Merge pull request #676 from hpcugent/develop

release EasyBuild v2.3.0

.gitignore

@@ -2,6 +2,7 @@
 .project
 LICENSE_HEADER
 *.pyc
+*.pyo
 *.nja
 build/
 dist/

RELEASE_NOTES

@@ -3,7 +3,28 @@ 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 150 software-specific easyblocks and 25 generic easyblocks.
+The latest version of easybuild-easyblocks provides 152 software-specific easyblocks and 25 generic easyblocks.
+
+v2.3.0 (September 2nd 2015)
+---------------------------
+
+feature + bugfix release
+- new easyblocks for 2 software packages that require customized support:
+    MCR (#623), Molpro (#665)
+- various other enhancements, including:
+    - enhance BWA easyblock to also install man pages (#650)
+    - enhance tbb easyblock to consider lib dirs in order and also define $CPATH, $LIBRARY_PATH, $TBBROOT (#653, #654)
+    - call PythonPackage.configure_step in ConfigureMakePythonPackage.configure_step (#668)
+    - add 'foldx3b6' as possible binary name in FoldX easyblock (#671)
+    - enhance/cleanup MATLAB easyblock (#672)
+    - move preparing of 'intel' subdir in $HOME to configure_step in IntelBase easyblock (#673)
+- various bug fixes, including:
+    - add missing super call in post_install_step of imkl easyblock (#648, #660)
+    - fix regex used to correct I_MPI_ROOT in impi mpivars.sh scripts (#662)
+    - fix regex used to patch .mk file in configure step of SuiteSparse easyblock (#666)
+    - correctly specify installation prefix via $GEM_HOME in RubyGem easyblock (#667)
+    - add custom sanity check in scipy easyblock (#669)
+    - specify to always use the bfd linker for OpenFOAM, to stay away from using ld.gold (#670)
 
 v2.2.0 (July 15th 2015)
 -----------------------
@@ -20,6 +41,7 @@ feature + bugfix release
     - make out-of-source build with CMake truly out-of-source (#615)
     - add support in Bundle easyblock to run full sanity check (#627)
     - also take platform-specific Python lib dirs into account in PythonPackage easyblock (#628)
+    - fix mpivars scripts in Intel MPI installation for versions where the installation is moved (#629)
     - don't restrict det_pylibdir function to only EasyBuild-provided Python (#631, #641)
     - support snappy and other optional native libs in Hadoop easyblock (#632, #638, #640, #642)
 - various bug fixes, including:

easybuild/easyblocks/__init__.py

@@ -37,7 +37,7 @@
 
 # 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('2.2.0')
+VERSION = LooseVersion('2.3.0')
 UNKNOWN = 'UNKNOWN'
 
 

easybuild/easyblocks/b/bwa.py

@@ -53,12 +53,18 @@ def install_step(self):
         """
         srcdir = self.cfg['start_dir']
         destdir = os.path.join(self.installdir, 'bin')
+        mandir = os.path.join(self.installdir, 'man')
+        manman1dir = os.path.join(self.installdir, 'man/man1')
+        manfile = os.path.join(srcdir, 'bwa.1')
         srcfile = None
         try:
             os.makedirs(destdir)
+            os.makedirs(mandir)
+            os.makedirs(manman1dir)
             for filename in self.files:
                 srcfile = os.path.join(srcdir, filename)
                 shutil.copy2(srcfile, destdir)
+            shutil.copy2(manfile, manman1dir)
         except OSError, err:
             raise EasyBuildError("Copying %s to installation dir %s failed: %s", srcfile, destdir, err)
 

easybuild/easyblocks/f/foldx.py

@@ -49,6 +49,7 @@ def install_step(self):
             'foldx_%s.linux' % self.version,  # FoldX v2.x
             'FoldX.linux64',  # FoldX 3.x
             'foldx64Linux',  # FoldX 3.0-beta6
+            'foldx3b6',  # FoldX 3.0 beta 6.1 >_<
         ]
         try:
             os.makedirs(bindir)

easybuild/easyblocks/generic/configuremakepythonpackage.py

@@ -52,8 +52,9 @@ def __init__(self, *args, **kwargs):
         """Initialize with PythonPackage."""
         PythonPackage.__init__(self, *args, **kwargs)
 
-    def configure_step(self):
+    def configure_step(self, *args, **kwargs):
         """Configure build using 'python configure'."""
+        PythonPackage.configure_step(self, *args, **kwargs)
         cmd = "%s python %s" % (self.cfg['preconfigopts'], self.cfg['configopts'])
         run_cmd(cmd, log_all=True)
 

easybuild/easyblocks/generic/intelbase.py

@@ -45,7 +45,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.run import run_cmd
 
