[petsc-dev] --download and spack
Smith, Barry F.
bsmith at mcs.anl.gov
Sun Oct 21 11:51:20 CDT 2018
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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