easyblocks_diff_cleaned.txt

diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/c/cgal.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/c/cgal.py
index 662796f..d2e63b5 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/c/cgal.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/c/cgal.py
@@ -62,6 +62,7 @@ class EB_CGAL(CMakeMake):
         libs = [tuple(os.path.join(d, 'libCGAL%s.%s' % (l, shlib_ext)) for d in libdirs) for l in ['', '_Core']]
         custom_paths = {
             'files': ['bin/cgal_%s' % x for x in ['create_cmake_script', 'make_macosx_app']] + libs,
-            'dirs': ['include/CGAL', ('lib/CGAL', 'lib64/CGAL')],
+#            'dirs': ['include/CGAL', ('lib/CGAL', 'lib64/CGAL')],
+            'dirs': ['include', ('lib', 'lib64')],
         }
         super(EB_CGAL, self).sanity_check_step(custom_paths=custom_paths)

diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/c/cp2k.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/c/cp2k.py
index e6f2f96..a2df30e 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/c/cp2k.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/c/cp2k.py
@@ -183,7 +183,7 @@ class EB_CP2K(EasyBlock):
             raise EasyBuildError("Don't know how to tweak configuration for compiler family %s" % comp_fam)
 
         # BLAS/LAPACK/FFTW
-        if get_software_root('imkl'):
+        if get_software_root('imkl') or os.getenv('MKLROOT'):
             options = self.configure_MKL(options)
         else:
             # BLAS
@@ -255,7 +255,9 @@ class EB_CP2K(EasyBlock):
         self.log.debug("Preparing module files")
 
         imkl = get_software_root('imkl')
-
+        if not imkl:
+            imkl = os.getenv('MKLROOT')
+        self.log.debug("MKLROOT: %s", imkl)
         if imkl:
 
             # prepare modinc target path
@@ -471,7 +473,11 @@ class EB_CP2K(EasyBlock):
         options['FCFLAGSOPT'] += ' $(INCFLAGS) -heap-arrays 64'
         options['FCFLAGSOPT2'] += ' $(INCFLAGS) -heap-arrays 64'
 
-        ifortver = LooseVersion(get_software_version('ifort'))
+        intelver = get_software_version('intel') # ifort
+        if intelver and len(intelver.split('.')[0]) == 2:
+            intelver = '20%s' % intelver
+        ifortver = LooseVersion(intelver) # ifort
+        self.log.debug("ifort loose version: %s" % ifortver)
 
         # -i-static has been deprecated prior to 2013, but was still usable. From 2015 it is not.
         if ifortver < LooseVersion("2013"):
@@ -497,7 +503,7 @@ class EB_CP2K(EasyBlock):
                 raise EasyBuildError(failmsg, "v12", "v2011.8")
 
         elif ifortver >= LooseVersion("11"):
-            if LooseVersion(get_software_version('ifort')) >= LooseVersion("11.1.072"):
+            if ifortver >= LooseVersion("11.1.072"):
                 self.make_instructions += "qs_vxc_atom.o: qs_vxc_atom.F\n\t$(FC) -c $(FCFLAGS2) $<\n"
 
             else:
diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/g/gromacs.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/g/gromacs.py
index 0519385..615d289 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/g/gromacs.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/g/gromacs.py
@@ -247,9 +247,9 @@ class EB_GROMACS(CMakeMake):
             else:
                 self.cfg.update('configopts', "-DGMX_GPU=OFF")
 
-            if get_software_root('imkl'):
+            if get_software_root('imkl') or os.getenv('MKLROOT'):
                 # using MKL for FFT, so it will also be used for BLAS/LAPACK
-                self.cfg.update('configopts', '-DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="$EBROOTMKL/mkl/include" ')
+                self.cfg.update('configopts', '-DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="$MKLROOT/include" ')
                 libs = os.getenv('LAPACK_STATIC_LIBS').split(',')
                 mkl_libs = [os.path.join(os.getenv('LAPACK_LIB_DIR'), lib) for lib in libs if lib != 'libgfortran.a']
                 mkl_libs = ['-Wl,--start-group'] + mkl_libs + ['-Wl,--end-group']

diff --git a/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/generic/buildscript.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/generic/buildscript.py
new file mode 100644
index 0000000..6ea4894
--- /dev/null
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/generic/buildscript.py
@@ -0,0 +1,77 @@
+##
+# Copyright 2009-2018 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for installing (precompiled) software which is supplied as a tarball,
+implemented as an easyblock
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+"""
+import shutil
+
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.run import run_cmd
+from easybuild.framework.easyconfig import CUSTOM
+
+class BuildScript(EasyBlock):
+    """
+    Softare builds from script provided as source
+    """
+
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Extra easyconfig parameters specific to BuildScript easyblock."""
+        extra_vars = EasyBlock.extra_options(extra_vars)
+        extra_vars.update({
+            'install_cmds': [None, "List of commands to run to install the software", CUSTOM],
+        })
+        return extra_vars
+
+    def configure_step(self):
+        """
+        Dummy configure method
+        """
+        pass
+
+    def build_step(self):
+        """
+        Dummy build method: nothing to build
+        """
+        pass
+
+    def install_step(self, src=None):
+        """Install by running specified install commands."""
+        if self.cfg['install_cmds'] is not None:
+     	    for cmd in self.cfg['install_cmds']:
+                run_cmd(cmd, log_all=True)        
+    
+    def sanity_check_rpath(self):
+        """Skip the rpath sanity check, this is binary software"""
+        self.log.info("RPATH sanity check is skipped when using %s easyblock (derived from Tarball)",
+                      self.__class__.__name__)

diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/generic/mesonninja.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/generic/mesonninja.py
index 0e8c480..ea2c150 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/generic/mesonninja.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/generic/mesonninja.py
@@ -56,7 +56,7 @@ class MesonNinja(EasyBlock):
         """
         # make sure both Meson and Ninja are included as build dependencies
         build_dep_names = [d['name'] for d in self.cfg.builddependencies()]
-        for tool in ['Ninja', 'Meson']:
+        for tool in ['ninja', 'meson']:
             if tool not in build_dep_names:
                 raise EasyBuildError("%s not included as build dependency", tool)
             cmd = tool.lower()

diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/generic/pythonpackage.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/generic/pythonpackage.py
index 2409118..f9a4cfc 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/generic/pythonpackage.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/generic/pythonpackage.py
@@ -587,9 +587,10 @@ class PythonPackage(ExtensionEasyBlock):
                 downloaded_deps.extend(re.compile(pattern, re.M).findall(self.install_cmd_output))
 
             if downloaded_deps:
-                success = False
-                fail_msg = "found one or more downloaded dependencies: %s" % ', '.join(downloaded_deps)
-                self.sanity_check_fail_msgs.append(fail_msg)
+                pass
+                #success = False
+                #fail_msg = "found one or more downloaded dependencies: %s" % ', '.join(downloaded_deps)
+                #self.sanity_check_fail_msgs.append(fail_msg)
         else:
             self.log.debug("Detection of downloaded dependencies not enabled")
 