-from vsc import fancylogger
+from vsc.utils import fancylogger
 _log = fancylogger.getLogger('generic.intelbase')
 
 
@@ -91,10 +91,6 @@ def __init__(self, *args, **kwargs):
         common_tmp_dir = os.path.dirname(tempfile.gettempdir())  # common tmp directory, same across nodes
         self.home_subdir_local = os.path.join(common_tmp_dir, os.getenv('USER'), 'easybuild_intel')
 
-        # prepare (local) 'intel' home subdir
-        self.setup_local_home_subdir()
-        self.clean_home_subdir()
-
     @staticmethod
     def extra_options(extra_vars=None):
         extra_vars = EasyBlock.extra_options(extra_vars)
@@ -165,6 +161,10 @@ def setup_local_home_subdir(self):
     def configure_step(self):
         """Configure: handle license file and clean home dir."""
 
+        # prepare (local) 'intel' home subdir
+        self.setup_local_home_subdir()
+        self.clean_home_subdir()
+
         lic_env_var = None  # environment variable that will be used
         default_lic_env_var = 'INTEL_LICENSE_FILE'
         lic_env_vars = [default_lic_env_var, 'LM_LICENSE_FILE']

easybuild/easyblocks/generic/pythonpackage.py

@@ -34,7 +34,7 @@
 import os
 import tempfile
 from os.path import expanduser
-from vsc import fancylogger
+from vsc.utils import fancylogger
 from vsc.utils.missing import nub
 
 import easybuild.tools.environment as env

easybuild/easyblocks/generic/rubygem.py

@@ -26,11 +26,15 @@
 EasyBuild support for Ruby Gems, implemented as an easyblock
 
 @author: Robert Schmidt (Ottawa Hospital Research Institute)
+@author: Kenneth Hoste (Ghent University)
 """
+import os
 import shutil
 
+import easybuild.tools.environment as env
 from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_cmd
 
 
@@ -81,4 +85,21 @@ def test_step(self):
 
     def install_step(self):
         """Install Ruby Gems using gem package manager"""
-        run_cmd('gem install --local %s' % self.ext_src)
+        ruby_root = get_software_root('Ruby')
+        if not ruby_root:
+            raise EasyBuildError("Ruby module not loaded?")
+
+        # this is the 'proper' way to specify a custom installation prefix: set $GEM_HOME
+        if not self.is_extension:
+            env.setvar('GEM_HOME', self.installdir)
+
+        bindir = os.path.join(self.installdir, 'bin')
+        run_cmd("gem install --bindir %s --local %s" % (bindir, self.ext_src))
+
+    def make_module_extra(self):
+        """Extend $GEM_PATH in module file."""
+        txt = super(RubyGem, self).make_module_extra()
+        # for stand-alone Ruby gem installs, $GEM_PATH needs to be updated
+        if not self.is_extension:
+            txt += self.module_generator.prepend_paths('GEM_PATH', [''])
+        return txt

easybuild/easyblocks/i/imkl.py

@@ -146,6 +146,8 @@ def post_install_step(self):
         """
         Install group libraries and interfaces (if desired).
         """
+        super(EB_imkl, self).post_install_step()
+
         # reload the dependencies
         self.load_dependency_modules()
 

easybuild/easyblocks/i/impi.py

@@ -138,7 +138,7 @@ def post_install_step(self):
                     sys.stdout.write(line)
             for script in [os.path.join('intel64', 'bin', 'mpivars.sh'), os.path.join('mic', 'bin', 'mpivars.sh')]:
                 for line in fileinput.input(os.path.join(self.installdir, script), inplace=1, backup='.orig.eb'):
-                    line = re.sub(r"^I_MPI_ROOT=", "I_MPI_ROOT=%s; export I_MPI_ROOT" % self.installdir, line)
+                    line = re.sub(r"^I_MPI_ROOT=.*", "I_MPI_ROOT=%s; export I_MPI_ROOT" % self.installdir, line)
                     sys.stdout.write(line)
 
     def sanity_check_step(self):

easybuild/easyblocks/m/matlab.py

@@ -32,14 +32,15 @@
 @author: Jens Timmerman (Ghent University)
 @author: Fotis Georgatos (Uni.Lu, NTUA)
 """
-
 import re
 import os
 import shutil
+import stat
 
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import adjust_permissions, read_file, write_file
 from easybuild.tools.run import run_cmd
 
 
@@ -50,7 +51,7 @@ def __init__(self, *args, **kwargs):
         """Add extra config options specific to MATLAB."""
         super(EB_MATLAB, self).__init__(*args, **kwargs)
         self.comp_fam = None
-        self.configfilename = "my_installer_input.txt"
+        self.configfile = os.path.join(self.builddir, 'my_installer_input.txt')
 
