Merge remote-tracking branch 'upstream/master'

Commiting upstream merge (including new struct layout), with a couple
important errata:
  - idump methods need to be disambiguated
  - The first field in a Stream must be a Pointer BitsType (unlike
    upstream where it must be an Array) or the logic in jl_show_* in
    builtins.c must be improved

Conflicts:
	Make.inc
	Makefile
	base/sysimg.jl
	deps/.gitignore
	deps/Makefile
	deps/Versions.make
	src/julia.expmap
	src/sys.c
	test/Makefile

.mailmap

@@ -55,3 +55,12 @@ Tim Holy <[email protected]> <[email protected]>
 Patrick O'Leary <[email protected]> <[email protected]>
 
 Ivan Mantova <[email protected]> <[email protected]>
+
+Keno Fischer <[email protected]> <[email protected]>
+Keno Fischer <[email protected]> <[email protected]>
+Keno Fischer <[email protected]> <[email protected]>
+
+Harlan Harris <[email protected]> <[email protected]>
+Harlan Harris <[email protected]> <[email protected]>
+
+Douglas Bates <[email protected]> <[email protected]>

LICENSE.md

@@ -50,6 +50,7 @@ External libraries, if used, include their own licenses:
 - [FDLIBM](http://www.netlib.org/fdlibm/fdlibm.h)
 - [FEMTOLISP](https://github.com/JeffBezanson/femtolisp)
 - [FFTW](http://fftw.org/doc/License-and-Copyright.html)
+- [GLPK](http://www.gnu.org/software/glpk)
 - [LAPACK](http://netlib.org/lapack/LICENSE.txt)
 - [LIBUNWIND](http://git.savannah.gnu.org/gitweb/?p=libunwind.git;a=blob_plain;f=LICENSE;hb=master)
 - [LLVM](http://llvm.org/releases/3.0/LICENSE.TXT)
@@ -58,3 +59,4 @@ External libraries, if used, include their own licenses:
 - [PCRE](http://www.pcre.org/licence.txt)
 - [READLINE](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html)
 - [SUITESPARSE](http://www.cise.ufl.edu/research/sparse/SuiteSparse/current/SuiteSparse/)
+- [ZLIB](http://zlib.net/zlib_license.html)

Make.inc

@@ -20,6 +20,7 @@ MKLLIB = /path/to/mkl/lib/intel64
 # or installed to usr/lib/libatlas from some another source (built as
 # a shared library, for your platform, single threaded)
 USE_ATLAS = 0
+ATLAS_LIBDIR = ${USRLIB}
 
 ifeq ($(OS), MINGW32_NT-6.1)
 OS=WINNT
@@ -60,7 +61,10 @@ CXX = g++
 JCFLAGS = -std=gnu99 -pipe $(fPIC) -fno-strict-aliasing -D_FILE_OFFSET_BITS=64
 JCXXFLAGS = -pipe $(fPIC) -fno-rtti
 DEBUGFLAGS = -ggdb3 -DDEBUG
-SHIPFLAGS = -O3 -DNDEBUG -falign-functions -momit-leaf-frame-pointer
+SHIPFLAGS = -O3 -DNDEBUG -falign-functions
+ifneq ($(ARCH), ppc64)
+  SHIPFLAGS += -momit-leaf-frame-pointer
+endif
 endif
 
 ifeq ($(USECLANG),1)
@@ -100,6 +104,7 @@ USE_SYSTEM_ARPACK=0
 USE_SYSTEM_SUITESPARSE=0
 USE_SYSTEM_GLPK=0
 USE_SYSTEM_NGINX=0
+USE_SYSTEM_ZLIB=0
 
 ifeq ($(USE_DEBIAN), 1)
 USE_SYSTEM_LLVM=1
@@ -114,13 +119,7 @@ USE_SYSTEM_GMP=1
 USE_SYSTEM_ARPACK=1
 USE_SYSTEM_SUITESPARSE=1
 USE_SYSTEM_GLPK=1
-endif
-
-# Use system BLAS and LAPACK on Mac
-# https://github.com/JuliaLang/julia/commit/7b6442f1db697d0bc8c39476e7d92afc11b169d2
-ifeq ($(OS), Darwin)
-USE_SYSTEM_BLAS=1
-USE_SYSTEM_LAPACK=1
+USE_SYSTEM_ZLIB=1
 endif
 