diff --git a/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/i/intel.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/i/intel.py
new file mode 100644
index 0000000..b7bd190
--- /dev/null
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/i/intel.py
@@ -0,0 +1,339 @@
+# #
+# Copyright 2009-2019 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+EasyBuild support for install the Intel C/C++ compiler suite, implemented as an easyblock
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+@author: Ward Poelmans (Ghent University)
+@author: Fokko Masselink
+"""
+
+import os
+import re
+import shutil
+from distutils.version import LooseVersion
+
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.easyblocks.generic.intelbase import IntelBase, ACTIVATION_NAME_2012, COMP_ALL
+from easybuild.easyblocks.generic.intelbase import LICENSE_FILE_NAME_2012
+from easybuild.easyblocks.t.tbb import get_tbb_gccprefix
+from easybuild.tools.run import run_cmd
+from easybuild.tools.systemtools import get_shared_lib_ext
+
+
+def get_icc_version():
+    """Obtain icc version string via 'icc --version'."""
+    cmd = "icc --version"
+    (out, _) = run_cmd(cmd, log_all=True, simple=False)
+
+    ver_re = re.compile("^icc \(ICC\) (?P<version>[0-9.]+) [0-9]+$", re.M)
+    version = ver_re.search(out).group('version')
+
+    return version
+
+
+class EB_intel(IntelBase):
+    """Support for installing icc
+
+    - tested with 11.1.046
+        - will fail for all older versions (due to newer silent installer)
+    """
+
+    @staticmethod
+    def extra_options():
+        """Add extra easyconfig parameters for Intel."""
+        extra_vars = {
+            'official_version': [None, "Official Intel version XXXX.X.XXX", CUSTOM],
+            'hide_mpi': [True, "LD_LIBRARY_PATH, CPATH, PATH are not including any reference to MPI libs or headers", CUSTOM],
+        }
+        return IntelBase.extra_options(extra_vars)
+
+
+    def __init__(self, *args, **kwargs):
+        """Constructor, initialize class variables."""
+        super(EB_intel, self).__init__(*args, **kwargs)
+
+        self.debuggerpath = None
+
+        self.comp_libs_subdir = None
+
+        if LooseVersion(self.cfg['official_version']) >= LooseVersion('2016'):
+
+            self.comp_libs_subdir = os.path.join('compilers_and_libraries_%s' % self.cfg['official_version'], 'linux')
+
+            if self.cfg['components'] is None:
+                # we need to use 'ALL' by default,
+                # using 'DEFAULTS' results in key things not being installed (e.g. bin/icc)
+                self.cfg['components'] = [COMP_ALL]
+                self.log.debug("Nothing specified for components, but required for version 2016, using %s instead",
+                               self.cfg['components'])
+    
+    
+    def install_step(self):
+        """
+        Actual installation
+        - create silent cfg file
+        - execute command
+        """
+        silent_cfg_names_map = None
+
+        if LooseVersion(self.cfg['official_version']) < LooseVersion('2013_sp1'):
+            # since icc v2013_sp1, silent.cfg has been slightly changed to be 'more standard'
+
+            silent_cfg_names_map = {
+                'activation_name': ACTIVATION_NAME_2012,
+                'license_file_name': LICENSE_FILE_NAME_2012,
+            }
+
+        super(EB_intel, self).install_step(silent_cfg_names_map=silent_cfg_names_map)
+        shutil.copy(self.license_file, os.path.join(self.installdir, '../'))
+
+
+    def sanity_check_step(self):
+        """Custom sanity check paths for icc."""
+
+        binprefix = 'bin/intel64'
+        libprefix = 'lib/intel64'
+        if LooseVersion(self.cfg['official_version']) >= LooseVersion('2011'):
+            if LooseVersion(self.cfg['official_version']) <= LooseVersion('2011.3.174'):
+                binprefix = 'bin'
+            elif LooseVersion(self.cfg['official_version']) >= LooseVersion('2013_sp1'):
+                binprefix = 'bin'
+            else:
+                libprefix = 'compiler/lib/intel64'
+
+        binfiles = ['icc', 'icpc']
+        if LooseVersion(self.cfg['official_version']) < LooseVersion('2014'):
+            binfiles += ['idb']
+
+        binaries = [os.path.join(binprefix, f) for f in binfiles]
+        libraries = [os.path.join(libprefix, 'lib%s' % l) for l in ['iomp5.a', 'iomp5.%s' % get_shared_lib_ext()]]
+        sanity_check_files = binaries + libraries
+        if LooseVersion(self.cfg['official_version']) > LooseVersion('2015'):
+            sanity_check_files.append('include/omp.h')
+
+        custom_paths = {
+            'files': sanity_check_files,
+            'dirs': [],
+        }
+
+        # make very sure that expected 'compilers_and_libraries_<VERSION>/linux' subdir is there for recent versions,
+        # since we rely on it being there in make_module_req_guess
+        if self.comp_libs_subdir:
+            custom_paths['dirs'].append(self.comp_libs_subdir)
+
+        custom_commands = ["which icc"]
+
+        super(EB_intel, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
+
+    def make_module_req_guess(self):
+        """
+        Additional paths to consider for prepend-paths statements in module file
+        """
+        prefix = None
+        docpath = 'documentation_%s' % self.cfg['official_version'].split('.')[0]
+        # guesses per environment variables
+        # some of these paths only apply to certain versions, but that doesn't really matter
+        # existence of paths is checked by module generator before 'prepend-paths' statements are included
+        
+        guesses = {
+            'CLASSPATH': ['daal/lib/daal.jar'],
+            # 'include' is deliberately omitted, including it causes problems, e.g. with complex.h and std::complex
+            # cfr. https://software.intel.com/en-us/forums/intel-c-compiler/topic/338378
+            'CPATH': ['ipp/include', 'mkl/include', 'mkl/include/fftw', 'tbb/include'],
+            'DAALROOT': ['daal'],
+            'IPPROOT': ['ipp'],
+            'LD_LIBRARY_PATH': ['lib'],
+            'MANPATH': ['debugger/gdb/intel64/share/man', 'man/common', 'man/en_US', 'share/man'],
+            'PATH': ['tbb/bin', 'mkl/bin'],
+            'TBBROOT': ['tbb'],
+            'MKLROOT': ['mkl'],
+            'PSTLROOT': ['pstl'],
+            'INFOPATH': [docpath],
+            'PKG_CONFIG_PATH': ['mkl/bin/pkgconfig']
+        }
+
+        if self.cfg['m32']:
+            # 32-bit toolchain
+            guesses['PATH'].extend(['bin/ia32', 'tbb/bin/ia32'])
+            # in the end we set 'LIBRARY_PATH' equal to 'LD_LIBRARY_PATH'
+            guesses['LD_LIBRARY_PATH'].append('lib/ia32')
+
+        else:
+            # 64-bit toolkit
+            guesses['PATH'].extend([
+                'bin/intel64',
+                'debugger/gdb/intel64/bin',
+                'ipp/bin/intel64',
+                'tbb/bin/emt64',
+                'tbb/bin/intel64',
+            ])
+
+            # in the end we set 'LIBRARY_PATH' equal to 'LD_LIBRARY_PATH'
+            guesses['LD_LIBRARY_PATH'].extend([
+                'tbb/lib/intel64/%s' % get_tbb_gccprefix(),
+                'mkl/lib/intel64',
+                'ipp/lib/intel64',
+                'debugger/ipt/intel64/lib',
+                'compiler/lib/intel64',
+            ])
+            guesses['MIC_LD_LIBRARY_PATH'] = [
+                'compiler/lib/mic',
+                'debugger/ipt/lib/mic',
+                'ipp/lib/mic',
+                'mkl/lib/mic',
+                'tbb/lib/mic',
+            ]
+
+
+            if not self.cfg['hide_mpi']:
+                guesses['LD_LIBRARY_PATH'].append('mpi/mic/lib', 'mpi/intel64/lib')
+                guesses['MIC_LD_LIBRARY_PATH'].append('/mpi/mic/lib')
+                guesses['PATH'].append('mpi/intel64/bin')
+                guesses['CPATH'].append('mpi/intel64/include')
+            if LooseVersion(self.cfg['official_version']) < LooseVersion('2016'):
+                prefix = 'composer_xe_%s' % self.cfg['official_version']
+                # for some older versions, name of subdirectory is slightly different
+                if not os.path.isdir(os.path.join(self.installdir, prefix)):
+                    cand_prefix = 'composerxe-%s' % self.cfg['official_version']
+                    if os.path.isdir(os.path.join(self.installdir, cand_prefix)):
+                        prefix = cand_prefix
+
+                # debugger is dependent on $INTEL_PYTHONHOME since version 2015 and newer
+                if LooseVersion(self.cfg['official_version']) >= LooseVersion('2015'):
+                    self.debuggerpath = os.path.join(prefix, 'debugger')
+
+            else:
+                # new directory layout for Intel Parallel Studio XE 2016
+                # https://software.intel.com/en-us/articles/new-directory-layout-for-intel-parallel-studio-xe-2016
+                prefix = self.comp_libs_subdir
+                # Debugger requires INTEL_PYTHONHOME, which only allows for a single value
+                self.debuggerpath = 'debugger_%s' % self.cfg['official_version'].split('.')[0]
+
+                guesses['LD_LIBRARY_PATH'].extend([
+                    os.path.join(self.debuggerpath, 'libipt/intel64/lib'),
+                    'daal/lib/intel64_lin',
+                ])
+
+            # 'lib/intel64' is deliberately listed last, so it gets precedence over subdirs
+            guesses['LD_LIBRARY_PATH'].append('lib/intel64') 
+
+        # set up advisor and inspector
+         
+        # set debugger path
+        if self.debuggerpath:
+            guesses['PATH'].append(os.path.join(self.debuggerpath, 'gdb', 'intel64', 'bin'))
+
+        # in recent Intel compiler distributions, the actual binaries are
+        # in deeper directories, and symlinked in top-level directories
+        # however, not all binaries are symlinked (e.g. mcpcom is not)
+        # we only need to include the deeper directories (same as compilervars.sh)
+        if prefix and os.path.isdir(os.path.join(self.installdir, prefix)):
+            for key, subdirs in guesses.items():
+                guesses[key] = [os.path.join(prefix, subdir) for subdir in subdirs]
+
+            # The for loop above breaks libipt library loading for gdb - this fixes that
+            guesses['LD_LIBRARY_PATH'].extend([
+                'daal/lib/intel64_lin',
+                # 'advisor/lib64',
+                # 'advisor_xe/lib64'
+                # 'inspector_xe/lib64',  # causes problems with libiomp5.so
+                # 'inspector/lib64',  # causes problems with libiomp5.so
+                ])
+            guesses['CPATH'].extend([
+                # 'daal/include',
+                # 'advisor/include',
+                # 'advisor_xe/include',
+                # 'inspector/include',
+                # 'inspector_xe/include',
+                ])
+            guesses['PATH'].extend([
+                'daal/bin',
+                'advisor/bin64',
+                'advisor_xe/bin64',
+                'inspector/bin64',
+                'inspector_xe/bin64'])
+            guesses['MANPATH'].extend([
+                'man/common',
+                '%s/en/debugger//gdb-mic/man' % docpath,
+                '%s/en/debugger//gdb-igfx/man' % docpath,
+                '%s/en/debugger//gdb-ia/man' % docpath,])
+            guesses['INFOPATH'].extend([
+                '%s/en/debugger//gdb-mic/info' % docpath,
+                '%s/en/debugger//gdb-ia/info' % docpath,
+                '%s/en/debugger//gdb-igfx/info' % docpath])
+            if self.debuggerpath:
+                guesses['LD_LIBRARY_PATH'].extend([
+                    os.path.join(self.debuggerpath, 'libipt/intel64/lib'),
+                    os.path.join(self.debuggerpath, 'iga/lib')])
+                guesses['GDB_CROSS'] = [
+                    os.path.join(self.debuggerpath, 'gdb/intel64_mic/bin/gdb-mic'),
+                    os.path.join(self.debuggerpath, 'gdb/intel64/bin/gdb-ia')]
+                for gdb in guesses['GDB_CROSS']:
+                    if os.path.isfile(os.path.join(self.installdir, gdb)):
+                        # pick first existing one and reset list
+                        guesses['GDB_CROSS'] = [gdb]
+                        break
+                guesses['GDBSERVER_MIC'] = [
+                    os.path.join(self.debuggerpath, 'gdb/targets/intel64/x200/bin/gdbserver'),
+                    os.path.join(self.debuggerpath, 'gdb/targets/mic/bin/gdbserver'),]
+
+        # only set $IDB_HOME if idb exists
+        idb_home_subdir = 'bin/intel64'
+        if os.path.isfile(os.path.join(self.installdir, idb_home_subdir, 'idb')):
+            guesses['IDB_HOME'] = [idb_home_subdir]
+        
+        guesses['LIBRARY_PATH'] = guesses['LD_LIBRARY_PATH']
+
+        return guesses
+
+
+    def make_module_extra(self, *args, **kwargs):
+        """Additional custom variables for icc: $INTEL_PYTHONHOME."""
+        txt = super(EB_intel, self).make_module_extra(*args, **kwargs)
+
+        if self.debuggerpath:
+            intel_pythonhome = os.path.join(self.installdir, self.debuggerpath, 'python', 'intel64')
+            if os.path.isdir(intel_pythonhome):
+                txt += self.module_generator.set_environment('INTEL_PYTHONHOME', intel_pythonhome)
+        
+        # use licence file in installdir/../
+        self.license_file = os.path.join(self.installdir, '..', os.path.basename(self.license_file))
+        
+        # on Debian/Ubuntu, /usr/include/x86_64-linux-gnu needs to be included in $CPATH for icc
+        out, ec = run_cmd("gcc -print-multiarch", simple=False, log_all=False, log_ok=False)
+        multiarch_inc_subdir = out.strip()
+        if ec == 0 and multiarch_inc_subdir:
+            multiarch_inc_dir = os.path.join('/usr', 'include', multiarch_inc_subdir)
+            self.log.info("Adding multiarch include path %s to $CPATH in generated module file", multiarch_inc_dir)
+            # system location must be appended at the end, so use append_paths
+            txt += self.module_generator.append_paths('CPATH', [multiarch_inc_dir], allow_abs=True)
+
+        return txt

diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/o/openfoam.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/o/openfoam.py
index 3a286b5..ff10c80 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/o/openfoam.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/o/openfoam.py
@@ -67,8 +67,12 @@ class EB_OpenFOAM(EasyBlock):
         self.openfoamdir = None
         self.thrdpartydir = None
 
+        # version may start with 'v' for some variants of OpenFOAM
+        # we need to strip this off to avoid problems when comparing LooseVersion instances in Python 3
+        self.looseversion = LooseVersion(self.version.strip('v+'))
+
         if 'extend' in self.name.lower():
-            if LooseVersion(self.version) >= LooseVersion('3.0'):
+            if self.looseversion >= LooseVersion('3.0'):
                 self.openfoamdir = 'foam-extend-%s' % self.version
             else:
                 self.openfoamdir = 'OpenFOAM-%s-ext' % self.version
@@ -145,10 +149,10 @@ class EB_OpenFOAM(EasyBlock):
                 extra_flags = '-fuse-ld=bfd'
 
             # older versions of OpenFOAM-Extend require -fpermissive
-            if 'extend' in self.name.lower() and LooseVersion(self.version) < LooseVersion('2.0'):
+            if 'extend' in self.name.lower() and self.looseversion < LooseVersion('2.0'):
                 extra_flags += ' -fpermissive'
 
-            if LooseVersion(self.version) < LooseVersion('3.0'):
+            if self.looseversion < LooseVersion('3.0'):
                 extra_flags += ' -fno-delete-null-pointer-checks'
 
         elif comp_fam == toolchain.INTELCOMP:  # @UndefinedVariable
@@ -166,13 +170,13 @@ class EB_OpenFOAM(EasyBlock):
             regex_subs = [(r"^(setenv|export) WM_THIRD_PARTY_USE_.*[ =].*$", r"# \g<0>")]
 