     @staticmethod
     def extra_options():
@@ -66,22 +67,16 @@ def configure_step(self):
         licserv = self.cfg['license_server']
         licport = self.cfg['license_server_port']
         lictxt = '\n'.join([
-                            "SERVER %s 000000000000 %s" % (licserv, licport),
-                            "USE_SERVER",
-                           ])
+            "SERVER %s 000000000000 %s" % (licserv, licport),
+            "USE_SERVER",
+        ])
 
-        licfile = "%s/matlab.lic" % self.builddir
-        try:
-            f = file(licfile, "w")
-            f.write(lictxt)
-            f.close()
-        except IOError, err:
-            raise EasyBuildError("Failed to create license file %s: %s", licfile, err)
+        licfile = os.path.join(self.builddir, 'matlab.lic')
+        write_file(licfile, lictxt)
 
-        configfile = os.path.join(self.builddir, self.configfilename)
         try:
-            shutil.copyfile("%s/%s/installer_input.txt" % (self.builddir, self.version), configfile)
-            config = file(configfile).read()
+            shutil.copyfile(os.path.join(self.cfg['start_dir'], 'installer_input.txt'), self.configfile)
+            config = read_file(self.configfile)
 
             regdest = re.compile(r"^# destinationFolder=.*", re.M)
             regkey = re.compile(r"^# fileInstallationKey=.*", re.M)
@@ -96,14 +91,12 @@ def configure_step(self):
             config = regmode.sub("mode=silent", config)
             config = reglicpath.sub("licensePath=%s" % licfile, config)
 
-            f = open(configfile, 'w')
-            f.write(config)
-            f.close()
+            write_file(self.configfile, config)
 
         except IOError, err:
-            raise EasyBuildError("Failed to create installation config file %s: %s", configfile, err)
+            raise EasyBuildError("Failed to create installation config file %s: %s", self.configfile, err)
 
-        self.log.debug('configuration file written to %s:\n %s' % (configfile, config))
+        self.log.debug('configuration file written to %s:\n %s', self.configfile, config)
 
     def build_step(self):
         """No building of MATLAB, no sources available."""
@@ -115,14 +108,7 @@ def install_step(self):
         src = os.path.join(self.cfg['start_dir'], 'install')
 
         # make sure install script is executable
-        try:
-            if os.path.isfile(src):
-                self.log.info("Doing chmod on source file %s" % src)
-                os.chmod(src, 0755)
-            else:
-                self.log.info("Did not find source file %s" % src)
-        except OSError, err:
-            raise EasyBuildError("Failed to chmod install script: %s", err)
+        adjust_permissions(src, stat.S_IXUSR)
 
         # make sure $DISPLAY is not defined, which may lead to (hard to trace) problems
         # this is a workaround for not being able to specify --nodisplay to the install scripts
@@ -131,27 +117,22 @@ def install_step(self):
 
         if not '_JAVA_OPTIONS' in self.cfg['preinstallopts']:
             self.cfg['preinstallopts'] = ('export _JAVA_OPTIONS="%s" && ' % self.cfg['java_options']) + self.cfg['preinstallopts']
-        configfile = "%s/%s" % (self.builddir, self.configfilename)
-        cmd = "%s ./install -v -inputFile %s %s" % (self.cfg['preinstallopts'], configfile, self.cfg['installopts'])
+        cmd = "%s ./install -v -inputFile %s %s" % (self.cfg['preinstallopts'], self.configfile, self.cfg['installopts'])
         run_cmd(cmd, log_all=True, simple=True)
 
     def sanity_check_step(self):
         """Custom sanity check for MATLAB."""
 
         custom_paths = {
-                        'files': ["bin/matlab", "bin/mcc", "bin/glnxa64/MATLAB", "bin/glnxa64/mcc",
-                                  "runtime/glnxa64/libmwmclmcrrt.so", "toolbox/local/classpath.txt"],
-                        'dirs': ["java/jar", "toolbox/compiler"],
-                       }
+            'files': ["bin/matlab", "bin/mcc", "bin/glnxa64/MATLAB", "bin/glnxa64/mcc",
+                      "runtime/glnxa64/libmwmclmcrrt.so", "toolbox/local/classpath.txt"],
+            'dirs': ["java/jar", "toolbox/compiler"],
+        }
 
         super(EB_MATLAB, self).sanity_check_step(custom_paths=custom_paths)
 
     def make_module_extra(self):
         """Extend PATH and set proper _JAVA_OPTIONS (e.g., -Xmx)."""
-
         txt = super(EB_MATLAB, self).make_module_extra()
-
         txt += self.module_generator.set_environment('_JAVA_OPTIONS', self.cfg['java_options'])
-
         return txt
-