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Update and simplify julia package (#14756)

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* Update and simplify julia package

The current Spack Julia package potentially installs a few julia
packages, with the installation being controlled by variants. There are
a couple of problems with this.

First, Julia handles packages very differently from systems such as R
and Python. Julia requires write access to the repository directories in
order for user installs of packages to work. If spack installs julia
packages then there will be a repository, DEPOT_PATH, in the
installation directory. If spack is used on an individual basis this
would work but would mean that package data is written to the spack
installation directory after installation. If spack is used to provide
packages for end users then user installs of julia packages will fail
due to lack of write access to the repository in the installation
directory. It seems best for spack to just install julia without any
julia packages, and drop the configuration for those packages.

Second, having spack install package as variants seems to be counter to
how spack works for other extendable systems, like R and Python. Julia
should be an extendable package in spack but it is not clear how to make
that work. As pointed out above, installing user packages requires write
access to the julia repositories, including the one in the install
directory. Essentially, a user package installation will try to update
metadata for *all* julia repositories.  Furthermore, each of those
repositories, assuming one per package with spack, would need to have
the Project.toml files merged to present the package stack to julia.
Again, it seems best for spack to just install julia itself and not try
to install julia packages, at least at this time. A good discussion on
this can be found at

https://discourse.julialang.org/t/how-does-one-set-up-a-centralized-julia-installation/13922.

This PR does the following:

- adds versions 1.2.0 and 1.3.1
- removes variants that correspond to julia packages
- changes python to build dependency as it seems to only be needed for
  LLVM
- the new versions can use Python-3
- removes dependencies for packages
- adds a conflict statement for Intel compiler, with comment
- add a setup_build_environment method to find GCC libraries
- make formatting consistent
- adds JULIA_CPU_TARGET option to correspond with target to help with
  running julia image on hardware older than build host
- added intel build options, for when they can be used
- removed code for installing packages
- removed code for julia config that was needed for packages

Note that versions below 0.5.1 fail to build, with or without these
changes. It is not clear why that is.

* Update var/spack/repos/builtin/packages/julia/package.py

Yes, need to use correct grammar even in the midst of numbers and symbols. Good catch!

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* More cleanup of Julia package

This commit does more cleanup and sets more constraints.

- Removed release-0.4 and release-0.5. I am not sure if those are
  actually useful but they are quite old and there are released versions
  from the same timeframe.
- Remove the binutils variant.
- Made cmake a build dependency for versions >= 1.
- Added git as a dependency for @master.
- Limit curl dependency to released versions.
- Do not use external curl for master. When I checked, using the
  external version failed but the internal curl worked.
- Versions <= 0.5.0 need an older version of openssl.
- Set conflicts directive for cxx variant.
- Added conflicts directive for needing +mkl with Intel compiler.
- Removed configuration settings as these prevented julia from working
  properly in all cases that I looked at.

* Fix flake8 error

Remove 'import sys' that is no longer used.

* More dependency tweaks

This commit sets further version constraints on dependencies. It really
looks like julia requires its internal dependencies more over time.

- curl only up to 0.5.0
- openssl only up to 0.5.0
- override with system curl up to version 0.5.0