             # this does not work for OpenFOAM Extend lower than 2.0
-            if 'extend' not in self.name.lower() or LooseVersion(self.version) >= LooseVersion('2.0'):
+            if 'extend' not in self.name.lower() or self.looseversion >= LooseVersion('2.0'):
                 key = "WM_PROJECT_VERSION"
                 regex_subs += [(r"^(setenv|export) %s=.*$" % key, r"export %s=%s #\g<0>" % (key, self.version))]
 
             WM_env_var = ['WM_COMPILER', 'WM_MPLIB', 'WM_THIRD_PARTY_DIR']
             # OpenFOAM >= 3.0.0 can use 64 bit integers
-            if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+            if 'extend' not in self.name.lower() and self.looseversion >= LooseVersion('3.0'):
                 WM_env_var.append('WM_LABEL_SIZE')
             for env_var in WM_env_var:
                 regex_subs.append((r"^(setenv|export) (?P<var>%s)[ =](?P<val>.*)$" % env_var,
@@ -181,6 +185,8 @@ class EB_OpenFOAM(EasyBlock):
 
         # inject compiler variables into wmake/rules files
         ldirs = glob.glob(os.path.join(self.builddir, self.openfoamdir, 'wmake', 'rules', 'linux*'))
+        if self.looseversion >= LooseVersion('1906'):
+            ldirs += glob.glob(os.path.join(self.builddir, self.openfoamdir, 'wmake', 'rules', 'General', '*'))
         langs = ['c', 'c++']
 
         # NOTE: we do not want to change the Debug rules files becuse
@@ -210,6 +216,9 @@ class EB_OpenFOAM(EasyBlock):
             'c++OPT': os.environ['CXXFLAGS'],
         }
         for wmake_rules_file in wmake_rules_files:
+            # the cOpt and c++Opt files don't exist in the General directories (which are included for recent versions)
+            if not os.path.isfile(wmake_rules_file):
+                continue
             fullpath = os.path.join(self.builddir, self.openfoamdir, wmake_rules_file)
             self.log.debug("Patching compiler variables in %s", fullpath)
             regex_subs = []
@@ -220,6 +229,7 @@ class EB_OpenFOAM(EasyBlock):
         # enable verbose build for debug purposes
         # starting with openfoam-extend 3.2, PS1 also needs to be set
         env.setvar("FOAM_VERBOSE", '1')
+        env.setvar("PS1", '1')
 
         # installation directory
         env.setvar("FOAM_INST_DIR", self.installdir)
@@ -241,15 +251,15 @@ class EB_OpenFOAM(EasyBlock):
         env.setvar("WM_NCOMPPROCS", str(self.cfg['parallel']))
 
         # OpenFOAM >= 3.0.0 can use 64 bit integers
-        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+        if 'extend' not in self.name.lower() and self.looseversion >= LooseVersion('3.0'):
             if self.toolchain.options['i8']:
                 env.setvar("WM_LABEL_SIZE", '64')
             else:
                 env.setvar("WM_LABEL_SIZE", '32')
 
         # make sure lib/include dirs for dependencies are found
-        openfoam_extend_v3 = 'extend' in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0')
-        if LooseVersion(self.version) < LooseVersion("2") or openfoam_extend_v3:
+        openfoam_extend_v3 = 'extend' in self.name.lower() and self.looseversion >= LooseVersion('3.0')
+        if self.looseversion < LooseVersion("2") or openfoam_extend_v3:
             self.log.debug("List of deps: %s" % self.cfg.dependencies())
             for dep in self.cfg.dependencies():
                 dep_name = dep['name'].upper(),
@@ -261,7 +271,7 @@ class EB_OpenFOAM(EasyBlock):
                     "%s_LIB_DIR": "%s/lib",
                     "%s_INCLUDE_DIR": "%s/include",
                 }
-                for var, val in dep_vars.iteritems():
+                for var, val in dep_vars.items():
                     env.setvar(var % dep_name, val % dep_root)
         else:
             for depend in ['SCOTCH', 'METIS', 'CGAL', 'Paraview']:
@@ -277,7 +287,7 @@ class EB_OpenFOAM(EasyBlock):
         """Build OpenFOAM using make after sourcing script to set environment."""
 
         precmd = "source %s" % os.path.join(self.builddir, self.openfoamdir, "etc", "bashrc")
-        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('4.0'):
+        if 'extend' not in self.name.lower() and self.looseversion >= LooseVersion('4.0'):
             cleancmd = "cd $WM_PROJECT_DIR && wcleanPlatform -all && cd -"
         else:
             cleancmd = "wcleanAll"
@@ -289,7 +299,7 @@ class EB_OpenFOAM(EasyBlock):
             'prebuildopts': self.cfg['prebuildopts'],
             'makecmd': os.path.join(self.builddir, self.openfoamdir, '%s'),
         }
-        if 'extend' in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+        if 'extend' in self.name.lower() and self.looseversion >= LooseVersion('3.0'):
             qa = {
                 "Proceed without compiling ParaView [Y/n]": 'Y',
                 "Proceed without compiling cudaSolvers? [Y/n]": 'Y',
@@ -305,12 +315,14 @@ class EB_OpenFOAM(EasyBlock):
                 r"\s*\^\s*",  # warning indicator
                 "Cleaning .*",
             ]
-            run_cmd_qa(cmd_tmpl % 'Allwmake.firstInstall', qa, no_qa=noqa, log_all=True, simple=True)
+            run_cmd_qa(cmd_tmpl % 'Allwmake.firstInstall', qa, no_qa=noqa, log_all=True, simple=True, maxhits=500)
         else:
             cmd = 'Allwmake'
-            if LooseVersion(self.version) >= LooseVersion('1606'):
+            if self.looseversion > LooseVersion('1606'):
                 # use Allwmake -log option if possible since this can be useful during builds, but also afterwards
-                cmd += ' -log'
+#                cmd += ' -log'
+                 cmd += ">log.make"
+            self.log.debug("CMD: %s"  % cmd )
             run_cmd(cmd_tmpl % cmd, log_all=True, simple=True, log_output=True)
 
     def install_step(self):
@@ -333,7 +345,7 @@ class EB_OpenFOAM(EasyBlock):
         shlib_ext = get_shared_lib_ext()
 
         # OpenFOAM >= 3.0.0 can use 64 bit integers
-        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+        if 'extend' not in self.name.lower() and self.looseversion >= LooseVersion('3.0'):
             if self.toolchain.options['i8']:
                 int_size = 'Int64'
             else:
@@ -343,8 +355,8 @@ class EB_OpenFOAM(EasyBlock):
 
         psubdir = "linux64%sDP%s%s" % (self.wm_compiler, int_size, self.build_type)
 
-        openfoam_extend_v3 = 'extend' in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0')
-        if openfoam_extend_v3 or LooseVersion(self.version) < LooseVersion("2"):
+        openfoam_extend_v3 = 'extend' in self.name.lower() and self.looseversion >= LooseVersion('3.0')
+        if openfoam_extend_v3 or self.looseversion < LooseVersion("2"):
             toolsdir = os.path.join(self.openfoamdir, "applications", "bin", psubdir)
             libsdir = os.path.join(self.openfoamdir, "lib", psubdir)
             dirs = [toolsdir, libsdir]
@@ -356,16 +368,24 @@ class EB_OpenFOAM(EasyBlock):
         # some randomly selected binaries
         # if one of these is missing, it's very likely something went wrong
         bins = [os.path.join(self.openfoamdir, "bin", x) for x in ["paraFoam"]] + \
-               [os.path.join(toolsdir, "buoyant%sSimpleFoam" % x) for x in ["", "Boussinesq"]] + \
-               [os.path.join(toolsdir, "%sFoam" % x) for x in ["boundary", "engine", "sonic"]] + \
+               [os.path.join(toolsdir, "buoyantSimpleFoam")] + \
+               [os.path.join(toolsdir, "%sFoam" % x) for x in ["boundary", "engine"]] + \
                [os.path.join(toolsdir, "surface%s" % x) for x in ["Add", "Find", "Smooth"]] + \
                [os.path.join(toolsdir, x) for x in ['blockMesh', 'checkMesh', 'deformedGeom', 'engineSwirl',
                                                     'modifyMesh', 'refineMesh']]
+
+        # only include Boussinesq and sonic since for OpenFOAM < 7, since those solvers have been deprecated
+        if self.looseversion < LooseVersion('7'):
+            bins.extend([
+                os.path.join(toolsdir, "buoyantBoussinesqSimpleFoam"),
+                os.path.join(toolsdir, "sonicFoam")
+            ])
+
         # check for the Pstream and scotchDecomp libraries, there must be a dummy one and an mpi one
         if 'extend' in self.name.lower():
             libs = [os.path.join(libsdir, "libscotchDecomp.%s" % shlib_ext),
                     os.path.join(libsdir, "libmetisDecomp.%s" % shlib_ext)]
-            if LooseVersion(self.version) < LooseVersion('3.2'):
+            if self.looseversion < LooseVersion('3.2'):
                 # Pstream should have both a dummy and a mpi one
                 libs.extend([os.path.join(libsdir, x, "libPstream.%s" % shlib_ext) for x in ["dummy", "mpi"]])
                 libs.extend([os.path.join(libsdir, "mpi", "libparMetisDecomp.%s" % shlib_ext)])
@@ -378,7 +398,7 @@ class EB_OpenFOAM(EasyBlock):
                    [os.path.join(libsdir, "libscotchDecomp.%s" % shlib_ext)] + \
                    [os.path.join(libsdir, "dummy", "libscotchDecomp.%s" % shlib_ext)]
 
-        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion("2.3.0"):
+        if 'extend' not in self.name.lower() and self.looseversion >= LooseVersion("2.3.0"):
             # surfaceSmooth is replaced by surfaceLambdaMuSmooth is OpenFOAM v2.3.0
             bins.remove(os.path.join(toolsdir, "surfaceSmooth"))
             bins.append(os.path.join(toolsdir, "surfaceLambdaMuSmooth"))
@@ -408,7 +428,7 @@ class EB_OpenFOAM(EasyBlock):
         ]
 
