Merge pull request #574 from hpcugent/develop

release EasyBuild v2.0.0

RELEASE_NOTES

@@ -3,7 +3,39 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyblocks provides 141 software-specific easyblocks and 20 generic easyblocks.
+The latest version of easybuild-easyblocks provides 143 software-specific easyblocks and 21 generic easyblocks.
+
+
+v2.0.0 (March 6th 2015)
+-----------------------
+
+feature + bugfix release
+- one new generic easyblock for installing a bundle of modules: Bundle (#550)
+    - and let the Toolchain generic easyblock derive from Bundle
+- new easyblocks for 2 software packages that require customized support:
+    - GAMESS-US (#470, #544, #558), Hadoop (#563)
+- various other enhancements, including:
+    - move support for staged_install from CPLEX easyblock to generic Binary easyblock (#502)
+    - fix sanity check in picard easyblock for v1.119 that doesn't include sam.jar (#522)
+    - log warning message when unlinking jellyfish symlink fails in Trinity easyblock (#534)
+    - revamp EB_libint2 easyblock into EB_Libint that works for both Libint v1x and v2.x (#536)
+    - update CP2K easyblock for recent versions (no more 'fes') (#537)
+    - update SuiteSparse easyblock for recent versions (#541)
+    - fix easyblock unit tests after dropping support for deprecated behaviour in framework (#543)
+    - rework PSI easyblock to support future releases (#545)
+    - enable always generating a 'verbose' Makefile in the generic CMakeMake easyblock (#546)
+    - remove functionality in (generic) easyblocks that was deprecated for EasyBuild v2.0 (#547)
+    - enhance generic RPackage easyblock to support installing extensions in a separate prefix (#551)
+    - deprecate GenomeAnalysisTK easyblock, since it's basically equivalent to Tarball (#557)
+    - update SAMtools easyblock for v1.2 (#562)
+    - take preconfigopts easyconfig parameter into account in ROOT easyblock (#566)
+    - update easyblock for installing EasyBuild
+        - to support bootstrapping with provided source tarballs (#559)
+        - to also cover vsc-base dependency, and verify easy-install.pth (#567)
+    - update disabling sanitizer tests for Clang 3.6 (#570)
+- various bug fixes, including:
+    - fix handling of LTO in GCC easyblock (#535)
+    - relocate FDTD RPM to fix installation on SL6 (#538)
 
 v1.16.2 (March 6th 2015)
 ------------------------
@@ -19,7 +51,7 @@ v1.16.0 (December 18th 2014)
 ----------------------------
 
 feature + bugfix release
-- new easyblocks for 2 software packages that requires customized support:
+- new easyblocks for 2 software packages that require customized support:
     - Chimera (#524), GATE (#518)
 - fix use of deprecated functionality, enhance unit tests to check for it (#523)
 - various other enhancements, including:
@@ -65,7 +97,7 @@ v1.15.0 (September 12th 2014)
 -----------------------------
 
 feature + bugfix release
-- added support for 2 new software packages that requires customized support: Modeller (#392), NAMD (#397)
+- added support for 2 new software packages that require customized support: Modeller (#392), NAMD (#397)
 - various enhancements, including:
     - fix locale used for running Perl unit tests (#425)
     - fix Rmpi easyblock to correctly configure for Intel MPI (#435)
@@ -90,7 +122,7 @@ v1.14.0 (July 9th 2014)
 
 feature + bugfix release
 - added one new generic easyblock: CmdCp (#395)
-- added support for 2 new software packages that requires customized support: ANSYS (#398), HPCG (#408)
+- added support for 2 new software packages that require customized support: ANSYS (#398), HPCG (#408)
 - various enhancements, including:
     - updated ABAQUS easyblock so that it works for version 13.2 (#406)
     - enhance BLAT easyblock by using super's build_step and prebuildopts/buildopts (#423)

easybuild/__init__.py

@@ -1,10 +1,10 @@
 ##
-# Copyright 2009-2012 Ghent University
-# Copyright 2009-2012 Stijn De Weirdt
+# Copyright 2009-2015 Ghent University
+# Copyright 2009-2015 Stijn De Weirdt
 # Copyright 2010 Dries Verdegem
-# Copyright 2010-2012 Kenneth Hoste
+# Copyright 2010-2015 Kenneth Hoste
 # Copyright 2011 Pieter De Baets
-# Copyright 2011-2012 Jens Timmerman
+# Copyright 2011-2015 Jens Timmerman
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/__init__.py