* Fix spec for curl certs

Only depending on curl through 0.5.0.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit is contained in:
Glenn Johnson 2020-02-18 15:59:09 -06:00 committed by GitHub
parent 6f95967e95
commit 3ee0295fb2
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1 changed files with 104 additions and 174 deletions
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274
var/spack/repos/builtin/packages/julia/package.py
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@ -6,7 +6,6 @@
from spack import *
import os
import sys
class Julia(Package):
@ -16,62 +15,55 @@ class Julia(Package):
url = "https://github.com/JuliaLang/julia/releases/download/v0.4.3/julia-0.4.3-full.tar.gz"
git = "https://github.com/JuliaLang/julia.git"
maintainers = ['glennpj']
version('master', branch='master')
version('1.3.1', sha256='053908ec2706eb76cfdc998c077de123ecb1c60c945b4b5057aa3be19147b723')
version('1.2.0', sha256='2419b268fc5c3666dd9aeb554815fe7cf9e0e7265bc9b94a43957c31a68d9184')
version('1.1.1', sha256='3c5395dd3419ebb82d57bcc49dc729df3b225b9094e74376f8c649ee35ed79c2')
version('1.0.0', sha256='1a2497977b1d43bb821a5b7475b4054b29938baae8170881c6b8dd4099d133f1')
version('0.6.2', sha256='1e34c13091c9ddb47cf87a51566d94a06613f3db3c483b8f63b276e416dd621b')
version('release-0.5', branch='release-0.5')
version('0.5.2', sha256='f5ef56d79ed55eacba9fe968bb175317be3f61668ef93e747d76607678cc01dd')
version('0.5.1', sha256='533b6427a1b01bd38ea0601f58a32d15bf403f491b8415e9ce4305b8bc83bb21')
version('0.5.0', sha256='732478536b6dccecbf56e541eef0aed04de0e6d63ae631b136e033dda2e418a9')
version('release-0.4', branch='release-0.4')
version('0.4.7', sha256='d658d5bd5fb79b19f3c01cadb9aba8622ca8a12a4b687acc7d99c21413623570')
version('0.4.6', sha256='4c23c9fc72398014bd39327c2f7efd3a301884567d4cb2a89105c984d4d633ba')
version('0.4.5', sha256='cbf361c23a77e7647040e8070371691083e92aa93c8a318afcc495ad1c3a71d9')
version('0.4.3', sha256='2b9df25a8f58df8e43038ec30bae195dfb160abdf925f3fa193b59d40e4113c5')
# TODO: Split these out into jl-hdf5, jl-mpi packages etc.
variant("cxx", default=False, description="Prepare for Julia Cxx package")
variant("hdf5", default=False, description="Install Julia HDF5 package")
variant("mpi", default=True, description="Install Julia MPI package")
variant("plot", default=False,
description="Install Julia plotting packages")
variant("python", default=False,
description="Install Julia Python package")
variant("simd", default=False, description="Install Julia SIMD package")
variant("mkl", default=False, description="Use Intel MKL")
variant('cxx', default=False, description='Prepare for Julia Cxx package')
variant('mkl', default=False, description='Use Intel MKL')
patch('gc.patch', when='@0.4:0.4.5')
patch('openblas.patch', when='@0.4:0.4.5')
patch('armgcc.patch', when='@1.0.0:1.1.1 %gcc@:5.9 target=aarch64:')
variant('binutils', default=sys.platform != 'darwin',
description="Build via binutils")
# Build-time dependencies:
# depends_on("awk")
depends_on("m4", type="build")
# depends_on("pkgconfig")
# depends_on('awk')
depends_on('m4', type='build')
# depends_on('pkgconfig')
# Python only needed to build LLVM?
depends_on('python@2.7:2.8', type='build', when='@:1.1')
depends_on('python@2.7:', type='build', when='@1.2:')
depends_on('cmake @2.8:', type='build', when='@1.0:')
depends_on('git', type='build', when='@master')
# Combined build-time and run-time dependencies:
# (Yes, these are run-time dependencies used by Julia's package manager.)
depends_on("binutils", when='+binutils')
depends_on("cmake @2.8:")
depends_on("curl")
depends_on("git", when='@:0.4')
depends_on("git", when='@release-0.4')
depends_on("openssl")
depends_on("python@2.7:2.8")
depends_on("mkl", when='+mkl')