         # OpenFOAM >= 3.0.0 can use 64 bit integers
-        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+        if 'extend' not in self.name.lower() and self.looseversion >= LooseVersion('3.0'):
             if self.toolchain.options['i8']:
                 env_vars += [('WM_LABEL_SIZE', '64')]
             else:

diff --git a/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/o/openfoam.py.old b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/o/openfoam.py.old
new file mode 100644
index 0000000..aa89dd9
--- /dev/null
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/o/openfoam.py.old
@@ -0,0 +1,423 @@
+##
+# Copyright 2009-2019 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for building and installing OpenFOAM, implemented as an easyblock
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+@author: Xavier Besseron (University of Luxembourg)
+@author: Ward Poelmans (Ghent University)
+@author: Balazs Hajgato (Free University Brussels (VUB))
+"""
+
+import glob
+import os
+import re
+import shutil
+import stat
+from distutils.version import LooseVersion
+
+import easybuild.tools.environment as env
+import easybuild.tools.toolchain as toolchain
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import adjust_permissions, apply_regex_substitutions, mkdir
+from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.run import run_cmd, run_cmd_qa
+from easybuild.tools.systemtools import get_shared_lib_ext
+
+
+class EB_OpenFOAM(EasyBlock):
+    """Support for building and installing OpenFOAM."""
+
+    def __init__(self, *args, **kwargs):
+        """Specify that OpenFOAM should be built in install dir."""
+
+        super(EB_OpenFOAM, self).__init__(*args, **kwargs)
+
+        self.build_in_installdir = True
+
+        self.wm_compiler = None
+        self.wm_mplib = None
+        self.openfoamdir = None
+        self.thrdpartydir = None
+
+        if 'extend' in self.name.lower():
+            if LooseVersion(self.version) >= LooseVersion('3.0'):
+                self.openfoamdir = 'foam-extend-%s' % self.version
+            else:
+                self.openfoamdir = 'OpenFOAM-%s-ext' % self.version
+        else:
+            self.openfoamdir = '-'.join([self.name, '-'.join(self.version.split('-')[:2])])
+        self.log.debug("openfoamdir: %s" % self.openfoamdir)
+
+        # Set build type to requested value
+        if self.toolchain.options['debug']:
+            self.build_type = 'Debug'
+        else:
+            self.build_type = 'Opt'
+
+    def extract_step(self):
+        """Extract sources as expected by the OpenFOAM(-Extend) build scripts."""
+        super(EB_OpenFOAM, self).extract_step()
+        # make sure that the expected subdir is really there after extracting
+        # if not, the build scripts (e.g., the etc/bashrc being sourced) will likely fail
+        openfoam_installdir = os.path.join(self.installdir, self.openfoamdir)
+        if not os.path.exists(openfoam_installdir):
+            self.log.warning("Creating expected directory %s, and moving everything there" % openfoam_installdir)
+            try:
+                contents_installdir = os.listdir(self.installdir)
+                source = os.path.join(self.installdir, contents_installdir[0])
+                # it's one directory but has a wrong name
+                if len(contents_installdir) == 1 and os.path.isdir(source):
+                    target = os.path.join(self.installdir, self.openfoamdir)
+                    self.log.debug("Renaming %s to %s", source, target)
+                    os.rename(source, target)
+                else:
+                    mkdir(openfoam_installdir)
+                    for fil in contents_installdir:
+                        if fil != self.openfoamdir:
+                            source = os.path.join(self.installdir, fil)
+                            target = os.path.join(openfoam_installdir, fil)
+                            self.log.debug("Moving %s to %s", source, target)
+                            shutil.move(source, target)
+                    os.chdir(openfoam_installdir)
+            except OSError as err:
+                raise EasyBuildError("Failed to move all files to %s: %s", openfoam_installdir, err)
+
+    def patch_step(self, beginpath=None):
+        """Adjust start directory and start path for patching to correct directory."""
+        self.cfg['start_dir'] = os.path.join(self.installdir, self.openfoamdir)
+        super(EB_OpenFOAM, self).patch_step(beginpath=self.cfg['start_dir'])
+
+    def prepare_step(self, *args, **kwargs):
+        """Prepare for OpenFOAM install procedure."""
+        super(EB_OpenFOAM, self).prepare_step(*args, **kwargs)
+
+        comp_fam = self.toolchain.comp_family()
+        if comp_fam == toolchain.GCC:  # @UndefinedVariable
+            self.wm_compiler = 'Gcc'
+        elif comp_fam == toolchain.INTELCOMP:  # @UndefinedVariable
+            self.wm_compiler = 'Icc'
+        else:
+            raise EasyBuildError("Unknown compiler family, don't know how to set WM_COMPILER")
+
+        # set to an MPI unknown by OpenFOAM, since we're handling the MPI settings ourselves (via mpicc, etc.)
+        # Note: this name must contain 'MPI' so the MPI version of the
+        # Pstream library is built (cf src/Pstream/Allwmake)
+        self.wm_mplib = "EASYBUILDMPI"
+
+    def configure_step(self):
+        """Configure OpenFOAM build by setting appropriate environment variables."""
+        # compiler & compiler flags
+        comp_fam = self.toolchain.comp_family()
+
+        extra_flags = ''
+        if comp_fam == toolchain.GCC:  # @UndefinedVariable
+            if get_software_version('GCC') >= LooseVersion('4.8'):
+                # make sure non-gold version of ld is used, since OpenFOAM requires it
+                # see http://www.openfoam.org/mantisbt/view.php?id=685
+                extra_flags = '-fuse-ld=bfd'
+
+            # older versions of OpenFOAM-Extend require -fpermissive
+            if 'extend' in self.name.lower() and LooseVersion(self.version) < LooseVersion('2.0'):
+                extra_flags += ' -fpermissive'
+
+            if LooseVersion(self.version) < LooseVersion('3.0'):
+                extra_flags += ' -fno-delete-null-pointer-checks'
+
+        elif comp_fam == toolchain.INTELCOMP:  # @UndefinedVariable
+            # make sure -no-prec-div is used with Intel compilers
+            extra_flags = '-no-prec-div'
+
+        for env_var in ['CFLAGS', 'CXXFLAGS']:
+            env.setvar(env_var, "%s %s" % (os.environ.get(env_var, ''), extra_flags))
+
+        # patch out hardcoding of WM_* environment variables
+        # for example, replace 'export WM_COMPILER=Gcc' with ': ${WM_COMPILER:=Gcc}; export WM_COMPILER'
+        for script in [os.path.join(self.builddir, self.openfoamdir, x) for x in ['etc/bashrc', 'etc/cshrc']]:
+            self.log.debug("Patching out hardcoded $WM_* env vars in %s", script)
+            # disable any third party stuff, we use EB controlled builds
+            regex_subs = [(r"^(setenv|export) WM_THIRD_PARTY_USE_.*[ =].*$", r"# \g<0>")]
+
+            # this does not work for OpenFOAM Extend lower than 2.0
+            if 'extend' not in self.name.lower() or LooseVersion(self.version) >= LooseVersion('2.0'):
+                key = "WM_PROJECT_VERSION"
+                regex_subs += [(r"^(setenv|export) %s=.*$" % key, r"export %s=%s #\g<0>" % (key, self.version))]
+
+            WM_env_var = ['WM_COMPILER', 'WM_MPLIB', 'WM_THIRD_PARTY_DIR']
+            # OpenFOAM >= 3.0.0 can use 64 bit integers
+            if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+                WM_env_var.append('WM_LABEL_SIZE')
+            for env_var in WM_env_var:
+                regex_subs.append((r"^(setenv|export) (?P<var>%s)[ =](?P<val>.*)$" % env_var,
+                                   r": ${\g<var>:=\g<val>}; export \g<var>"))
+            apply_regex_substitutions(script, regex_subs)
+
+        # inject compiler variables into wmake/rules files
+        ldirs = glob.glob(os.path.join(self.builddir, self.openfoamdir, 'wmake', 'rules', 'linux*'))
+        langs = ['c', 'c++']
+
+        # NOTE: we do not want to change the Debug rules files becuse
+        # that would change the cOPT/c++OPT values from their empty setting.
+        suffixes = ['', 'Opt']
+        wmake_rules_files = [os.path.join(ldir, lang + suff) for ldir in ldirs for lang in langs for suff in suffixes]
+
+        mpicc = os.environ['MPICC']
+        mpicxx = os.environ['MPICXX']
+        cc_seq = os.environ.get('CC_SEQ', os.environ['CC'])
+        cxx_seq = os.environ.get('CXX_SEQ', os.environ['CXX'])
+
+        if self.toolchain.mpi_family() == toolchain.OPENMPI:
+            # no -cc/-cxx flags supported in OpenMPI compiler wrappers
+            c_comp_cmd = 'OMPI_CC="%s" %s' % (cc_seq, mpicc)
+            cxx_comp_cmd = 'OMPI_CXX="%s" %s' % (cxx_seq, mpicxx)
+        else:
+            # -cc/-cxx should work for all MPICH-based MPIs (including Intel MPI)
+            c_comp_cmd = '%s -cc="%s"' % (mpicc, cc_seq)
+            cxx_comp_cmd = '%s -cxx="%s"' % (mpicxx, cxx_seq)
+
+        comp_vars = {
+            # specify MPI compiler wrappers and compiler commands + sequential compiler that should be used by them
+            'cc': c_comp_cmd,
+            'CC': cxx_comp_cmd,
+            'cOPT': os.environ['CFLAGS'],
+            'c++OPT': os.environ['CXXFLAGS'],
+        }
+        for wmake_rules_file in wmake_rules_files:
+            fullpath = os.path.join(self.builddir, self.openfoamdir, wmake_rules_file)
+            self.log.debug("Patching compiler variables in %s", fullpath)
+            regex_subs = []
+            for comp_var, newval in comp_vars.items():
+                regex_subs.append((r"^(%s\s*=\s*).*$" % re.escape(comp_var), r"\1%s" % newval))
+            apply_regex_substitutions(fullpath, regex_subs)
+
+        # enable verbose build for debug purposes
+        # starting with openfoam-extend 3.2, PS1 also needs to be set
+        env.setvar("FOAM_VERBOSE", '1')
+
+        # installation directory
+        env.setvar("FOAM_INST_DIR", self.installdir)
+
+        # third party directory
+        self.thrdpartydir = "ThirdParty-%s" % self.version
+        # only if third party stuff is actually installed
+        if os.path.exists(self.thrdpartydir):
+            os.symlink(os.path.join("..", self.thrdpartydir), self.thrdpartydir)
+            env.setvar("WM_THIRD_PARTY_DIR", os.path.join(self.installdir, self.thrdpartydir))
+
+        env.setvar("WM_COMPILER", self.wm_compiler)
+        env.setvar("WM_MPLIB", self.wm_mplib)
+
+        # Set Compile options according to build type
+        env.setvar("WM_COMPILE_OPTION", self.build_type)
+
+        # parallel build spec
+        env.setvar("WM_NCOMPPROCS", str(self.cfg['parallel']))
+
+        # OpenFOAM >= 3.0.0 can use 64 bit integers
+        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+            if self.toolchain.options['i8']:
+                env.setvar("WM_LABEL_SIZE", '64')
+            else:
+                env.setvar("WM_LABEL_SIZE", '32')
+
+        # make sure lib/include dirs for dependencies are found
+        openfoam_extend_v3 = 'extend' in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0')
+        if LooseVersion(self.version) < LooseVersion("2") or openfoam_extend_v3:
+            self.log.debug("List of deps: %s" % self.cfg.dependencies())
+            for dep in self.cfg.dependencies():
+                dep_name = dep['name'].upper(),
+                dep_root = get_software_root(dep['name'])
+                env.setvar("%s_SYSTEM" % dep_name, "1")
+                dep_vars = {
+                    "%s_DIR": "%s",
+                    "%s_BIN_DIR": "%s/bin",
+                    "%s_LIB_DIR": "%s/lib",
+                    "%s_INCLUDE_DIR": "%s/include",
+                }
+                for var, val in dep_vars.iteritems():
+                    env.setvar(var % dep_name, val % dep_root)
+        else:
+            for depend in ['SCOTCH', 'METIS', 'CGAL', 'Paraview']:
+                dependloc = get_software_root(depend)
+                if dependloc:
+                    if depend == 'CGAL' and get_software_root('Boost'):
+                        env.setvar("CGAL_ROOT", dependloc)
+                        env.setvar("BOOST_ROOT", get_software_root('Boost'))
+                    else:
+                        env.setvar("%s_ROOT" % depend.upper(), dependloc)
+
+    def build_step(self):
+        """Build OpenFOAM using make after sourcing script to set environment."""
+
+        precmd = "source %s" % os.path.join(self.builddir, self.openfoamdir, "etc", "bashrc")
+        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('4.0'):
+            cleancmd = "cd $WM_PROJECT_DIR && wcleanPlatform -all && cd -"
+        else:
+            cleancmd = "wcleanAll"
+
+        # make directly in install directory
+        cmd_tmpl = "%(precmd)s && %(cleancmd)s && %(prebuildopts)s %(makecmd)s" % {
+            'precmd': precmd,
+            'cleancmd': cleancmd,
+            'prebuildopts': self.cfg['prebuildopts'],
+            'makecmd': os.path.join(self.builddir, self.openfoamdir, '%s'),
+        }
+        if 'extend' in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+            qa = {
+                "Proceed without compiling ParaView [Y/n]": 'Y',
+                "Proceed without compiling cudaSolvers? [Y/n]": 'Y',
+            }
+            noqa = [
+                ".* -o .*",
+                "checking .*",
+                "warning.*",
+                "configure: creating.*",
+                "%s .*" % os.environ['CC'],
+                "wmake .*",
+                "Making dependency list for source file.*",
+                r"\s*\^\s*",  # warning indicator
+                "Cleaning .*",
+            ]
+            run_cmd_qa(cmd_tmpl % 'Allwmake.firstInstall', qa, no_qa=noqa, log_all=True, simple=True)
+        else:
+            cmd = 'Allwmake'
+            if LooseVersion(self.version) >= LooseVersion('1606'):
+                # use Allwmake -log option if possible since this can be useful during builds, but also afterwards
+                #cmd += ' -log'
+                pass
+            run_cmd(cmd_tmpl % cmd, log_all=True, simple=True, log_output=True)
+
+    def install_step(self):
+        """Building was performed in install dir, so just fix permissions."""
+
+        # fix permissions of OpenFOAM dir
+        fullpath = os.path.join(self.installdir, self.openfoamdir)
+        adjust_permissions(fullpath, stat.S_IROTH, add=True, recursive=True, ignore_errors=True)
+        adjust_permissions(fullpath, stat.S_IXOTH, add=True, recursive=True, onlydirs=True, ignore_errors=True)
+
+        # fix permissions of ThirdParty dir and subdirs (also for 2.x)
+        # if the thirdparty tarball is installed
+        fullpath = os.path.join(self.installdir, self.thrdpartydir)
+        if os.path.exists(fullpath):
+            adjust_permissions(fullpath, stat.S_IROTH, add=True, recursive=True, ignore_errors=True)
+            adjust_permissions(fullpath, stat.S_IXOTH, add=True, recursive=True, onlydirs=True, ignore_errors=True)
+
+    def sanity_check_step(self):
+        """Custom sanity check for OpenFOAM"""
+        shlib_ext = get_shared_lib_ext()
+
+        # OpenFOAM >= 3.0.0 can use 64 bit integers
+        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+            if self.toolchain.options['i8']:
+                int_size = 'Int64'
+            else:
+                int_size = 'Int32'
+        else:
+            int_size = ''
+
+        psubdir = "linux64%sDP%s%s" % (self.wm_compiler, int_size, self.build_type)
+
+        openfoam_extend_v3 = 'extend' in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0')
+        if openfoam_extend_v3 or LooseVersion(self.version) < LooseVersion("2"):
+            toolsdir = os.path.join(self.openfoamdir, "applications", "bin", psubdir)
+            libsdir = os.path.join(self.openfoamdir, "lib", psubdir)
+            dirs = [toolsdir, libsdir]
+        else:
+            toolsdir = os.path.join(self.openfoamdir, "platforms", psubdir, "bin")
+            libsdir = os.path.join(self.openfoamdir, "platforms", psubdir, "lib")
+            dirs = [toolsdir, libsdir]
+
+        # some randomly selected binaries
+        # if one of these is missing, it's very likely something went wrong
+        bins = [os.path.join(self.openfoamdir, "bin", x) for x in ["paraFoam"]] + \
+               [os.path.join(toolsdir, "buoyant%sSimpleFoam" % x) for x in ["", "Boussinesq"]] + \
+               [os.path.join(toolsdir, "%sFoam" % x) for x in ["boundary", "engine", "sonic"]] + \
+               [os.path.join(toolsdir, "surface%s" % x) for x in ["Add", "Find", "Smooth"]] + \
+               [os.path.join(toolsdir, x) for x in ['blockMesh', 'checkMesh', 'deformedGeom', 'engineSwirl',
+                                                    'modifyMesh', 'refineMesh']]
+        # check for the Pstream and scotchDecomp libraries, there must be a dummy one and an mpi one
+        if 'extend' in self.name.lower():
+            libs = [os.path.join(libsdir, "libscotchDecomp.%s" % shlib_ext),
+                    os.path.join(libsdir, "libmetisDecomp.%s" % shlib_ext)]
+            if LooseVersion(self.version) < LooseVersion('3.2'):
+                # Pstream should have both a dummy and a mpi one
+                libs.extend([os.path.join(libsdir, x, "libPstream.%s" % shlib_ext) for x in ["dummy", "mpi"]])
+                libs.extend([os.path.join(libsdir, "mpi", "libparMetisDecomp.%s" % shlib_ext)])
+            else:
+                libs.extend([os.path.join(libsdir, "libparMetisDecomp.%s" % shlib_ext)])
+        else:
+            # there must be a dummy one and an mpi one for both
+            libs = [os.path.join(libsdir, x, "libPstream.%s" % shlib_ext) for x in ["dummy", "mpi"]] + \
+                   [os.path.join(libsdir, x, "libptscotchDecomp.%s" % shlib_ext) for x in ["dummy", "mpi"]] +\
+                   [os.path.join(libsdir, "libscotchDecomp.%s" % shlib_ext)] + \
+                   [os.path.join(libsdir, "dummy", "libscotchDecomp.%s" % shlib_ext)]
+
+        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion("2.3.0"):
+            # surfaceSmooth is replaced by surfaceLambdaMuSmooth is OpenFOAM v2.3.0
+            bins.remove(os.path.join(toolsdir, "surfaceSmooth"))
+            bins.append(os.path.join(toolsdir, "surfaceLambdaMuSmooth"))
+
+        custom_paths = {
+            'files': [os.path.join(self.openfoamdir, 'etc', x) for x in ["bashrc", "cshrc"]] + bins + libs,
+            'dirs': dirs,
+        }
+
+        super(EB_OpenFOAM, self).sanity_check_step(custom_paths=custom_paths)
+
+    def make_module_extra(self, altroot=None, altversion=None):
+        """Define extra environment variables required by OpenFOAM"""
+
+        txt = super(EB_OpenFOAM, self).make_module_extra()
+
+        env_vars = [
+            # Set WM_COMPILE_OPTION in the module file
+            # $FOAM_BASH will then pick it up correctly.
+            ('WM_COMPILE_OPTION', self.build_type),
+            ('WM_PROJECT_VERSION', self.version),
+            ('FOAM_INST_DIR', self.installdir),
+            ('WM_COMPILER', self.wm_compiler),
+            ('WM_MPLIB', self.wm_mplib),
+            ('FOAM_BASH', os.path.join(self.installdir, self.openfoamdir, 'etc', 'bashrc')),
+            ('FOAM_CSH', os.path.join(self.installdir, self.openfoamdir, 'etc', 'cshrc')),
+        ]
+
+        # OpenFOAM >= 3.0.0 can use 64 bit integers
+        if 'extend' not in self.name.lower() and LooseVersion(self.version) >= LooseVersion('3.0'):
+            if self.toolchain.options['i8']:
+                env_vars += [('WM_LABEL_SIZE', '64')]
+            else:
+                env_vars += [('WM_LABEL_SIZE', '32')]
+
+        for (env_var, val) in env_vars:
+            # check whether value is defined for compatibility with --module-only
+            if val:
+                txt += self.module_generator.set_environment(env_var, val)
+
+        return txt

