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Merge pull request #26 from mariux64/Add-julia-0.6.4
Julia: Add version 0.6.4
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,207 @@ | ||
| #! /bin/bash | ||
|
|
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| PKG=julia | ||
| VERSION=0.6.4 | ||
| BUILD=0 | ||
|
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| PREFIX=/pkg/$PKG-$VERSION-$BUILD | ||
| #PREFIX=/dev/shm/$PKG-$VERSION-$BUILD | ||
|
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| set -xe | ||
| umask 022 | ||
|
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| BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp | ||
| test -d $BUILD_TMPDIR && rm -rf $BUILD_TMPDIR | ||
| mkdir -p $BUILD_TMPDIR/home | ||
| export TMPDIR=$BUILD_TMPDIR | ||
| export HOME=$BUILD_TMPDIR/home | ||
|
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| exec </dev/null | ||
|
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| mkdir -p $PREFIX | ||
| cat >$PREFIX/profile <<-EOF | ||
| PATH=$PREFIX/bin:\$PATH | ||
| EOF | ||
| . $PREFIX/profile | ||
|
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| export MAKEFLAGS="-j $(nproc)" | ||
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| BUILDDIR=$PREFIX/build | ||
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| mkdir -p $BUILDDIR | ||
| cd $BUILDDIR | ||
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| test -e julia-${VERSION}-full.tar.gz || wget https://github.com/JuliaLang/julia/releases/download/v${VERSION}/julia-${VERSION}-full.tar.gz | ||
| test -d julia || tar xvf julia-${VERSION}-full.tar.gz | ||
| cd julia | ||
|
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||
| patch -p1 <<'EOF' | ||
| From 44d590277454035841803083f57af1b861192595 Mon Sep 17 00:00:00 2001 | ||
| From: Donald Buczek <buczek@molgen.mpg.de> | ||
| Date: Fri, 30 Jun 2017 11:41:41 +0200 | ||
| Subject: [PATCH 1/2] Allow OpenBLAS NUM_THREADS to be overwritten | ||
| When building OpenBLAS we have some default for its NUM_THREADS build | ||
| option. Allow this default to be overwritten by a new | ||
| OPENBLAS_NUM_THREADS make variable. | ||
| --- | ||
| deps/blas.mk | 9 +++++---- | ||
| 1 file changed, 5 insertions(+), 4 deletions(-) | ||
| diff --git a/deps/blas.mk b/deps/blas.mk | ||
| index 55216c8..b9bf8ed 100644 | ||
| --- a/deps/blas.mk | ||
| +++ b/deps/blas.mk | ||
| @@ -14,17 +14,18 @@ OPENBLAS_BUILD_OPTS += GEMM_MULTITHREADING_THRESHOLD=50 | ||
| ifneq ($(ARCH),x86_64) | ||
| # Assume we can't address much memory to spawn many threads | ||
| # It is also unlikely that 32-bit architectures have too many cores | ||
| -OPENBLAS_BUILD_OPTS += NUM_THREADS=8 | ||
| +OPENBLAS_NUM_THREADS:=8 | ||
| else ifeq ($(OS),WINNT) | ||
| # Windows seems unable to handle very many | ||
| -OPENBLAS_BUILD_OPTS += NUM_THREADS=16 | ||
| +OPENBLAS_NUM_THREADS:=16 | ||
| else ifeq ($(OS),Darwin) | ||
| # This should suffice for the largest macs | ||
| -OPENBLAS_BUILD_OPTS += NUM_THREADS=16 | ||
| +OPENBLAS_NUM_THREADS:=16 | ||
| else | ||
| # On linux, try to provision for the largest possible machine currently | ||
| -OPENBLAS_BUILD_OPTS += NUM_THREADS=16 | ||
| +OPENBLAS_NUM_THREADS:=16 | ||
| endif | ||
| +OPENBLAS_BUILD_OPTS += NUM_THREADS=$(OPENBLAS_NUM_THREADS) | ||
| else | ||
| OPENBLAS_BUILD_OPTS += USE_THREAD=0 | ||
| endif | ||
| -- | ||
| 2.4.1 | ||
| From 93dd6a3b0e45708b902e5b7ad459d554ce45b7ab Mon Sep 17 00:00:00 2001 | ||
| From: Donald Buczek <buczek@molgen.mpg.de> | ||
| Date: Fri, 30 Jun 2017 14:41:53 +0200 | ||
| Subject: [PATCH 2/2] Start up OpenBLAS with 1 thread per default. | ||
| --- | ||
| base/initdefs.jl | 5 ++--- | ||
| 1 file changed, 2 insertions(+), 3 deletions(-) | ||