depends_on('cmake @2.8:', type=('build', 'run'), when='@:0.6')
depends_on('curl', when='@:0.5.0')
depends_on('git', type=('build', 'run'), when='@:0.4')
depends_on('openssl@:1.0', when='@:0.5.0')
depends_on('mkl', when='+mkl')
# Run-time dependencies:
# depends_on("arpack")
# depends_on("fftw +float")
# depends_on("gmp")
# depends_on("libgit")
# depends_on("mpfr")
# depends_on("openblas")
# depends_on("pcre2")
# depends_on('arpack')
# depends_on('fftw +float')
# depends_on('gmp')
# depends_on('libgit')
# depends_on('mpfr')
# depends_on('openblas')
# depends_on('pcre2')
# ARPACK: Requires BLAS and LAPACK; needs to use the same version
# as Julia.
@ -97,162 +89,100 @@ class Julia(Package):
# USE_SYSTEM_UTF8PROC=0
# USE_SYSTEM_LIBGIT2=0
# Run-time dependencies for Julia packages:
depends_on("hdf5", when="+hdf5", type="run")
depends_on("mpi", when="+mpi", type="run")
depends_on("py-matplotlib", when="+plot", type="run")
conflicts('+cxx', when='@:0.6', msg='Variant cxx requires Julia >= 1.0.0')
conflicts("@:0.7.0", when="target=aarch64:")
conflicts('@:0.7.0', when='target=aarch64:')
# GCC conflicts
conflicts('@:0.5.1', when='%gcc@8:', msg='Julia <= 0.5.1 needs GCC <= 7')
# Building recent versions of Julia with Intel is untested and unsupported
# by the Julia project, https://github.com/JuliaLang/julia/issues/23407.
conflicts('@0.6:', when='%intel',
msg='Only Julia <= 0.5.x can be built with the Intel compiler.')
conflicts('%intel', when='~mkl',
msg='Building with the Intel compiler requires the mkl variant '
'(+mkl)')
def setup_build_environment(self, env):
# The julia build can have trouble with finding GCC libraries with the
# spack compiler.
if self.compiler.name == 'gcc':
gcc_base = os.path.split(os.path.split(self.compiler.cc)[0])[0]
env.prepend_path('LD_LIBRARY_PATH', join_path(gcc_base, 'lib64'))
def install(self, spec, prefix):
# Julia needs git tags
if os.path.isfile(".git/shallow"):
git = which("git")
git("fetch", "--unshallow")
if os.path.isfile('.git/shallow'):
git = which('git')
git('fetch', '--unshallow')
# Explicitly setting CC, CXX, or FC breaks building libuv, one
# of Julia's dependencies. This might be a Darwin-specific
# problem. Given how Spack sets up compilers, Julia should
# still use Spack's compilers, even if we don't specify them
# explicitly.
# explicitly. Potential options are
# 'CC=cc',
# 'CXX=c++',
# 'FC=fc',
# 'USE_SYSTEM_ARPACK=1',
# 'override USE_SYSTEM_CURL=1',
# 'USE_SYSTEM_FFTW=1',
# 'USE_SYSTEM_GMP=1',
# 'USE_SYSTEM_MPFR=1',
# 'USE_SYSTEM_PCRE=1',
options = [
# "CC=cc",
# "CXX=c++",
# "FC=fc",
# "USE_SYSTEM_ARPACK=1",
"override USE_SYSTEM_CURL=1",
# "USE_SYSTEM_FFTW=1",
# "USE_SYSTEM_GMP=1",
# "USE_SYSTEM_MPFR=1",
# "USE_SYSTEM_PCRE=1",
"prefix=%s" % prefix]
if "+cxx" in spec:
if "@master" not in spec:
raise InstallError(
"Variant +cxx requires the @master version of Julia")
'prefix={0}'.format(prefix)
]
if '@:0.5.0' in spec:
options += [
"BUILD_LLVM_CLANG=1",
"LLVM_ASSERTIONS=1",
"USE_LLVM_SHLIB=1"]
'override USE_SYSTEM_CURL=1'
]
if '+cxx' in spec:
options += [
'BUILD_LLVM_CLANG=1',
'LLVM_ASSERTIONS=1',
'USE_LLVM_SHLIB=1'
]
if spec.target.family == 'aarch64':
options += [
'JULIA_CPU_TARGET=generic',
'MARCH=armv8-a+crc']
'MARCH=armv8-a+crc'
]
if spec.target.family == 'x86_64' or spec.target.family == 'x86':
if spec.target == 'x86_64':
options += [
'JULIA_CPU_TARGET=generic'
]
else:
options += [
'JULIA_CPU_TARGET={0}'.format(spec.target)
]
if '%intel' in spec:
options += [
'USEICC=1',
'USEIFC=1',
'USE_INTEL_LIBM=1'
]
if '+mkl' in spec:
options += [
'USE_INTEL_MKL=1']
'USE_INTEL_MKL=1',
]
with open('Make.user', 'w') as f:
f.write('\n'.join(options) + '\n')
make()
make("install")
make('install')
