Merge pull request #2613 from easybuilders/4.5.x

release EasyBuild v4.5.0

RELEASE_NOTES

@@ -3,7 +3,47 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyblocks provides 241 software-specific easyblocks and 37 generic easyblocks.
+The latest version of easybuild-easyblocks provides 242 software-specific easyblocks and 37 generic easyblocks.
+
+
+v4.5.0 (October 29th 2021)
+--------------------------
+
+feature release
+
+- new software-specific easyblock for imkl-FFTW (#2599)
+- minor enhancements and updates, including:
+  - add support for installing R extensions in parallel (#2408)
+  - update MotionCor2 easyblock to consider to locations for built binary (#2541, #2598)
+  - let GROMACS runtime logs show EasyBuild was used by setting -DGMX_VERSION_STRING_OF_FORK configuration option (#2571)
+  - adjust qa list in WIEN2k easyblock to handle new questions + fix sanity check for v21.1 (#2572)
+  - enhance GCC easyblock to add support for AMD GPU offloading (#2578)
+  - add support for specifying subdirectory for target installation directory in CMakMake (#2579)
+  - enhance COMSOL easyblock to change permission on build directory during extract step (to allow using patches) (#2584)
+  - enhance FlexiBLAS easyblock to support building with Intel MKL (imkl) as backend (#2588)
+  - update MATLAB easyblock for 2021b (jre is no longer included) (#2589)
+  - update OpenCV easyblock to detect GTK3 and GTK2 dependencies (next to GTK+) (#2591)
+  - avoid that path to CUDA install directory is added to $PATH (#2593)
+  - enhance imkl easyblock to add support for installing with NVHPC (#2595)
+  - enhance PETSc easyblock to run tests in parallel (#2601)
+  - update ELSI easyblock to support two new external dependencies (#2602)
+  - add custom custom easyconfig parameter 'backends' in FlexiBLAS easyblock to specify backends (#2605)
+  - detect problem with compiling CPU detection code in configure output in GROMACS easyblock (#2609)
+  - use correct include directory for FlexiBLAS (#2610)
+- various bug fixes, including:
+  - unset $EASYBUILD_* environment variables when running sanity check in EasyBuildMeta easyblock + also unset $MODULES_LMCONFLICT to avoid conflict when loading EasyBuild module (#2568)
+  - ensure that all ABAQUS components get installed for ABAQUS 2021.x (+ add support for enabling/disabling fe-safe) (#2569)
+  - fix subdir path in VTune easyblock for 2021.x versions + add sanity check command (#2576)
+  - make sure custom easyblock for installing EasyBuild respects requested version of Python (like $EB_PYTHON) (#2581)
+  - restore RPATH wrappers for OpenMPI sanity check (#2582)
+  - fix installation of libcp2k for recent CP2K versions (#2585)
+  - make version regex in OpenSSL wrapper easyblock less strict (version string does not always end with a letter) (#2597)
+  - redefine collect_exts_file_info instead of now deprecated fetch_extension_sources in OCaml easyblock (#2603)
+- other changes:
+  - don't use --config=mkl for TensorFlow 2.4+ (#2583)
+    - this fixes some performance related issues for TensorFlow, see https://github.com/easybuilders/easybuild-easyblocks/issues/2577 and https://github.com/easybuilders/easybuild-easyconfigs/issues/14120
+  - fix support for recent imkl version in numexpr easyblock (#2606)
+  - derive custom easyblock from MotionCor2 from PackedBinary instead of EasyBlock (#2607)
 
 
 v4.4.2 (September 7th 2021)
@@ -29,7 +69,7 @@ update/bugfix release
   - fix motorBike test in sanity check for OpenFOAM 9 (#2544)
   - generate and install pkg-config files for OpenSSL wrapper (#2549)
   - don't run 'setup.py config' for numpy >= 1.21, since it's no longer supported (#2554)
-  - update WIEK2k easyblock to handle new Intel versions, WIEN2k v21, Perl dependency, and tuning of dimension parameters (#2558)
+  - update WIEN2k easyblock to handle new Intel versions, WIEN2k v21, Perl dependency, and tuning of dimension parameters (#2558)
   - remove PCRE from list of system libraries for TensorFlow 2.6.0 (#2559)
   - add support for also installing Tosca component in ABAQUS (#2560)
   - update ABAQUS easyblock to support installing of version 2021 with hot fixes (#2562)

easybuild/easyblocks/__init__.py

@@ -43,7 +43,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = LooseVersion('4.4.2')
+VERSION = LooseVersion('4.5.0')
 UNKNOWN = 'UNKNOWN'
 