@@ -1,10 +1,10 @@
 # #
-# Copyright 2009-2014 Ghent University
-# Copyright 2009-2014 Stijn De Weirdt
+# Copyright 2009-2015 Ghent University
+# Copyright 2009-2015 Stijn De Weirdt
 # Copyright 2010 Dries Verdegem
-# Copyright 2010-2014 Kenneth Hoste
+# Copyright 2010-2015 Kenneth Hoste
 # Copyright 2011 Pieter De Baets
-# Copyright 2011-2014 Jens Timmerman
+# Copyright 2011-2015 Jens Timmerman
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -33,7 +33,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware
-VERSION = LooseVersion("1.16.2")
+VERSION = LooseVersion("2.0.0")
 UNKNOWN = "UNKNOWN"
 
 

easybuild/easyblocks/a/abaqus.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/acml.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/aladin.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/ansys.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/ant.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/arb.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/armadillo.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/atlas.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/b/bamtools.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 The Cyprus Institute 
+# Copyright 2009-2015 The Cyprus Institute 
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/b/bioconductor.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/b/bisearch.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/b/blacs.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/b/blat.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 the Cyprus Institute
+# Copyright 2009-2015 the Cyprus Institute
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/b/boost.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/b/bowtie2.py

@@ -1,7 +1,7 @@
 ##
 # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
 #
-# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Copyright:: Copyright 2012-2015 Uni.Lu/LCSB, NTUA
 # Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>, Kenneth Hoste
 # License::   MIT/GPL
 # $Id$

easybuild/easyblocks/b/bwa.py

@@ -1,7 +1,7 @@
 ##
 # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
 #
-# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Copyright:: Copyright 2012-2015 Uni.Lu/LCSB, NTUA
 # Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Kenneth Hoste
 # Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>
 # License::   MIT/GPL

easybuild/easyblocks/b/bzip2.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/c/cgal.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/c/chapel.py

@@ -1,7 +1,7 @@
 ## 
 # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
 #
-# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Copyright:: Copyright 2012-2015 Uni.Lu/LCSB, NTUA
 # Authors::   Fotis Georgatos <fotis@cern.ch>, Kenneth Hoste
 # License::   MIT/GPL
 # $Id$

easybuild/easyblocks/c/clang.py

@@ -35,6 +35,7 @@
 import fileinput
 import glob
 import os
+import re
 import shutil
 import sys
 from distutils.version import LooseVersion
@@ -196,36 +197,54 @@ def configure_step(self):
         super(EB_Clang, self).configure_step(srcdir=self.llvm_src_dir)
 
