mariux64 · donald · Sep 12, 2018 · Sep 12, 2018
diff --git a/julia-0.6.4-0.build.sh b/julia-0.6.4-0.build.sh
@@ -0,0 +1,207 @@
+#! /bin/bash
+
+PKG=julia
+VERSION=0.6.4
+BUILD=0
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+#PREFIX=/dev/shm/$PKG-$VERSION-$BUILD
+
+set -xe
+umask 022
+
+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
+
+exec </dev/null
+
+mkdir -p $PREFIX
+cat >$PREFIX/profile <<-EOF
+	PATH=$PREFIX/bin:\$PATH
+EOF
+. $PREFIX/profile
+
+export MAKEFLAGS="-j $(nproc)"
+
+BUILDDIR=$PREFIX/build
+
+mkdir -p $BUILDDIR
+cd $BUILDDIR
+
+test -e julia-${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-${VERSION}-full.tar.gz
+cd julia
+
+patch -p1 <<'EOF'
+From 44d590277454035841803083f57af1b861192595 Mon Sep 17 00:00:00 2001
+From: Donald Buczek <buczek@molgen.mpg.de>
+Date: Fri, 30 Jun 2017 11:41:41 +0200
+Subject: [PATCH 1/2] Allow OpenBLAS NUM_THREADS to be overwritten
+
+When building OpenBLAS we have some default for its NUM_THREADS build
+option. Allow this default to be overwritten by a new
+OPENBLAS_NUM_THREADS make variable.
+---
+ deps/blas.mk | 9 +++++----
+ 1 file changed, 5 insertions(+), 4 deletions(-)
+
+diff --git a/deps/blas.mk b/deps/blas.mk
+index 55216c8..b9bf8ed 100644
+--- a/deps/blas.mk
++++ b/deps/blas.mk
+@@ -14,17 +14,18 @@ OPENBLAS_BUILD_OPTS += GEMM_MULTITHREADING_THRESHOLD=50
+ ifneq ($(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
+
+make -j $(nproc) prefix="${PREFIX}" MARCH=x86-64 OPENBLAS_NUM_THREADS=80
+make install prefix="${PREFIX}" MARCH=x86-64
+
+patchelf --remove-rpath ${PREFIX}/lib/julia/libpcre2-posix.so.1.0.1
+
+for i in `ls ${PREFIX}/bin`; do
+	ln -sv ${PREFIX}/bin/$i{,-$VERSION}
+done
+
+exit