[petsc-dev] --download and spack

Sun Oct 21 12:31:33 CDT 2018

   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.
> 