoying. They should have some simple spack command to run that sets up the file for you.
> 
> > 
> > But I haven't figured out how to specify vecLib on Mac to spack..
> 
>     This is how I did it (still seems to work)
> 
>     all:
>         providers:
>             # prefer OpenMPI over MPICH by default
>             mpi: [mpich, openmpi]
>             # Use Apple BLAS/LAPACK accelerator library instead of installing one
>             blas: [veclibfort]
>             lapack: [veclibfort]

Ah - ok 'veclibfort' is what I have to remember..

Satish
> 
> 
> > [one of the packages in xsdk need cblas interfaces - so I end up using
> > openblas for most of my installs]
> > 
> > Satish
> > 
> > On Sun, 21 Oct 2018, Smith, Barry F. wrote:
> > 
> >> 
> >>   Still prefers OpenBLAS over system BLAS.
> >> 
> >> 
> >> 
> >>> On Oct 21, 2018, at 12:31 PM, Barry Smith <bsmith at anl.gov> wrote:
> >>> 
> >>> 
> >>>  How does one set the compiler for Spack to use. I read all of https://spack.readthedocs.io/en/latest/getting_started.html and it showed how to find compilers and add them to the spack compiler list but nothing about how to tell spack to use a particular compiler?
> >>> 
> >>> 
> >>> 
> >>>> On Oct 21, 2018, at 11:51 AM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
> >>>> 
> >>>> 
> >>>> Needs some more work
> >>>> 
> >>>> 
> >>>> ./bin/spack install petsc+hypre
> >>>> ==> mpich at 3.2 : externally installed in /usr/local
> >>>> ==> mpich at 3.2 : generating module file
> >>>> ==> mpich at 3.2 : registering into DB
> >>>> ==> zlib at 1.2.8 : externally installed in /usr
> >>>> ==> zlib at 1.2.8 : generating module file
> >>>> ==> zlib at 1.2.8 : registering into DB
> >>>> ==> Installing hdf5
> >>>> ==> Fetching https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.3/src/hdf5-1.10.3.tar.gz
> >>>> ######################################################################## 100.0%
> >>>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/hdf5-1.10.3-qe62ngz3szijov3frsc6sclbfylst3qk/hdf5-1.10.3.tar.gz
> >>>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/hdf5-1.10.3-qe62ngz3szijov3frsc6sclbfylst3qk
> >>>> ==> No patches needed for hdf5
> >>>> ==> Building hdf5 [AutotoolsPackage]
> >>>> ==> Executing phase: 'autoreconf'
> >>>> ==> Executing phase: 'configure'
> >>>> ==> Executing phase: 'build'
> >>>> ==> Executing phase: 'install'
> >>>> ==> Successfully installed hdf5
> >>>> Fetch: 4.37s.  Build: 2m 5.47s.  Total: 2m 9.84s.
> >>>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/hdf5-1.10.3-qe62ngz3szijov3frsc6sclbfylst3qk
> >>>> ==> Installing veclibfort
> >>>> ==> Fetching https://github.com/mcg1969/vecLibFort/archive/0.4.2.tar.gz
> >>>> ######################################################################## 100.0%
> >>>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/veclibfort-0.4.2-jgzyxocuu54r2lqckfugttbk3gpvhthk/0.4.2.tar.gz
> >>>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/veclibfort-0.4.2-jgzyxocuu54r2lqckfugttbk3gpvhthk
> >>>> ==> No patches needed for veclibfort
> >>>> ==> Building veclibfort [Package]
> >>>> ==> Executing phase: 'install'
> >>>> ==> Successfully installed veclibfort
> >>>> Fetch: 1.02s.  Build: 1.73s.  Total: 2.75s.
> >>>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/veclibfort-0.4.2-jgzyxocuu54r2lqckfugttbk3gpvhthk
> >>>> ==> Installing hypre
> >>>> ==> Fetching https://github.com/LLNL/hypre/archive/v2.15.0.tar.gz
> >>>> ######################################################################## 100.0%
> >>>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/hypre-2.15.0-zzqagb6smd7uzznitrlvx3eor4oay3dg/v2.15.0.tar.gz
> >>>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/hypre-2.15.0-zzqagb6smd7uzznitrlvx3eor4oay3dg
> >>>> ==> No patches needed for hypre
> >>>> ==> Building hypre [Package]
> >>>> ==> Executing phase: 'install'
> >>>> ==> Successfully installed hypre
> >>>> Fetch: 1.68s.  Build: 45.02s.  Total: 46.70s.
> >>>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/hypre-2.15.0-zzqagb6smd7uzznitrlvx3eor4oay3dg
> >>>> ==> cmake at 3.7.1 : externally installed in /usr/local/bin
> >>>> ==> cmake at 3.7.1 : generating module file
> >>>> ==> cmake at 3.7.1 : registering into DB
> >>>> ==> Installing metis
> >>>> ==> Fetching http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz
> >>>> ######################################################################## 100.0%
> >>>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/metis-5.1.0-x7k25qyuivjq4t4jb32gxagfa3qc4b3y/metis-5.1.0.tar.gz
> >>>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/metis-5.1.0-x7k25qyuivjq4t4jb32gxagfa3qc4b3y
> >>>> ==> Applied patch install_gklib_defs_rename.patch
> >>>> ==> Ran patch() for metis
> >>>> ==> Building metis [Package]
> >>>> ==> Executing phase: 'install'
> >>>> ==> Successfully installed metis
> >>>> Fetch: 3.86s.  Build: 8.33s.  Total: 12.19s.
> >>>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/metis-5.1.0-x7k25qyuivjq4t4jb32gxagfa3qc4b3y