diff --git a/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/p/paraview.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/p/paraview.py
new file mode 100644
index 0000000..dde2d0e
--- /dev/null
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/p/paraview.py
@@ -0,0 +1,146 @@
+##
+# Copyright 2009-2019 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for software that is configured with CMake, implemented as an easyblock
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+@author: Ward Poelmans (Ghent University)
+@author: Maxime Boissonneault (Compute Canada - Universite Laval)
+"""
+import os
+
+from easybuild.easyblocks.generic.cmakemake import CMakeMake
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.config import build_option
+from easybuild.tools.filetools import change_dir, mkdir, which
+from easybuild.tools.environment import setvar
+from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd
+from vsc.utils.missing import nub
+
+
+DEFAULT_CONFIGURE_CMD = 'cmake'
+
+
+class EB_ParaView(CMakeMake):
+    """Support for configuring build with CMake instead of traditional configure script"""
+
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Define extra easyconfig parameters specific to CMakeMake."""
+        extra_vars = CMakeMake.extra_options(extra_vars)
+        extra_vars.update({
+            'abs_path_compilers': [False, "Specify compilers via absolute file path (not via command names)", CUSTOM],
+            'allow_system_boost': [False, "Always allow CMake to pick up on Boost installed in OS "
+                                          "(even if Boost is included as a dependency)", CUSTOM],
+            'configure_cmd': [DEFAULT_CONFIGURE_CMD, "Configure command to use", CUSTOM],
+            'srcdir': [None, "Source directory location to provide to cmake command", CUSTOM],
+            'separate_build_dir': [False, "Perform build in a separate directory", CUSTOM],
+            'build_in_installdir': [True, "Perform build in installation directory", CUSTOM],
+        })
+        return extra_vars
+
+    def configure_step(self, srcdir=None, builddir=None):
+        """Configure build using cmake"""
+
+        # Set the search paths for CMake
+        tc_ipaths = self.toolchain.get_variable("CPPFLAGS", list)
+        tc_lpaths = self.toolchain.get_variable("LDFLAGS", list)
+        cpaths = os.getenv('CPATH', '').split(os.pathsep)
+        lpaths = os.getenv('LD_LIBRARY_PATH', '').split(os.pathsep)
+        include_paths = os.pathsep.join(nub(tc_ipaths + cpaths))
+        library_paths = os.pathsep.join(nub(tc_lpaths + lpaths))
+        setvar("CMAKE_INCLUDE_PATH", include_paths)
+        setvar("CMAKE_LIBRARY_PATH", library_paths)
+
+        if builddir is None and self.cfg.get('separate_build_dir', False):
+            builddir = os.path.join(self.builddir, 'easybuild_obj')
+
+        if builddir:
+            mkdir(builddir, parents=True)
+            change_dir(builddir)
+            default_srcdir = self.cfg['start_dir']
+        else:
+            default_srcdir = '.'
+
+        if srcdir is None:
+            if self.cfg.get('srcdir', None) is not None:
+                srcdir = self.cfg['srcdir']
+            else:
+                srcdir = default_srcdir
+
+        options = ['-DCMAKE_INSTALL_PREFIX=%s' % self.installdir]
+        env_to_options = {
+            'CC': 'CMAKE_C_COMPILER',
+            'CFLAGS': 'CMAKE_C_FLAGS',
+            'CXX': 'CMAKE_CXX_COMPILER',
+            'CXXFLAGS': 'CMAKE_CXX_FLAGS',
+            'F90': 'CMAKE_Fortran_COMPILER',
+            'FFLAGS': 'CMAKE_Fortran_FLAGS',
+        }
+        for env_name, option in env_to_options.items():
+            value = os.getenv(env_name)
+            if value is not None:
+                if option.endswith('_COMPILER') and self.cfg.get('abs_path_compilers', False):
+                    value = which(value)
+                    self.log.info("Using absolute path to compiler command: %s", value)
+                options.append("-D%s='%s'" % (option, value))
+
+        if build_option('rpath'):
+            # instruct CMake not to fiddle with RPATH when --rpath is used, since it will undo stuff on install...
+            # https://github.com/LLNL/spack/blob/0f6a5cd38538e8969d11bd2167f11060b1f53b43/lib/spack/spack/build_environment.py#L416
+            options.append('-DCMAKE_SKIP_RPATH=ON')
+
+        # show what CMake is doing by default
+        options.append('-DCMAKE_VERBOSE_MAKEFILE=ON')
+
+        if not self.cfg.get('allow_system_boost', False):
+            # don't pick up on system Boost if Boost is included as dependency
+            # - specify Boost location via -DBOOST_ROOT
+            # - instruct CMake to not search for Boost headers/libraries in other places
+            # - disable search for Boost CMake package configuration file
+            boost_root = get_software_root('Boost')
+            if boost_root:
+                options.extend([
+                    '-DBOOST_ROOT=%s' % boost_root,
+                    '-DBoost_NO_SYSTEM_PATHS=ON',
+                    '-DBoost_NO_BOOST_CMAKE=ON',
+                ])
+
+        options_string = ' '.join(options)
+
+        command = ' '.join([
+            self.cfg['preconfigopts'],
+            self.cfg.get('configure_cmd') or DEFAULT_CONFIGURE_CMD,
+            options_string,
+            self.cfg['configopts'],
+            srcdir])
+        (out, _) = run_cmd(command, log_all=True, simple=False)
+
+        return out

diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/p/python.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/p/python.py
index 3a3fc00..7c56884 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/p/python.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/p/python.py
@@ -258,13 +258,13 @@ class EB_Python(ConfigureMake):
         # make sure hashlib is installed correctly, there should be no errors/output when 'import hashlib' is run
         # (python will exit with 0 regardless of whether or not errors are printed...)
         # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/6484
-        cmd = "python -c 'import hashlib'"
-        (out, _) = run_cmd(cmd)
-        regex = re.compile('error', re.I)
-        if regex.search(out):
-            raise EasyBuildError("Found one or more errors in output of %s: %s", cmd, out)
-        else:
-            self.log.info("No errors found in output of %s: %s", cmd, out)
+        #cmd = "python -c 'import hashlib'"
+        #(out, _) = run_cmd(cmd)
+        #regex = re.compile('error', re.I)
+        #if regex.search(out):
+        #    raise EasyBuildError("Found one or more errors in output of %s: %s", cmd, out)
+        #else:
+        #    self.log.info("No errors found in output of %s: %s", cmd, out)
 
         pyver = 'python' + self.pyshortver
         custom_paths = {

diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/q/quantumespresso.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/q/quantumespresso.py
index 14f760c..9199d45 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/q/quantumespresso.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/q/quantumespresso.py
@@ -141,14 +141,15 @@ class EB_QuantumESPRESSO(ConfigureMake):
                 raise EasyBuildError("QuantumESPRESSO %s needs ELPA to be " +
                                      "version %s or newer" % (self.version, elpa_min_ver))
 
-            elpa_include = os.path.join(elpa, 'include')
-            repls.append(('IFLAGS', '-I%s' % os.path.join(elpa_include, 'modules'), True))
-            self.cfg.update('configopts', '--with-elpa-include=%s' % elpa_include)
             if self.toolchain.options.get('openmp', False):
+                elpa_include = 'elpa_openmp-%s' % elpa_v
                 elpa_lib = 'libelpa_openmp.a'
             else:
+                elpa_include = 'elpa-%s' % elpa_v
                 elpa_lib = 'libelpa.a'
-
+            elpa_include = os.path.join(elpa, 'include', elpa_include)
+            repls.append(('IFLAGS', '-I%s' % os.path.join(elpa_include, 'modules'), True))
+            self.cfg.update('configopts', '--with-elpa-include=%s' % elpa_include)
             elpa_lib = os.path.join(elpa, 'lib', elpa_lib)
             self.cfg.update('configopts', '--with-elpa-lib=%s' % elpa_lib)
 
@@ -343,46 +344,28 @@ class EB_QuantumESPRESSO(ConfigureMake):
         copy_dir(os.path.join(self.cfg['start_dir'], 'bin'), bindir)
 
         # Pick up files not installed in bin
-        upftools = []
+        def copy_binaries(path, extension='.x'):
+            full_dir = os.path.join(self.cfg['start_dir'], path)
+            self.log.info("Looking for binaries in %s" % full_dir)
+            for filename in os.listdir(full_dir):
+                full_path = os.path.join(full_dir, filename)
+                if os.path.isfile(full_path):
+                    if extension and not filename.endswith(extension):
+                        continue
+                    copy_file(full_path, bindir)
+
         if 'upf' in targets or 'all' in targets:
-            upftools = ["casino2upf.x", "cpmd2upf.x", "fhi2upf.x", "fpmd2upf.x", "ncpp2upf.x",
-                        "oldcp2upf.x", "read_upf_tofile.x", "rrkj2upf.x", "uspp2upf.x", "vdb2upf.x",
-                        "virtual.x"]
-            if LooseVersion(self.version) > LooseVersion("5"):
-                upftools.extend(["interpolate.x", "upf2casino.x"])
-            if LooseVersion(self.version) >= LooseVersion("6.3"):
-                upftools.extend(["fix_upf.x"])
-        upf_bins = [os.path.join('upftools', x) for x in upftools]
-        for upf_bin in upf_bins:
-            copy_file(os.path.join(self.cfg['start_dir'], upf_bin), bindir)
+            copy_binaries('upftools')
 
-        wanttools = []
         if 'want' in targets:
-            wanttools = ["blc2wan.x", "conductor.x", "current.x", "disentangle.x",
-                         "dos.x", "gcube2plt.x", "kgrid.x", "midpoint.x", "plot.x", "sumpdos",
-                         "wannier.x", "wfk2etsf.x"]
-            if LooseVersion(self.version) > LooseVersion("5"):
-                wanttools.extend(["cmplx_bands.x", "decay.x", "sax2qexml.x", "sum_sgm.x"])
-        want_bins = [os.path.join('WANT', 'bin', x) for x in wanttools]
-        for want_bin in want_bins:
-            copy_file(os.path.join(self.cfg['start_dir'], want_bin), bindir)
+            copy_binaries('WANT') # this seems to be the wrong dir, (some) executable are in WANT/bin
+            copy_binaries(os.path.join('WANT','bin'), extension=None)
 
-        w90tools = []
         if 'w90' in targets:
-            if LooseVersion(self.version) >= LooseVersion("5.4"):
-                w90tools = ["postw90.x"]
-                if LooseVersion(self.version) < LooseVersion("6.1"):
-                    w90tools = ["w90chk2chk.x"]
-        w90_bins = [os.path.join('W90', x) for x in w90tools]
-        for w90_bin in w90_bins:
-            copy_file(os.path.join(self.cfg['start_dir'], w90_bin), bindir)
+            copy_binaries('W90')
 
-        yambo_bins = []
         if 'yambo' in targets:
-            yambo_bins = ["a2y", "p2y", "yambo", "ypp"]
-        yambo_bins = [os.path.join('YAMBO', 'bin', x) for x in yambo_bins]
-        for yambo_bin in yambo_bins:
-            copy_file(os.path.join(self.cfg['start_dir'], yambo_bin), bindir)
+            copy_binaries('YAMBO')
 
     def sanity_check_step(self):
         """Custom sanity check for Quantum ESPRESSO."""
@@ -394,7 +377,10 @@ class EB_QuantumESPRESSO(ConfigureMake):
         bins = ["iotk", "iotk.x", "iotk_print_kinds.x"]
 
         if 'cp' in targets or 'all' in targets:
-            bins.extend(["cp.x", "cppp.x", "wfdd.x"])
+            bins.extend(["cp.x", "wfdd.x"])
+            if LooseVersion(self.version) < LooseVersion("6.4"):
+                bins.append("cppp.x")
+
 
         # only for v4.x, not in v5.0 anymore, called gwl in 6.1 at least
         if 'gww' in targets or 'gwl' in targets:
@@ -420,12 +406,14 @@ class EB_QuantumESPRESSO(ConfigureMake):
         if 'pp' in targets or 'pwall' in targets or 'all' in targets:
             bins.extend(["average.x", "bands.x", "dos.x", "epsilon.x", "initial_state.x",
                          "plan_avg.x", "plotband.x", "plotproj.x", "plotrho.x", "pmw.x", "pp.x",
-                         "projwfc.x", "sumpdos.x", "pw2wannier90.x", "pw_export.x", "pw2gw.x",
+                         "projwfc.x", "sumpdos.x", "pw2wannier90.x", "pw2gw.x",
                          "wannier_ham.x", "wannier_plot.x"])
-            if LooseVersion(self.version) > LooseVersion("5"):
+            if LooseVersion(self.version) > LooseVersion("5") and LooseVersion(self.version) < LooseVersion("6.4"):
                 bins.extend(["pw2bgw.x", "bgw2pw.x"])
-            else:
+            elif LooseVersion(self.version) <= LooseVersion("5"):
                 bins.extend(["pw2casino.x"])
+            if LooseVersion(self.version) < LooseVersion("6.4"):
+                bins.extend(["pw_export.x"])
 
         if 'pw' in targets or 'all' in targets:
             bins.extend(["dist.x", "ev.x", "kpoints.x", "pw.x", "pwi2xsf.x"])
@@ -448,22 +436,25 @@ class EB_QuantumESPRESSO(ConfigureMake):
         upftools = []
         if 'upf' in targets or 'all' in targets:
             upftools = ["casino2upf.x", "cpmd2upf.x", "fhi2upf.x", "fpmd2upf.x", "ncpp2upf.x",
-                        "oldcp2upf.x", "read_upf_tofile.x", "rrkj2upf.x", "uspp2upf.x", "vdb2upf.x",
-                        "virtual.x"]
+                        "oldcp2upf.x", "read_upf_tofile.x", "rrkj2upf.x", "uspp2upf.x", "vdb2upf.x"]
             if LooseVersion(self.version) > LooseVersion("5"):
                 upftools.extend(["interpolate.x", "upf2casino.x"])
             if LooseVersion(self.version) >= LooseVersion("6.3"):
                 upftools.extend(["fix_upf.x"])
+            if LooseVersion(self.version) < LooseVersion("6.4"):
+                upftools.extend(["virtual.x"])
+            else:
+                upftools.extend(["virtual_v2.x"])
 
         if 'vdw' in targets:  # only for v4.x, not in v5.0 anymore
             bins.extend(["vdw.x"])
 
         if 'w90' in targets:
             bins.extend(["wannier90.x"])
-            if LooseVersion(self.version) >= LooseVersion("5.4"):
-                bins.extend(["postw90.x"])
-                if LooseVersion(self.version) < LooseVersion("6.1"):
-                    bins.extend(["w90chk2chk.x"])
+            #if LooseVersion(self.version) > LooseVersion("5.4"):
+            #    bins.extend(["postw90.x"])
+            #    if LooseVersion(self.version) < LooseVersion("6.1"):
+            #        bins.extend(["w90chk2chk.x"])
 
         want_bins = []
         if 'want' in targets:

diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/s/samtools.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/s/samtools.py
index e0a8590..a3145f9 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/s/samtools.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/s/samtools.py
@@ -39,12 +39,15 @@ class EB_SAMtools(ConfigureMake):
         self.bin_files = ["misc/blast2sam.pl",
                           "misc/bowtie2sam.pl", "misc/export2sam.pl", "misc/interpolate_sam.pl",
                           "misc/novo2sam.pl", "misc/psl2sam.pl", "misc/sam2vcf.pl", "misc/samtools.pl",
-                          "misc/soap2sam.pl", "misc/varfilter.py", "misc/wgsim_eval.pl",
+                          "misc/soap2sam.pl", "misc/wgsim_eval.pl",
                           "misc/zoom2sam.pl", "misc/md5sum-lite", "misc/md5fa", "misc/maq2sam-short",
                           "misc/maq2sam-long", "misc/wgsim", "samtools"]
+# "misc/varfilter.py" not available in 1.10
 
         self.include_files = ["bam.h", "bam2bcf.h", "bam_endian.h",
-                              "sam.h", "sam_header.h", "sample.h"]
+                              "sam.h", "sample.h"]
+# "sam_header.h" not available in 1.10
+
         self.include_dirs = []
 
         if LooseVersion(self.version) == LooseVersion('0.1.18'):

diff --git a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/s/siesta.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/s/siesta.py
index aac30ee..46af47e 100644
--- a/home/uvacse/git/easybuild-easyblocks/easybuild/easyblocks/s/siesta.py
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/s/siesta.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2019 Ghent University
+# Copyright 2009-2017 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -8,7 +8,7 @@
 # Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #
-# https://github.com/easybuilders/easybuild
+# http://github.com/hpcugent/easybuild
 #
 # EasyBuild is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -68,10 +68,8 @@ class EB_Siesta(ConfigureMake):
         arch_make = os.path.join(obj_dir, 'arch.make')
         bindir = os.path.join(start_dir, 'bin')
 