 -include $(JULIAHOME)/Make.user
@@ -258,13 +257,14 @@ endif
 endif
 
 ifeq ($(USE_ATLAS), 1)
-USE_SYSTEM_BLAS=1
-USE_SYSTEM_LAPACK=1
-LIBBLAS = -lsatlas
-LIBLAPACK = -lsatlas
+USE_SYSTEM_BLAS = 1
+USE_SYSTEM_LAPACK = 1
+LIBBLAS = -L$(ATLAS_LIBDIR) -lsatlas
+LIBLAPACK = $(LIBBLAS)
 LIBBLASNAME = libsatlas
-LIBLAPACKNAME = libsatlas
+LIBLAPACKNAME = $(LIBBLASNAME)
 endif
+
 # Make tricks
 
 define dir_target

Makefile

@@ -43,7 +43,7 @@ ifeq ($(OS), Darwin)
 endif
 	cd $(PREFIX)/bin && ln -s julia-release-$(DEFAULT_REPL) julia
 	cp -R -L $(BUILD)/lib/julia/* $(PREFIX)/lib/julia
-	-cp $(BUILD)/lib/lib{Rmath,amd,amos,arpack,cholmod,colamd,suitesparseconfig,fdm,fftw3,fftw3f,fftw3_threads,fftw3f_threads,glpk,glpk_wrapper,gmp,gmp_wrapper,grisu,history,julia-release,openblas,openlibm,pcre,random,readline,suitesparse_wrapper,umfpack}.$(SHLIB_EXT) $(PREFIX)/lib
+	-cp $(BUILD)/lib/lib{Rmath,amd,amos,arpack,cholmod,colamd,suitesparseconfig,fdm,fftw3,fftw3f,fftw3_threads,fftw3f_threads,glpk,glpk_wrapper,gmp,gmp_wrapper,grisu,history,julia-release,$(OPENBLASNAME),openlibm,pcre,random,readline,suitesparse_wrapper,umfpack,z}.$(SHLIB_EXT) $(PREFIX)/lib
 # Web-REPL stuff
 	-cp $(BUILD)/lib/mod* $(PREFIX)/lib
 	-cp $(BUILD)/sbin/* $(PREFIX)/sbin
@@ -57,6 +57,7 @@ endif
 
 dist: cleanall
 	rm -fr julia-*.tar.gz julia-$(JULIA_COMMIT)
+#	$(MAKE) -C deps clean-openblas
 	$(MAKE) install OPENBLAS_DYNAMIC_ARCH=1
 	tar zcvf julia-$(JULIA_COMMIT)-$(OS)-$(ARCH).tar.gz julia-$(JULIA_COMMIT)
 	rm -fr julia-$(JULIA_COMMIT)

README.md

@@ -79,7 +79,7 @@ On Ubuntu systems, You may also need to install the package `libncurses5-dev`.
 
 #### OS X
 
-Download and install [gfortran from hpc.sf.net](http://hpc.sf.net/), if necessary.
+It is essential to use a 64-bit gfortran. Download and install [gfortran and gcc from hpc.sf.net](http://hpc.sf.net/), if necessary. The HPC gfortran requires gcc to function properlyl.
 
 If you get link errors mentioning `gfortran`, it might help to put `/usr/local/gfortran/lib` at the beginning of the `DYLD_LIBRARY_PATH` environment variable.
 

base/signal.jl → base/DSP.jl

@@ -1,6 +1,8 @@
-module FFT
+module DSP
+
 import Base.*
 import Base.FFTW.*
+
 export FFTW, filt, deconv, conv, conv2, xcorr, fftshift, ifftshift,
        # the rest are defined imported from FFTW:
        bfft, bfftn, brfft, brfftn, fft, fft2, fft3, fftn,

base/signal_fftw.jl → base/DSP_fftw.jl

@@ -1,5 +1,7 @@
 module FFTW
+
 import Base.*
+
 global transpose
 export bfft, bfftn, brfft, brfftn, fft, fft2, fft3, fftn,
        ifft, ifft2, ifft3, ifftn, irfft, irfftn, rfft, rfftn

base/abstractarray.jl

@@ -23,20 +23,7 @@ length(t::AbstractArray) = prod(size(t))
 first(a::AbstractArray) = a[1]
 last(a::AbstractArray) = a[end]
 
-function stride(a::AbstractArray, i::Integer)
-    s = 1
-    if i > ndims(a)
-        return numel(a)
-    end
-    for n=1:(i-1)
-        s *= size(a, n)
-    end
-    return s
-end
-strides{T}(a::AbstractArray{T,1}) = (1,)
-strides{T}(a::AbstractArray{T,2}) = (1, size(a,1))
-strides{T}(a::AbstractArray{T,3}) = (1, size(a,1), size(a,1)*size(a,2))
-strides   (a::AbstractArray)      = ntuple(ndims(a), i->stride(a,i))
+strides(a::AbstractArray) = ntuple(ndims(a), i->stride(a,i))::Dims
 
 isinteger{T<:Integer}(::AbstractArray{T}) = true
 isinteger(::AbstractArray) = false