| diff --git a/base/initdefs.jl b/base/initdefs.jl | ||
| index 20437a4..4f8f6e6 100644 | ||
| --- a/base/initdefs.jl | ||
| +++ b/base/initdefs.jl | ||
| @@ -62,9 +62,8 @@ function early_init() | ||
| # make sure OpenBLAS does not set CPU affinity (#1070, #9639) | ||
| ENV["OPENBLAS_MAIN_FREE"] = get(ENV, "OPENBLAS_MAIN_FREE", | ||
| get(ENV, "GOTOBLAS_MAIN_FREE", "1")) | ||
| - if Sys.CPU_CORES > 8 && !("OPENBLAS_NUM_THREADS" in keys(ENV)) && !("OMP_NUM_THREADS" in keys(ENV)) | ||
| - # Prevent openblas from starting too many threads, unless/until specifically requested | ||
| - ENV["OPENBLAS_NUM_THREADS"] = 8 | ||
| + if !("OPENBLAS_NUM_THREADS" in keys(ENV)) && !("OMP_NUM_THREADS" in keys(ENV)) | ||
| + Base.LinAlg.BLAS.set_num_threads(1) | ||
| end | ||
| end | ||
| -- | ||
| 2.4.1 | ||
| From 36e4a82ba8714bd76828d56bde4431758af552fc Mon Sep 17 00:00:00 2001 | ||
| From: Donald Buczek <buczek@molgen.mpg.de> | ||
| Date: Fri, 30 Jun 2017 15:44:42 +0200 | ||
| Subject: [PATCH 3/3] Remove html docs | ||
| The building of html docs pull something not versioned from the internet | ||
| and made the build sudddenly fail. | ||
| Building HTML documentation. | ||
| INFO: Initializing package repository /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6 | ||
| INFO: Cloning METADATA from https://github.com/JuliaLang/METADATA.jl | ||
| INFO: Updating METADATA... | ||
| INFO: Computing changes... | ||
| INFO: Cloning cache of Compat from https://github.com/JuliaLang/Compat.jl.git | ||
| INFO: Cloning cache of DocStringExtensions from https://github.com/JuliaDocs/DocStringExtensions.jl.git | ||
| INFO: Cloning cache of Documenter from https://github.com/JuliaDocs/Documenter.jl.git | ||
| INFO: Installing Compat v0.25.2 | ||
| INFO: Installing DocStringExtensions v0.3.3 | ||
| INFO: Installing Documenter v0.11.1 | ||
| INFO: No packages to install, update or remove | ||
| Documenter: setting up build directory. | ||
| Documenter: expanding markdown templates. | ||
| Documenter: building cross-references. | ||
| Documenter: running document checks. | ||
| !! Skipped doctesting. | ||
| > checking footnote links. | ||
| Documenter: populating indices. | ||
| Documenter: rendering document. | ||
| !! Overwriting '/dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/_build/html/en/assets/arrow.svg'. | ||
| !! Overwriting '/dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/_build/html/en/assets/documenter.js'. | ||
| !! Overwriting '/dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/_build/html/en/assets/search.js'. | ||
| !! Overwriting '/dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/_build/html/en/assets/highlightjs/highlight.js'. | ||
| !! Overwriting '/dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/_build/html/en/assets/highlightjs/default.css'. | ||
| !! Overwriting '/dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/_build/html/en/assets/documenter.css'. | ||
| fatal: Not a git repository (or any parent up to mount point /dev/shm) | ||
| Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). | ||
| ERROR: LoadError: failed process: Process(`git rev-parse --show-toplevel`, ProcessExited(128)) [128] | ||
| Stacktrace: | ||
| [1] pipeline_error(::Base.Process) at ./process.jl:682 | ||
| [2] read(::Cmd, ::Base.DevNullStream) at ./process.jl:629 | ||
| [3] readstring at ./process.jl:634 [inlined] (repeats 2 times) | ||
| [4] readchomp at ./io.jl:491 [inlined] | ||
| [5] (::Documenter.Utilities.##2#3)() at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Utilities/Utilities.jl:423 | ||
| [6] cd(::Documenter.Utilities.##2#3, ::String) at ./file.jl:70 | ||
| [7] url(::String, ::String) at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Utilities/Utilities.jl:422 | ||