-        loose_ver = LooseVersion(self.version)
-
         par = ''
-        if loose_ver >= LooseVersion('4.1'):
+        if LooseVersion(self.version) >= LooseVersion('4.1'):
             par = '-j %s' % self.cfg['parallel']
 
         # enable OpenMP support if desired
@@ -98,7 +96,7 @@ class EB_Siesta(ConfigureMake):
             (r"^(LDFLAGS\s*=).*$", r"\1 %s %s" % (os.environ['FCFLAGS'], os.environ['LDFLAGS'])),
         ]
 
-        netcdff_loc = get_software_root('netCDF-Fortran')
+        netcdff_loc = get_software_root('netcdf')
         if netcdff_loc:
             # Needed for gfortran at least
             regex_newlines.append((r"^(ARFLAGS_EXTRA\s*=.*)$", r"\1\nNETCDF_INCFLAGS = -I%s/include" % netcdff_loc))
@@ -117,7 +115,7 @@ class EB_Siesta(ConfigureMake):
         # Populate start_dir with makefiles
         run_cmd(os.path.join(start_dir, 'Src', 'obj_setup.sh'), log_all=True, simple=True, log_output=True)
 
-        if loose_ver < LooseVersion('4.1-b2'):
+        if LooseVersion(self.version) < LooseVersion('4.1-b2'):
             # MPI?
             if self.toolchain.options.get('usempi', None):
                 self.cfg.update('configopts', '--enable-mpi')
@@ -137,16 +135,17 @@ class EB_Siesta(ConfigureMake):
             # Configure is run in obj_dir, configure script is in ../Src
             super(EB_Siesta, self).configure_step(cmd_prefix='../Src/')
 
-            if loose_ver > LooseVersion('4.0'):
+            if LooseVersion(self.version) > LooseVersion('4.0'):
                 regex_subs_Makefile = [
                     (r'CFLAGS\)-c', r'CFLAGS) -c'),
                 ]
                 apply_regex_substitutions('Makefile', regex_subs_Makefile)
 
         else: # there's no configure on newer versions
-
+            fortran_flags = ''
             if self.toolchain.comp_family() in [toolchain.INTELCOMP]:
                 copy_file(os.path.join(obj_dir, 'intel.make'), arch_make)
+                fortran_flags = '-heap-arrays'
             elif self.toolchain.comp_family() in [toolchain.GCC]:
                 copy_file(os.path.join(obj_dir, 'gfortran.make'), arch_make)
             else:
@@ -164,19 +163,18 @@ class EB_Siesta(ConfigureMake):
                 complibs = lapack
 
             regex_subs.extend([
-                (r"^(LIBS\s*=).*$", r"\1 %s" % complibs),
+                (r"^(LIBS\s*=\s).*$", r"\1 %s" % complibs),
                 # Needed for a couple of the utils
-                (r"^(FFLAGS\s*=\s*).*$", r"\1 -fPIC %s" % os.environ['FCFLAGS']),
+                (r"^(FFLAGS\s*=\s*).*$", r"\1 -fPIC %s %s" % (fortran_flags, os.environ['FCFLAGS'])),
             ])
             regex_newlines.append((r"^(COMP_LIBS\s*=.*)$", r"\1\nWXML = libwxml.a"))
 
             if netcdff_loc:
                 regex_subs.extend([
                     (r"^(LIBS\s*=.*)$", r"\1 $(NETCDF_LIBS)"),
-                    (r"^(FPPFLAGS\s*=.*)$", r"\1 -DCDF $(NETCDF_INCLUDE)"),
+                    (r"^(FPPFLAGS\s*=.*)$", r"\1 -DCDF"),
                 ])
-                netcdf_lib_and_inc = "NETCDF_LIBS = -lnetcdff\nNETCDF_INCLUDE = -I%s/include" % netcdff_loc
-                regex_newlines.append((r"^(COMP_LIBS\s*=.*)$", r"\1\n%s" % netcdf_lib_and_inc))
+                regex_newlines.append((r"^(COMP_LIBS\s*=.*)$", r"\1\nNETCDF_LIBS = -lnetcdff"))
 
         apply_regex_substitutions(arch_make, regex_subs)
 
@@ -184,6 +182,9 @@ class EB_Siesta(ConfigureMake):
         for regex_nl in regex_newlines:
             apply_regex_substitutions(arch_make, [regex_nl])
 
+        # new line error and missing -lnetcdff - Ruoshi Sun 2020-04-21
+        apply_regex_substitutions(arch_make, [(r"^(LIBS\s*=)", r"LIBS = -lnetcdff \\")])
+
         run_cmd('make %s' % par, log_all=True, simple=True, log_output=True)
 
         # Put binary in temporary install dir
@@ -193,12 +194,11 @@ class EB_Siesta(ConfigureMake):
             # Make the utils
             change_dir(os.path.join(start_dir, 'Util'))
 
-            if loose_ver >= LooseVersion('4'):
-                # clean_all.sh might be missing executable bit...
-                adjust_permissions('./clean_all.sh', stat.S_IXUSR, recursive=False, relative=True)
-                run_cmd('./clean_all.sh', log_all=True, simple=True, log_output=True)
+            # clean_all.sh might be missing executable bit...
+            adjust_permissions('./clean_all.sh', stat.S_IXUSR, recursive=False, relative=True)
+            run_cmd('./clean_all.sh', log_all=True, simple=True, log_output=True)
 
-            if loose_ver >= LooseVersion('4.1'):
+            if LooseVersion(self.version) >= LooseVersion('4.1'):
                 regex_subs_TS = [
                     (r"^default:.*$", r""),
                     (r"^EXE\s*=.*$", r""),
@@ -209,58 +209,45 @@ class EB_Siesta(ConfigureMake):
                 makefile = os.path.join(start_dir, 'Util', 'TS', 'tshs2tshs', 'Makefile')
                 apply_regex_substitutions(makefile, regex_subs_TS)
 
-            if loose_ver >= LooseVersion('4'):
-                # SUFFIX rules in wrong place
-                regex_subs_suffix = [
-                    (r'^(\.SUFFIXES:.*)$', r''),
-                    (r'^(include\s*\$\(ARCH_MAKE\).*)$', r'\1\n.SUFFIXES:\n.SUFFIXES: .c .f .F .o .a .f90 .F90'),
-                ]
-                makefile = os.path.join(start_dir, 'Util', 'Sockets', 'Makefile')
-                apply_regex_substitutions(makefile, regex_subs_suffix)
-                makefile = os.path.join(start_dir, 'Util', 'SiestaSubroutine', 'SimpleTest', 'Src', 'Makefile')
-                apply_regex_substitutions(makefile, regex_subs_suffix)
+            # SUFFIX rules in wrong place
+            regex_subs_suffix = [
+                (r'^(\.SUFFIXES:.*)$', r''),
+                (r'^(include\s*\$\(ARCH_MAKE\).*)$', r'\1\n.SUFFIXES:\n.SUFFIXES: .c .f .F .o .a .f90 .F90'),
+            ]
+            makefile = os.path.join(start_dir, 'Util', 'Sockets', 'Makefile')
+            apply_regex_substitutions(makefile, regex_subs_suffix)
+            makefile = os.path.join(start_dir, 'Util', 'SiestaSubroutine', 'SimpleTest', 'Src', 'Makefile')
+            apply_regex_substitutions(makefile, regex_subs_suffix)
 
             regex_subs_UtilLDFLAGS = [
                 (r'(\$\(FC\)\s*-o\s)', r'$(FC) %s %s -o ' % (os.environ['FCFLAGS'], os.environ['LDFLAGS'])),
             ]
             makefile = os.path.join(start_dir, 'Util', 'Optimizer', 'Makefile')
             apply_regex_substitutions(makefile, regex_subs_UtilLDFLAGS)
-            if loose_ver >= LooseVersion('4'):
-                makefile = os.path.join(start_dir, 'Util', 'JobList', 'Src', 'Makefile')
-                apply_regex_substitutions(makefile, regex_subs_UtilLDFLAGS)
-
-            # remove clean at the end of default target
-            # And yes, they are re-introducing this bug.
-            is_ver40_to_401 = loose_ver >= LooseVersion('4.0') and loose_ver < LooseVersion('4.0.2')
-            if (is_ver40_to_401 or loose_ver == LooseVersion('4.1-b3')):
-                    makefile = os.path.join(start_dir, 'Util', 'SiestaSubroutine', 'SimpleTest', 'Src', 'Makefile')
-                    apply_regex_substitutions(makefile, [(r"simple_mpi_parallel clean", r"simple_mpi_parallel")])
-                    makefile = os.path.join(start_dir, 'Util', 'SiestaSubroutine', 'ProtoNEB', 'Src', 'Makefile')
-                    apply_regex_substitutions(makefile, [(r"protoNEB clean", r"protoNEB")])
-
-            # build_all.sh might be missing executable bit...
-            adjust_permissions('./build_all.sh', stat.S_IXUSR, recursive=False, relative=True)
+            makefile = os.path.join(start_dir, 'Util', 'JobList', 'Src', 'Makefile')
+            apply_regex_substitutions(makefile, regex_subs_UtilLDFLAGS)
+
             run_cmd('./build_all.sh', log_all=True, simple=True, log_output=True)
 