> >>>> ==> Installing parmetis
> >>>> ==> Fetching http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz
> >>>> ######################################################################## 100.0%
> >>>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/parmetis-4.0.3-st6cbngrj2r5jgtenru4f6jbtrbvhp3h/parmetis-4.0.3.tar.gz
> >>>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/parmetis-4.0.3-st6cbngrj2r5jgtenru4f6jbtrbvhp3h
> >>>> ==> Applied patch enable_external_metis.patch
> >>>> ==> Applied patch pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch
> >>>> ==> Applied patch pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch
> >>>> ==> Building parmetis [CMakePackage]
> >>>> ==> Executing phase: 'cmake'
> >>>> ==> Executing phase: 'build'
> >>>> ==> Executing phase: 'install'
> >>>> ==> Successfully installed parmetis
> >>>> Fetch: 3.71s.  Build: 8.08s.  Total: 11.79s.
> >>>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/parmetis-4.0.3-st6cbngrj2r5jgtenru4f6jbtrbvhp3h
> >>>> ==> python at 2.7.1 : externally installed in /usr
> >>>> ==> python at 2.7.1 : generating module file
> >>>> ==> python at 2.7.1 : registering into DB
> >>>> ==> Installing superlu-dist
> >>>> ==> Fetching https://github.com/xiaoyeli/superlu_dist/archive/v5.4.0.tar.gz
> >>>> ######################################################################## 100.0%
> >>>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/superlu-dist-5.4.0-zfeg63fl3jxidb2irxucgz7nvmintbzn/v5.4.0.tar.gz
> >>>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/superlu-dist-5.4.0-zfeg63fl3jxidb2irxucgz7nvmintbzn
> >>>> ==> No patches needed for superlu-dist
> >>>> ==> Building superlu-dist [CMakePackage]
> >>>> ==> Executing phase: 'cmake'
> >>>> ==> Executing phase: 'build'
> >>>> ==> Executing phase: 'install'
> >>>> ==> Successfully installed superlu-dist
> >>>> Fetch: 2.03s.  Build: 22.54s.  Total: 24.57s.
> >>>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/superlu-dist-5.4.0-zfeg63fl3jxidb2irxucgz7nvmintbzn
> >>>> ==> Installing petsc
> >>>> ==> Fetching http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.10.2.tar.gz
> >>>> ######################################################################## 100.0%
> >>>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/petsc-3.10.2-7fmmtqrr42secdvbosssdjc5lxnohh6b/petsc-3.10.2.tar.gz
> >>>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/petsc-3.10.2-7fmmtqrr42secdvbosssdjc5lxnohh6b
> >>>> ==> No patches needed for petsc
> >>>> ==> Building petsc [Package]
> >>>> ==> Executing phase: 'install'
> >>>> ==> Error: ProcessError: Command exited with status 2:
> >>>>  'make' 'MAKE_NP=8'
> >>>> 
> >>>> 1 error found in build log:
> >>>>   52    
> >>>>   53    ==> 'make' 'MAKE_NP=8'
> >>>>   54    makefile:15: lib/petsc/conf/petscvariables: No such file or directory
> >>>>   55    makefile:16: /lib/petsc/conf/variables: No such file or directory
> >>>>   56    makefile:17: /lib/petsc/conf/rules: No such file or directory
> >>>>   57    makefile:18: /lib/petsc/conf/test.common: No such file or directory
> >>>>>> 58    make: *** No rule to make target `/lib/petsc/conf/test.common'.  Stop.
> >>>> 
> >>>> See build log for details:
> >>>> /Users/barrysmith/Src/spack/var/spack/stage/petsc-3.10.2-7fmmtqrr42secdvbosssdjc5lxnohh6b/petsc-3.10.2/spack-build.out
> >>>> 
> >>>> Then in the build log
> >>>> 
> >>>> File "/private/var/folders/c1/ldz_dt8n2r3dtwv_chp5pfr40000gn/T/barrysmith/spack-stage/spack-stage-hFL0xI/petsc-3.10.2/config/BuildSystem/nargs.py", line 360, in setValue
> >>>>  raise ValueError('Invalid directory: '+str(dir)+' for key '+str(self.key))
> >>>> ===============================================================================
> >>>>           Configuring PETSc to compile on your system                       
> >>>> ===============================================================================
> >>>> *******************************************************************************
> >>>>              ERROR in COMMAND LINE ARGUMENT to ./configure 
> >>>> -------------------------------------------------------------------------------
> >>>> Invalid directory: /usr/include for key with-zlib-include
> >>>> *******************************************************************************
> >>>> 
> >>>> 
> >>>> Apple OS doesn't come with a /usr/include 
> >>>> 
> >>>> 
> >>>>> On Oct 20, 2018, at 10:47 PM, Jed Brown <jed at jedbrown.org> wrote:
> >>>>> 
> >>>>> We're currently maintaining a (somewhat clumsy and limited, albeit
> >>>>> functional) package manager in the form of the --download functionality.
> >>>>> What do people think of outsourcing this to Spack, which would handle
> >>>>> dependency resolution and report includes/libraries to PETSc?  That
> >>>>> would enable reuse of installed packages between different PETSC_ARCH
> >>>>> and be more reliable regarding upgrade/downgrade when switching
> >>>>> branches.
> >>>> 
> >>> 
> >> 
> > 
>

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