 

easybuild/easyblocks/a/abaqus.py

@@ -52,6 +52,7 @@ class EB_ABAQUS(Binary):
     @staticmethod
     def extra_options():
         extra_vars = {
+            'with_fe_safe': [None, "Enable installation of fe-safe (if None: auto-enable for ABAQUS >= 2020)", CUSTOM],
             'with_tosca': [None, "Enable installation of Tosca (if None: auto-enable for ABAQUS >= 2020)", CUSTOM],
         }
         return Binary.extra_options(extra_vars)
@@ -62,9 +63,13 @@ def __init__(self, *args, **kwargs):
         self.replayfile = None
 
         if self.cfg['with_tosca'] is None and LooseVersion(self.version) >= LooseVersion('2020'):
-            self.log.info("Auto-enabling installation of Tosca component for ABAQUS versions >= 2020")
+            self.log.info("Auto-enabling installation of Tosca components for ABAQUS versions >= 2020")
             self.cfg['with_tosca'] = True
 
+        if self.cfg['with_fe_safe'] is None and LooseVersion(self.version) >= LooseVersion('2020'):
+            self.log.info("Auto-enabling installation of fe-safe components for ABAQUS versions >= 2020")
+            self.cfg['with_fe_safe'] = True
+
     def extract_step(self):
         """Use default extraction procedure instead of the one for the Binary easyblock."""
         EasyBlock.extract_step(self)
@@ -124,6 +129,19 @@ def install_step(self):
             # Enable Abaqus CAE (docs)
             std_qa[selectionstr % (r"\[ \]", "Abaqus CAE")] = "%(nr)s"
 
+            # enable all ABAQUS components
+            std_qa[selectionstr % (r"\[ \]", "Abaqus.*")] = "%(nr)s"
+            std_qa[selectionstr % (r"\[ \]", "Cosimulation Services")] = "%(nr)s"
+
+            # enable 3DSFlow Solver (used to be called "Abaqus/CFD Solver")
+            std_qa[selectionstr % (r"\[ \]", "3DSFlow Solver")] = "%(nr)s"
+
+            # disable/enable fe-safe components
+            if self.cfg['with_fe_safe']:
+                std_qa[selectionstr % (r"\[ \]", ".*fe-safe")] = "%(nr)s"
+            else:
+                std_qa[selectionstr % (r"\[*\]", ".*fe-safe")] = "%(nr)s"
+
             # Disable/enable Tosca
             if self.cfg['with_tosca']:
                 std_qa[selectionstr % (r"\[\ \]", "Tosca")] = "%(nr)s"
@@ -285,6 +303,11 @@ def sanity_check_step(self):
             custom_paths['dirs'].append('%s-%s' % ('.'.join(verparts[0:2]), verparts[2]))
             custom_commands.append("abaqus information=all")
 
+        if LooseVersion(self.version) >= LooseVersion('2020'):
+            custom_paths['files'].append(os.path.join('cae', 'linux_a64', 'code', 'bin', 'abaqusstd'))
+            if self.cfg['with_fe_safe']:
+                custom_paths['files'].append(os.path.join('cae', 'linux_a64', 'code', 'bin', 'fe-safe'))
+
         if self.cfg['with_tosca']:
             custom_commands.append("ToscaPython.sh --help")
 

easybuild/easyblocks/c/comsol.py

@@ -49,11 +49,15 @@ def __init__(self, *args, **kwargs):
         super(EB_COMSOL, self).__init__(*args, **kwargs)
         self.configfile = os.path.join(self.builddir, 'my_setupconfig.ini')
 
-    def configure_step(self):
-        """Configure COMSOL installation: create license file."""
+    def extract_step(self):
+        """Need to adjust the permissions on the top dir, the DVD has 0444."""
+        super(EB_COMSOL, self).extract_step()
 
         # The tar file comes from the DVD and has 0444 as permission at the top dir.
-        adjust_permissions(self.start_dir, stat.S_IWUSR)
+        adjust_permissions(self.builddir, stat.S_IWUSR)
+
+    def configure_step(self):
+        """Configure COMSOL installation: create license file."""
 
         default_lic_env_var = 'LMCOMSOL_LICENSE_FILE'
         lic_specs, self.license_env_var = find_flexlm_license(custom_env_vars=[default_lic_env_var],

easybuild/easyblocks/c/cp2k.py

@@ -668,9 +668,13 @@ def build_step(self):
         run_cmd(cmd + " clean", log_all=True, simple=True, log_output=True)
 
         # build and install
+        # compile regularly first with the default make target
+        # and only then build the library
+        run_cmd(cmd + ' all', log_all=True, simple=True, log_output=True)
+
+        # build as a library
         if self.cfg['library']:
-            cmd += ' libcp2k'
-        run_cmd(cmd + " all", log_all=True, simple=True, log_output=True)
+            run_cmd(cmd + 'libcp2k', log_all=True, simple=True, log_output=True)
 
     def test_step(self):
         """Run regression test."""

easybuild/easyblocks/c/cuda.py

@@ -270,6 +270,12 @@ def sanity_check_step(self):
 
     def make_module_extra(self):
         """Set the install directory as CUDA_HOME, CUDA_ROOT, CUDA_PATH."""
+
+        # avoid adding of installation directory to $PATH (cfr. Binary easyblock) since that may cause trouble,
+        # for example when there's a clash between command name and a subdirectory in the installation directory
+        # (like compute-sanitizer)
+        self.cfg['prepend_to_path'] = False
+
         txt = super(EB_CUDA, self).make_module_extra()
         txt += self.module_generator.set_environment('CUDA_HOME', self.installdir)
         txt += self.module_generator.set_environment('CUDA_ROOT', self.installdir)

easybuild/easyblocks/e/easybuildmeta.py

@@ -30,6 +30,7 @@
 import copy
 import os
 import re
+import sys
 from distutils.version import LooseVersion
 
