Merge branch 'it4i-salomon'

b/binutils/binutils-2.30-GCCcore-7.3.0.eb

@@ -0,0 +1,28 @@
+# IT4Innovations 2018
+
+name = 'binutils'
+version = '2.30'
+
+homepage = 'http://directory.fsf.org/project/binutils/'
+description = "binutils: GNU binary utilities"
+
+toolchain = {'name': 'GCCcore', 'version': '7.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+patches = ['binutils-%(version)s_fix-assertion-fail-elf.patch']
+checksums = [
+    '8c3850195d1c093d290a716e20ebcaa72eda32abf5e3d8611154b39cff79e9ea',  # binutils-2.30.tar.gz
+    '7a661190c973287642296dd9fb30ff45dc26ae2138f7761cd8362f7e412ff5ab',  # binutils-2.30_fix-assertion-fail-elf.patch
+]
+
+builddependencies = [
+    ('flex', '2.6.4', '', True),
+    ('Bison', '3.0.4', '', True),
+    # zlib required, but being linked in statically, so not a runtime dep
+    ('zlib', '1.2.11', '', True),
+    # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils
+    ('binutils', version, '', True)
+]
+
+moduleclass = 'tools'

b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb

@@ -0,0 +1,25 @@
+
+# IT4Innovations 2018
+
+name = 'binutils'
+version = '2.31.1'
+
+homepage = 'http://directory.fsf.org/project/binutils/'
+description = "binutils: GNU binary utilities"
+
+toolchain = {'name': 'GCCcore', 'version': '8.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88']
+
+builddependencies = [
+    ('flex', '2.6.4', '', True),
+    ('Bison', '3.0.5', '', True),
+    # zlib required, but being linked in statically, so not a runtime dep
+    ('zlib', '1.2.11', '', True),
+    # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils
+    ('binutils', version, '', True)
+]
+
+moduleclass = 'tools'

c/CMake/CMake-3.13.1.eb

@@ -0,0 +1,30 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'CMake'
+version = '3.13.1'
+
+homepage = 'http://www.cmake.org'
+description = """CMake, the cross-platform, open-source build system.
+ CMake is a family of tools designed to build, test and package software."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = '-- -DCMAKE_USE_OPENSSL=1'
+
+dependencies = [
+    ('ncurses', '6.1'),
+]
+
+osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

e/ed/ed-1.9.eb

@@ -0,0 +1,25 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'ed'
+version = '1.9'
+
+homepage = 'http://www.gnu.org/software/ed/ed.html'
+description = """GNU ed is a line-oriented text editor."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = [
+    'https://launchpad.net/ed/main/%(version)s/+download/',
+    GNU_SOURCE,
+]
+sources = [SOURCE_TAR_GZ]
+checksums = ['d5b372cfadf073001823772272fceac2cfa87552c5cd5a8efc1c8aae61f45a88']
+
+sanity_check_paths = {
+    'files': ['bin/ed'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

f/flex/flex-2.6.4.eb

@@ -9,7 +9,7 @@ toolchain = {'name': 'dummy', 'version': ''}
 toolchainopts = {'pic': True}
 
 sources = [SOURCELOWER_TAR_GZ]
-source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s']
+source_urls = ['https://sources.voidlinux.eu/flex-2.6.4/']
 
 dependencies = [('Bison', '3.0.4')]
 

g/GCC/GCC-7.3.0-2.30.eb

@@ -0,0 +1,25 @@
+easyblock = 'Bundle'
+
+name = 'GCC'
+version = '7.3.0'
+
+binutilsver = '2.30'
+versionsuffix = '-%s' % binutilsver
+
+homepage = 'http://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+dependencies = [
+    ('GCCcore', version),
+    # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils
+    ('binutils', binutilsver, '', ('GCCcore', version)),
+]
+
+altroot = 'GCCcore'
+altversion = 'GCCcore'
+
+# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS)
+moduleclass = 'compiler'

g/GCCcore/GCCcore-6.3.0.eb

@@ -13,11 +13,16 @@ mpfr_version = '3.1.5'
 
 source_urls = [
     # GCC auto-resolving HTTP mirror
+#    'https://ftp.gnu.org/gnu/gcc/gcc-%(version)/',
     'http://ftpmirror.gnu.org/gcc/gcc-%(version)s',
+#    'https://ftp.gnu.org/gnu/gmp/',
     'http://ftpmirror.gnu.org/gmp',  # idem for GMP
+#    'https://ftp.gnu.org/gnu/mpfr/',
     'http://ftpmirror.gnu.org/mpfr',  # idem for MPFR
+#    'https://ftp.gnu.org/gnu/mpc/',
     'http://www.multiprecision.org/mpc/download',  # MPC official
-    'ftp://gcc.gnu.org/pub/gcc/infrastructure/',  # GCC dependencies
+    'http://ftp.nluug.nl/languages/gcc/infrastructure/',
+#    'ftp://gcc.gnu.org/pub/gcc/infrastructure/',  # GCC dependencies
     'http://gcc.cybermirror.org/infrastructure/',  # HTTP mirror for GCC dependencies
     'http://isl.gforge.inria.fr/',  # original HTTP source for ISL
 ]