| [8] render_article(::Documenter.Writers.HTMLWriter.HTMLContext, ::Documenter.Documents.NavNode) at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Writers/HTMLWriter.jl:403 | ||
| [9] render_page(::Documenter.Writers.HTMLWriter.HTMLContext, ::Documenter.Documents.NavNode) at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Writers/HTMLWriter.jl:170 | ||
| [10] render(::Documenter.Documents.Document) at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Writers/HTMLWriter.jl:118 | ||
| [11] dispatch(::Type{Documenter.Writers.FormatSelector}, ::Symbol, ::Documenter.Documents.Document) at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Selectors.jl:164 | ||
| [12] render(::Documenter.Documents.Document) at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Writers/Writers.jl:66 | ||
| [13] runner(::Type{Documenter.Builder.RenderDocument}, ::Documenter.Documents.Document) at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Builder.jl:205 | ||
| [14] dispatch(::Type{Documenter.Builder.DocumentPipeline}, ::Documenter.Documents.Document) at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Selectors.jl:164 | ||
| [15] cd(::Documenter.##2#3{Documenter.Documents.Document}, ::String) at ./file.jl:70 | ||
| [16] #makedocs#1(::Bool, ::Array{Any,1}, ::Function) at /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/deps/v0.6/Documenter/src/Documenter.jl:198 | ||
| [17] (::Documenter.#kw##makedocs)(::Array{Any,1}, ::Documenter.#makedocs) at ./<missing>:0 | ||
| [18] include_from_node1(::String) at ./loading.jl:569 | ||
| [19] include(::String) at ./sysimg.jl:14 | ||
| [20] process_options(::Base.JLOptions) at ./client.jl:305 | ||
| [21] _start() at ./client.jl:371 | ||
| while loading /dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/make.jl, in expression starting on line 118 | ||
| Makefile:33: recipe for target 'html' failed | ||
| make[2]: *** [html] Error 1 | ||
| make[2]: Leaving directory '/dev/shm/bee-root/julia/julia-0.6.0-0/source/doc' | ||
| Makefile:119: recipe for target 'docs' failed | ||
| make[1]: *** [docs] Error 2 | ||
| make[1]: Leaving directory '/dev/shm/bee-root/julia/julia-0.6.0-0/source' | ||
| Makefile:59: recipe for target '/dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/_build/html/en/index.html' failed | ||
| make: *** [/dev/shm/bee-root/julia/julia-0.6.0-0/source/doc/_build/html/en/index.html] Error 2 | ||
| --- | ||
| Makefile | 2 +- | ||
| 1 file changed, 1 insertion(+), 1 deletion(-) | ||
| diff --git a/Makefile b/Makefile | ||
| index 9dfbf52..e0f3f0f 100644 | ||
| --- a/Makefile | ||
| +++ b/Makefile | ||
| @@ -332,7 +332,7 @@ define stringreplace | ||
| $(build_depsbindir)/stringreplace $$(strings -t x - $1 | grep '$2' | awk '{print $$1;}') '$3' 255 "$(call cygpath_w,$1)" | ||
| endef | ||
| -install: $(build_depsbindir)/stringreplace $(BUILDROOT)/doc/_build/html/en/index.html | ||
| +install: $(build_depsbindir)/stringreplace | ||
| @$(MAKE) $(QUIET_MAKE) all | ||
| @for subdir in $(bindir) $(datarootdir)/julia/site/$(VERSDIR) $(docdir) $(man1dir) $(includedir)/julia $(libdir) $(private_libdir) $(sysconfdir); do \ | ||
| mkdir -p $(DESTDIR)$$subdir; \ | ||
| -- | ||
| 2.4.1 | ||
| EOF | ||
|
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| make -j $(nproc) prefix="${PREFIX}" MARCH=x86-64 OPENBLAS_NUM_THREADS=80 | ||
| make install prefix="${PREFIX}" MARCH=x86-64 | ||
|
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| patchelf --remove-rpath ${PREFIX}/lib/julia/libpcre2-posix.so.1.0.1 | ||
|
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| for i in `ls ${PREFIX}/bin`; do | ||
| ln -sv ${PREFIX}/bin/$i{,-$VERSION} | ||
| done | ||
|
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| exit |