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage
@@ -48,7 +49,8 @@ class EB_EasyBuildMeta(PythonPackage):
     def __init__(self, *args, **kwargs):
         """Initialize custom class variables."""
         super(EB_EasyBuildMeta, self).__init__(*args, **kwargs)
-        self.real_initial_environ = None
+
+        self.real_initial_environ = copy.deepcopy(self.initial_environ)
 
         self.easybuild_pkgs = ['easybuild-framework', 'easybuild-easyblocks', 'easybuild-easyconfigs']
         if LooseVersion(self.version) >= LooseVersion('2.0') and LooseVersion(self.version) <= LooseVersion('3.999'):
@@ -64,6 +66,17 @@ def __init__(self, *args, **kwargs):
             # consider setuptools first, in case it is listed as a sources
             self.easybuild_pkgs.insert(0, 'setuptools')
 
+    # Override this function since we want to respect the user choice for the python installation to use
+    # (which can be influenced by EB_PYTHON and EB_INSTALLPYTHON)
+    def prepare_python(self):
+        """Python-specific preparations."""
+
+        self.python_cmd = sys.executable
+        # set Python lib directories
+        self.set_pylibdirs()
+
+        self.log.info("Python command being used: %s", self.python_cmd)
+
     def check_readiness_step(self):
         """Make sure EasyBuild can be installed with a loaded EasyBuild module."""
         env_var_name = get_software_root_env_var_name(self.name)
@@ -208,13 +221,19 @@ def sanity_check_step(self):
         ]
 
         # (temporary) cleanse copy of initial environment to avoid conflict with (potentially) loaded EasyBuild module
-        self.real_initial_environ = copy.deepcopy(self.initial_environ)
-        for env_var in ['_LMFILES_', 'LOADEDMODULES']:
+        for env_var in ['_LMFILES_', 'LOADEDMODULES', 'MODULES_LMCONFLICT', '__MODULES_LMCONFLICT']:
             if env_var in self.initial_environ:
                 self.initial_environ.pop(env_var)
                 os.environ.pop(env_var)
                 self.log.debug("Unset $%s in current env and copy of original env to make sanity check work" % env_var)
 
+        # unset all $EASYBUILD_* environment variables when running sanity check commands,
+        # to prevent failing sanity check for old EasyBuild versions when configuration options are defined
+        # via $EASYBUILD_* environment variables
+        for key in [k for k in self.initial_environ if k.startswith('EASYBUILD_')]:
+            val = self.initial_environ.pop(key)
+            self.log.info("$%s found in environment, unset for running sanity check (was: %s)", key, val)
+
         super(EB_EasyBuildMeta, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
 
     def make_module_extra(self):

easybuild/easyblocks/e/elsi.py

@@ -42,6 +42,7 @@ def __init__(self, *args, **kwargs):
         """Initialize ELSI-specific variables."""
         super(EB_ELSI, self).__init__(*args, **kwargs)
         self.enable_sips = False
+        self.internal_ntpoly = True
         self.env_suff = '_MT' if self.toolchain.options.get('openmp', None) else ''
 
     @staticmethod
@@ -115,6 +116,21 @@ def configure_step(self):
             else:
                 raise EasyBuildError("Could not find FFTW library or interface.")
 
+        ntpoly = get_software_root('NTPoly')
+        if ntpoly:
+            self.internal_ntpoly = False
+            self.log.info("Using external NTPoly.")
+            self.cfg.update('configopts', "-DUSE_EXTERNAL_NTPOLY=ON")
+            external_libs.append('NTPoly')
+        else:
+            self.log.info("No external NTPoly specified as dependency, building internal NTPoly.")
+
+        bsepack = get_software_root('bsepack')
+        if bsepack:
+            self.log.info("Using external BSEPACK.")
+            self.cfg.update('configopts', "-DENABLE_BSEPACK=ON -DUSE_EXTERNAL_BSEPACK=ON")
+            external_libs.extend(['bsepack', 'sseig'])
+
         if get_software_root('imkl') or get_software_root('ScaLAPACK'):
             external_libs.extend(re.findall(r'lib(.*?)\.a', os.environ['SCALAPACK%s_STATIC_LIBS' % self.env_suff]))
         else:
@@ -131,7 +147,9 @@ def configure_step(self):
     def sanity_check_step(self):
         """Custom sanity check for ELSI."""
 
-        libs = ['elsi', 'fortjson', 'MatrixSwitch', 'NTPoly', 'OMM']
+        libs = ['elsi', 'fortjson', 'MatrixSwitch', 'OMM']
+        if self.internal_ntpoly:
+            libs.append('NTPoly')
         modules = [lib.lower() for lib in libs if lib != 'OMM']
         modules.extend(['omm_ops', 'omm_params', 'omm_rand'])