# Julia's package manager needs a certificate
cacert_dir = join_path(prefix, "etc", "curl")
if '@:0.5.0' in spec:
cacert_dir = join_path(prefix, 'etc', 'curl')
mkdirp(cacert_dir)
cacert_file = join_path(cacert_dir, "cacert.pem")
curl = which("curl")
curl("--create-dirs",
"--output", cacert_file,
"https://curl.haxx.se/ca/cacert.pem")
# Put Julia's compiler cache into a private directory
cachedir = join_path(prefix, "var", "julia", "cache")
mkdirp(cachedir)
# Store Julia packages in a private directory
pkgdir = join_path(prefix, "var", "julia", "pkg")
mkdirp(pkgdir)
# Configure Julia
if spec.satisfies('@master') or spec.satisfies("@0.7:"):
julia_config = 'startup.jl'
cache_path = 'DEPOT_PATH'
unshift = 'pushfirst!'
else:
julia_config = 'juliarc.jl'
cache_path = 'LOAD_CACHE_PATH'
unshift = 'unshift!'
with open(join_path(prefix, "etc", "julia", julia_config),
"a") as juliarc:
if "@master" in spec or "@release-0.5" in spec or "@0.5" in spec:
# This is required for versions @0.5:
juliarc.write(
'# Point package manager to working certificates\n')
if spec.satisfies('@master') or spec.satisfies('@0,7'):
juliarc.write('import LibGit2;')
juliarc.write('LibGit2.set_ssl_cert_locations("%s")\n' %
cacert_file)
juliarc.write('\n')
juliarc.write('# Put compiler cache into a private directory\n')
juliarc.write('empty!(Base.%s)\n' % cache_path)
juliarc.write('%s(Base.%s, "%s")\n' %
(unshift, cache_path, cachedir))
juliarc.write('\n')
juliarc.write('# Put Julia packages into a private directory\n')
juliarc.write('ENV["JULIA_PKGDIR"] = "%s"\n' % pkgdir)
juliarc.write('\n')
# Install some commonly used packages
julia = spec['julia'].command
if spec.satisfies("@:0.7"):
julia("-e", 'Pkg.init(); Pkg.update()')
pkgstart = ''
else:
pkgstart = 'import Pkg;'
# Install HDF5
if "+hdf5" in spec:
with open(join_path(prefix, "etc", "julia", julia_config),
"a") as juliarc:
juliarc.write('# HDF5\n')
juliarc.write('push!(Libdl.DL_LOAD_PATH, "%s")\n' %
spec["hdf5"].prefix.lib)
juliarc.write('\n')
julia("-e", pkgstart + 'Pkg.add("HDF5"); using HDF5')
julia("-e", pkgstart + 'Pkg.add("JLD"); using JLD')
# Install MPI
if "+mpi" in spec:
with open(join_path(prefix, "etc", "julia", julia_config),
"a") as juliarc:
juliarc.write('# MPI\n')
juliarc.write('ENV["JULIA_MPI_C_COMPILER"] = "%s"\n' %
join_path(spec["mpi"].prefix.bin, "mpicc"))
juliarc.write('ENV["JULIA_MPI_Fortran_COMPILER"] = "%s"\n' %
join_path(spec["mpi"].prefix.bin, "mpifort"))
juliarc.write('\n')
julia("-e", pkgstart + 'Pkg.add("MPI"); using MPI')
# Install Python
if "+python" in spec or "+plot" in spec:
with open(join_path(prefix, "etc", "julia", julia_config),
"a") as juliarc:
juliarc.write('# Python\n')
juliarc.write('ENV["PYTHON"] = "%s"\n' % spec["python"].home)
juliarc.write('\n')
# Python's OpenSSL package installer complains:
# Error: PREFIX too long: 166 characters, but only 128 allowed
# Error: post-link failed for: openssl-1.0.2g-0
julia("-e", pkgstart + 'Pkg.add("PyCall"); using PyCall')
if "+plot" in spec:
julia("-e", pkgstart + 'Pkg.add("PyPlot"); using PyPlot')
julia("-e", pkgstart + 'Pkg.add("Colors"); using Colors')
# These require maybe gtk and imagemagick
julia("-e", pkgstart + 'Pkg.add("Plots"); using Plots')
julia("-e", pkgstart + 'Pkg.add("PlotRecipes"); using PlotRecipes')
julia(
"-e",
pkgstart + 'Pkg.add("UnicodePlots"); using UnicodePlots'
)
julia("-e", """\
using Plots
using UnicodePlots
unicodeplots()
plot(x->sin(x)*cos(x), linspace(0, 2pi))
""")
# Install SIMD
if "+simd" in spec:
julia("-e", pkgstart + 'Pkg.add("SIMD"); using SIMD')
julia("-e", pkgstart + 'Pkg.status()')
cacert_file = join_path(cacert_dir, 'cacert.pem')
curl = which('curl')
curl('--create-dirs',
'--output', cacert_file,
'https://curl.haxx.se/ca/cacert.pem')