g/GCCcore/GCCcore-8.2.0.eb

@@ -0,0 +1,54 @@
+easyblock = 'EB_GCC'
+
+name = 'GCCcore'
+version = '8.2.0'
+
+homepage = 'http://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+mpfr_version = '4.0.1'
+
+source_urls = [
+    'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s',  # GCC auto-resolving HTTP mirror
+    'http://ftpmirror.gnu.org/gnu/gmp',  # idem for GMP
+    'http://ftpmirror.gnu.org/gnu/mpfr',  # idem for MPFR
+    'http://ftpmirror.gnu.org/gnu/mpc',  # idem for MPC
+#    'ftp://gcc.gnu.org/pub/gcc/infrastructure/',  # GCC dependencies
+    'http://ftp.nluug.nl/languages/gcc/infrastructure/'
+    'http://gcc.cybermirror.org/infrastructure/',  # HTTP mirror for GCC dependencies
+    'http://isl.gforge.inria.fr/',  # original HTTP source for ISL
+]
+sources = [
+    'gcc-%(version)s.tar.gz',
+    'gmp-6.1.2.tar.bz2',
+    'mpfr-%s.tar.bz2' % mpfr_version,
+    'mpc-1.1.0.tar.gz',
+    'isl-0.20.tar.bz2',
+]
+patches = [
+    'GCCcore-6.2.0-fix-find-isl.patch',
+    'gcc-8.2.0-isl-0.20-missing-include.patch',
+]
+checksums = [
+    '1b0f36be1045ff58cbb9c83743835367b860810f17f0195a4e093458b372020f',  # gcc-8.2.0.tar.gz
+    '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2',  # gmp-6.1.2.tar.bz2
+    'a4d97610ba8579d380b384b225187c250ef88cfe1d5e7226b89519374209b86b',  # mpfr-4.0.1.tar.bz2
+    '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e',  # mpc-1.1.0.tar.gz
+    'b587e083eb65a8b394e833dea1744f21af3f0e413a448c17536b5549ae42a4c2',  # isl-0.20.tar.bz2
+    '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68',  # GCCcore-6.2.0-fix-find-isl.patch
+    '62fa14c3ba2e59cb1d172251cd9d429534394388b10796cf437f65e94ce81c7f',  # gcc-8.2.0-isl-0.20-missing-include.patch
+]
+
+builddependencies = [
+    ('M4', '1.4.18'),
+    ('binutils', '2.31.1'),
+]
+
+languages = ['c', 'c++', 'fortran']
+
+withisl = True
+
+moduleclass = 'compiler'

g/GMP/GMP-6.0.0a.eb

@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'GMP'
+version = '6.0.0a'
+
+homepage = 'http://gmplib.org/'
+description = """GMP is a free library for arbitrary precision arithmetic, 
+operating on signed integers, rational numbers, and floating point numbers. """
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ["%(namelower)s-%(version)s.tar.bz2"]
+source_urls = [GNU_SOURCE]
+
+builddependencies = [
+    ('Autotools', '20150215'),
+]
+
+# enable C++ interface
+configopts = '--enable-cxx'
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'],
+    'dirs': [],
+}
+
+moduleclass = 'math'

l/libtool/libtool-2.4.6.eb

@@ -0,0 +1,19 @@
+# It4innovations 2018
+easyblock = 'ConfigureMake'
+
+name = 'libtool'
+version = '2.4.6'
+
+homepage = 'http://www.gnu.org/software/libtool'
+description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries
+ behind a consistent, portable interface."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3']
+
+dependencies = [('M4', '1.4.18')]
+
+moduleclass = 'lib'

l/libzip/libzip-1.2.0.eb

@@ -0,0 +1,22 @@
+easyblock = 'ConfigureMake'
+
+name = 'libzip'
+version = '1.2.0'
+
+homepage = 'https://nih.at/libzip/'
+description = """libzip is a C library for reading, creating, and modifying zip archives. 
+Files can be added from data buffers, files, or compressed data copied directly from other 
+zip archives. Changes made without closing the archive can be reverted. The API is documented 
+by man pages."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['https://nih.at/libzip']
+sources = ['%(name)s-%(version)s.tar.gz']
+
+sanity_check_paths = {
+    'files': ['bin/zipcmp', 'bin/zipmerge', 'bin/ziptool'],
+    'dirs': ['bin', 'include', 'lib', 'share'],
+}
+
+moduleclass = 'lib'

r/RapidJSON/RapidJSON-1.1.0-GCC-6.3.0-2.27.eb

@@ -17,8 +17,8 @@ toolchainopts = {'pic': True}
 source_urls = ['https://github.com/Tencent/rapidjson/archive/']
 sources = ['v%(version)s.tar.gz']
 
-dependencies = [
-    ('CMake', '3.11.4'),
+builddependencies = [
+    ('CMake', '3.13.1'),
 ]
 
 sanity_check_paths = {

s/Szip/Szip-2.1.eb

@@ -1,3 +1,5 @@
+# IT4Innovations 2018
+
 easyblock = 'ConfigureMake'
 
 name = 'Szip'
@@ -9,7 +11,7 @@ description = "Szip compression software, providing lossless compression of scie
 toolchain = {'name': 'dummy', 'version': ''}
 toolchainopts = {'optarch': True, 'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/previous/2.1/src/']
 sources = [SOURCELOWER_TAR_GZ]
 
 configopts = "--with-pic"