     def disable_sanitizer_tests(self):
-        """Disable the tests of all the sanitizers"""
-        patchfiles = [
-            "projects/compiler-rt/lib/asan/CMakeLists.txt",
-            "projects/compiler-rt/lib/dfsan/CMakeLists.txt",
-            "projects/compiler-rt/lib/lsan/CMakeLists.txt",
-            "projects/compiler-rt/lib/msan/CMakeLists.txt",
-            "projects/compiler-rt/lib/tsan/CMakeLists.txt",
-            "projects/compiler-rt/lib/ubsan/CMakeLists.txt",
-        ]
-
-        for patchfile in patchfiles:
+        """Disable the tests of all the sanitizers by removing the test directories from the build system"""
+        if LooseVersion(self.version) < LooseVersion('3.6'):
+            # for Clang 3.5 and lower, the tests are scattered over several CMakeLists.
+            # We loop over them, and patch out the rule that adds the sanitizers tests to the testsuite
+            patchfiles = [
+                "lib/asan",
+                "lib/dfsan",
+                "lib/lsan",
+                "lib/msan",
+                "lib/tsan",
+                "lib/ubsan",
+            ]
+
+            for patchfile in patchfiles:
+                patchfile_fp = os.path.join(self.llvm_src_dir, "projects/compiler-rt", patchfile, "CMakeLists.txt")
+                if os.path.exists(patchfile_fp):
+                    self.log.debug("Patching %s in %s" % (patchfile, self.llvm_src_dir))
+                    try:
+                        for line in fileinput.input(patchfile_fp, inplace=1, backup='.orig'):
+                            if "add_subdirectory(lit_tests)" not in line:
+                                sys.stdout.write(line)
+                    except (IOError, OSError), err:
+                        self.log.error("Failed to patch %s: %s" % (patchfile_fp, err))
+                else:
+                    self.log.debug("Not patching non-existent %s in %s" % (patchfile, self.llvm_src_dir))
+
+            # There is a common part seperate for the specific saniters, we disable all
+            # the common tests
+            patchfile = "projects/compiler-rt/lib/sanitizer_common/CMakeLists.txt"
+            try:
+                for line in fileinput.input("%s/%s" % (self.llvm_src_dir, patchfile), inplace=1, backup='.orig'):
+                    if "add_subdirectory(tests)" not in line:
+                        sys.stdout.write(line)
+            except IOError, err:
+                self.log.error("Failed to patch %s/%s: %s" % (self.llvm_src_dir, patchfile, err))
+        else:
+            # In Clang 3.6, the sanitizer tests are grouped together in one CMakeLists
+            # We patch out adding the subdirectories with the sanitizer tests
+            patchfile = "projects/compiler-rt/test/CMakeLists.txt"
             patchfile_fp = os.path.join(self.llvm_src_dir, patchfile)
-            if os.path.exists(patchfile_fp):
-                self.log.debug("Patching %s in %s" % (patchfile, self.llvm_src_dir))
-                try:
-                    for line in fileinput.input(patchfile_fp, inplace=1, backup='.orig'):
-                        if "add_subdirectory(lit_tests)" not in line:
-                            sys.stdout.write(line)
-                except (IOError, OSError), err:
-                    self.log.error("Failed to patch %s: %s" % (patchfile_fp, err))
-            else:
-                self.log.debug("Not patching non-existent %s in %s" % (patchfile, self.llvm_src_dir))
-
-        patchfile = "projects/compiler-rt/lib/sanitizer_common/CMakeLists.txt"
-        try:
-            for line in fileinput.input("%s/%s" % (self.llvm_src_dir, patchfile), inplace=1, backup='.orig'):
-                if "add_subdirectory(tests)" not in line:
-                    sys.stdout.write(line)
-        except IOError, err:
-            self.log.error("Failed to patch %s/%s: %s" % (self.llvm_src_dir, patchfile, err))
+            self.log.debug("Patching %s in %s" % (patchfile, self.llvm_src_dir))
+            patch_regex = re.compile(r'add_subdirectory\((.*san|sanitizer_common)\)')
+            try:
+                for line in fileinput.input(patchfile_fp, inplace=1, backup='.orig'):
+                    if not patch_regex.search(line):
+                        sys.stdout.write(line)
+            except IOError, err:
+                self.log.error("Failed to patch %s: %s" % (patchfile_fp, err))
 
     def build_with_prev_stage(self, prev_obj, next_obj):
         """Build Clang stage N using Clang stage N-1"""

easybuild/easyblocks/c/cp2k.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2013 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -774,7 +774,7 @@ def sanity_check_step(self):
 
         cp2k_type = self.cfg['type']
         custom_paths = {
-            'files': ["bin/%s.%s" % (x, cp2k_type) for x in ["cp2k", "cp2k_shell", "fes"]],
+            'files': ["bin/%s.%s" % (x, cp2k_type) for x in ["cp2k", "cp2k_shell"]],
             'dirs': ["tests"]
         }