             # Now move all the built utils to the temp installdir
             expected_utils = [
+                'Bands/eigfat2plot',
                 'CMLComp/ccViz',
-                'Contrib/APostnikov/eig2bxsf', 'Contrib/APostnikov/fmpdos',
-                'Contrib/APostnikov/md2axsf', 'Contrib/APostnikov/rho2xsf',
-                'Contrib/APostnikov/vib2xsf', 'Contrib/APostnikov/xv2xsf',
-                'COOP/fat', 'COOP/mprop',
+                'Contrib/APostnikov/eig2bxsf', 'Contrib/APostnikov/rho2xsf',
+                'Contrib/APostnikov/vib2xsf', 'Contrib/APostnikov/fmpdos',
+                'Contrib/APostnikov/xv2xsf', 'Contrib/APostnikov/md2axsf',
+                'COOP/mprop', 'COOP/fat',
                 'Denchar/Src/denchar',
-                'DensityMatrix/cdf2dm', 'DensityMatrix/dm2cdf',
+                'DensityMatrix/dm2cdf', 'DensityMatrix/cdf2dm',
                 'Eig2DOS/Eig2DOS',
-                'Gen-basis/gen-basis', 'Gen-basis/ioncat',
-                'Gen-basis/ionplot.sh',
-                'Grid/cdf2grid', 'Grid/cdf2xsf', 'Grid/cdf_laplacian',
-                'Grid/g2c_ng', 'Grid/grid2cdf', 'Grid/grid2cube',
-                'Grid/grid2val', 'Grid/grid_rotate',
+                'Gen-basis/ioncat', 'Gen-basis/gen-basis',
+                'Grid/cdf2grid', 'Grid/cdf_laplacian', 'Grid/cdf2xsf',
+                'Grid/grid2cube',
+                'Grid/grid_rotate', 'Grid/g2c_ng', 'Grid/grid2cdf', 'Grid/grid2val',
                 'Helpers/get_chem_labels',
                 'HSX/hs2hsx', 'HSX/hsx2hs',
-                'JobList/Src/countJobs', 'JobList/Src/getResults',
-                'JobList/Src/horizontal', 'JobList/Src/runJobs',
+                'JobList/Src/getResults', 'JobList/Src/countJobs',
+                'JobList/Src/runJobs', 'JobList/Src/horizontal',
                 'Macroave/Src/macroave',
                 'ON/lwf2cdf',
                 'Optimizer/simplex', 'Optimizer/swarm',
@@ -269,69 +256,33 @@ class EB_Siesta(ConfigureMake):
                 'SiestaSubroutine/FmixMD/Src/driver',
                 'SiestaSubroutine/FmixMD/Src/para',
                 'SiestaSubroutine/FmixMD/Src/simple',
-                'STM/ol-stm/Src/stm', 'STM/simple-stm/plstm',
-                'VCA/fractional', 'VCA/mixps',
-                'Vibra/Src/fcbuild', 'Vibra/Src/vibra',
-                'WFS/info_wfsx',
-                'WFS/readwf', 'WFS/readwfx', 'WFS/wfs2wfsx',
-                'WFS/wfsnc2wfsx', 'WFS/wfsx2wfs',
+                'STM/simple-stm/plstm', 'STM/ol-stm/Src/stm',
+                'VCA/mixps', 'VCA/fractional',
+                'Vibra/Src/vibra', 'Vibra/Src/fcbuild',
+                'WFS/info_wfsx', 'WFS/wfsx2wfs',
+                'WFS/readwfx', 'WFS/wfsnc2wfsx', 'WFS/readwf', 'WFS/wfs2wfsx',
             ]
 
-            if loose_ver >= LooseVersion('3.2'):
+            if LooseVersion(self.version) <= LooseVersion('4.0'):
                 expected_utils.extend([
-                    'Bands/eigfat2plot',
+                    'Bands/new.gnubands',
+                    'TBTrans/tbtrans',
                 ])
 
-            if loose_ver >= LooseVersion('4.0'):
+            if LooseVersion(self.version) >= LooseVersion('4.0'):
                 expected_utils.extend([
                     'SiestaSubroutine/ProtoNEB/Src/protoNEB',
                     'SiestaSubroutine/SimpleTest/Src/simple_pipes_parallel',
                     'SiestaSubroutine/SimpleTest/Src/simple_pipes_serial',
-                    'SiestaSubroutine/SimpleTest/Src/simple_sockets_parallel',
-                    'SiestaSubroutine/SimpleTest/Src/simple_sockets_serial',
                     'Sockets/f2fmaster', 'Sockets/f2fslave',
                 ])
-                if self.toolchain.options.get('usempi', None):
-                    expected_utils.extend([
-                        'SiestaSubroutine/SimpleTest/Src/simple_mpi_parallel',
-                        'SiestaSubroutine/SimpleTest/Src/simple_mpi_serial',
-                    ])
-
-            if loose_ver < LooseVersion('4.1'):
-                if loose_ver >= LooseVersion('4.0'):
-                    expected_utils.extend([
-                        'COOP/dm_creator',
-                        'TBTrans_rep/tbtrans',
-                    ])
-                else:
-                    expected_utils.extend([
-                        'TBTrans/tbtrans',
-                    ])
-
-            if loose_ver < LooseVersion('4.0.2'):
-                expected_utils.extend([
-                    'Bands/new.gnubands',
-                ])
-            else:
+
+            if LooseVersion(self.version) >= LooseVersion('4.1'):
                 expected_utils.extend([
                     'Bands/gnubands',
-                ])
-                # Need to revisit this when 4.1 is officialy released.
-                # This is based on b1-b3 releases
-                if loose_ver < LooseVersion('4.1'):
-                    expected_utils.extend([
-                        'Contour/grid1d', 'Contour/grid2d',
-                        'Optical/optical', 'Optical/optical_input',
-                        'sies2arc/sies2arc',
-                    ])
-
-            if loose_ver >= LooseVersion('4.1'):
-                expected_utils.extend([
-                    'DensityMatrix/dmbs2dm', 'DensityMatrix/dmUnblock',
                     'Grimme/fdf2grimme',
                     'SpPivot/pvtsp',
-                    'TS/TBtrans/tbtrans', 'TS/tselecs.sh',
-                    'TS/ts2ts/ts2ts', 'TS/tshs2tshs/tshs2tshs',
+                    'TS/ts2ts/ts2ts', 'TS/tshs2tshs/tshs2tshs', 'TS/TBtrans/tbtrans',
                 ])
 
             for util in expected_utils:
@@ -341,25 +292,15 @@ class EB_Siesta(ConfigureMake):
             # Build transiesta
             change_dir(obj_dir)
 
-            ts_clean_target = 'clean'
-            if loose_ver >= LooseVersion('4.1-b4'):
-                ts_clean_target += '-transiesta'
-
-            run_cmd('make %s' % ts_clean_target, log_all=True, simple=True, log_output=True)
+            run_cmd('make clean', log_all=True, simple=True, log_output=True)
             run_cmd('make %s transiesta' % par, log_all=True, simple=True, log_output=True)
 
             copy_file(os.path.join(obj_dir, 'transiesta'), bindir)
 
-
     def build_step(self):
         """No build step for Siesta."""
         pass
 
-    def test_step(self):
-        """Custom test step for Siesta."""
-        change_dir(os.path.join(self.cfg['start_dir'], 'Obj', 'Tests'))
-        super(EB_Siesta, self).test_step()
-
     def install_step(self):
         """Custom install procedure for Siesta: copy binaries."""
         bindir = os.path.join(self.installdir, 'bin')
@@ -382,10 +323,10 @@ class EB_Siesta(ConfigureMake):
         }
         custom_commands = []
         if self.toolchain.options.get('usempi', None):
+            
             # make sure Siesta was indeed built with support for running in parallel
-            # The "cd to builddir" is required to not contaminate the install dir with cruft from running siesta
-            mpi_test_cmd = "cd %s && " % self.builddir
-            mpi_test_cmd = mpi_test_cmd + "echo 'SystemName test' | mpirun -np 2 siesta 2>/dev/null | grep PARALLEL"
-            custom_commands.append(mpi_test_cmd)
-
+            
+            # mpirun does not work on frontend
+            # custom_commands.append("echo 'SystemName test' | mpirun -np 2 siesta 2>/dev/null | grep PARALLEL")
+            s = 3 # mock statement
         super(EB_Siesta, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)

diff --git a/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/s/singularityimage.py b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/s/singularityimage.py
new file mode 100644
index 0000000..759bb0e
--- /dev/null
+++ b/apps/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/s/singularityimage.py
@@ -0,0 +1,122 @@
+##
+# Copyright 2009-2017 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+General EasyBuild support for software with a binary installer
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+"""
+
+import shutil
+import os
+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 mkdir, rmtree2
+from easybuild.tools.run import run_cmd
+from easybuild.easyblocks.generic.binary import Binary
+
+class EB_SingularityImage(Binary):
+    """
+    Support for installing software that comes in binary form.
+    Just copy the sources to the install dir, or use the specified install command.
+    """
+
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Extra easyconfig parameters specific to Binary easyblock."""
+        extra_vars = Binary.extra_options(extra_vars)
+        extra_vars.update({
+            'deffile': [None, "Definition (spec) file used to build the container.", CUSTOM],
+            'use_gpu': [False, "Use GPU for running container applications.", CUSTOM], 
+        })
+        return extra_vars
+
+    def __init__(self, *args, **kwargs):
+        """Initialize Binary-specific variables."""
+        super(EB_SingularityImage, self).__init__(*args, **kwargs)
+
+        #self.actual_installdir = None
+        #if self.cfg['staged_install']:
+        #    self.actual_installdir = self.installdir
+        #    self.installdir = os.path.join(self.builddir, 'staged')
+        #    mkdir(self.installdir, parents=True)
+        #    self.log.info("Performing staged installation via %s" % self.installdir)
+        
+        container_run_cmd ='singularity run'
+        if self.cfg['use_gpu']:
+            container_run_cmd = 'singularity run --nv'
+        containerfile = self.cfg['sources'][0]
+        for srcfile in self.cfg['sources']:
+            if srcfile != self.cfg['deffile']:
+                containerfile = srcfile 
+        msg = "Before using this container for the FIRST time, copy it to your personal home (or /scratch) directory using this command:\n"
+        msg+= "cp $CONTAINERDIR/%s /home/$USER\n\n" % containerfile
+        msg+= "To execute the default application inside the container, run this command:\n"
+        msg+= "%s /home/$USER/%s\n\n" % (container_run_cmd,containerfile)
+        if self.cfg['modloadmsg']:
+            msg += self.cfg['modloadmsg']
+        self.cfg['modloadmsg'] = msg
+        self.log.debug(self.cfg['modloadmsg'])
+        
+
+    def post_install_step(self):
+        """Copy installation to actual installation directory in case of a staged installation."""
+        if self.cfg['staged_install']:
+            staged_installdir = self.installdir
+            self.installdir = self.actual_installdir
+            try:
+                # copytree expects target directory to not exist yet
+                if os.path.exists(self.installdir):
+                    rmtree2(self.installdir)
+                shutil.copytree(staged_installdir, self.installdir)
+            except OSError, err:
+                raise EasyBuildError("Failed to move staged install from %s to %s: %s",
+                                     staged_installdir, self.installdir, err)
+
+        deffile = self.cfg['deffile']
+        if deffile is not None:
+            easybuilddir = os.path.join(self.installdir, 'easybuild')
+            try:
+                os.makedirs(easybuilddir)
+                shutil.copy(os.path.join(self.cfg['start_dir'], deffile), easybuilddir)
+            except OSError, err:
+                raise EasyBuildError("Failed to copy %s to %s: %s", self.cfg['deffile'], easybuilddir, err)
+
+        super(Binary, self).post_install_step()
+
+
+    def make_module_extra(self):
+        """Add the install directory to the PATH."""
+        txt = super(EB_SingularityImage, self).make_module_extra()
+        txt += self.module_generator.set_environment("CONTAINERDIR", self.installdir)
+        self.log.debug("make_module_extra added this: %s" % txt)
+        self.log.debug(self.cfg)
+        return txt