Merge pull request #3367 from boegel/5.0.x

sync with develop (20240619)

RELEASE_NOTES

@@ -3,7 +3,34 @@ 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 255 software-specific easyblocks and 43 generic easyblocks.
+The latest version of easybuild-easyblocks provides 259 software-specific easyblocks and 43 generic easyblocks.
+
+
+v4.9.2 (12 June 2024)
+---------------------
+
+update/bugfix release
+
+- 4 new software-specific easyblocks: QuantumESPRESSO with CMake (#3257), AEDT (#3281), optiSLang (#3300), MetalWalls (#3311, #3331)
+- minor enhancements and updates, including:
+  - refactor GAMESS-US easyblock to directly write install.info (#3047)
+  - add ABAQUS license server to generated module (#3277)
+  - allow 'nosource: True' in PythonPackage extensions (#3305)
+  - auto-disable FFTW quad precision on RISC-V (#3314)
+  - use regular 'configure' instead of wrapper script in easyblock for UCX plugins (#3315)
+  - add libjpeg-turbo to include dir for torchvision easyblock (#3322, #3353)
+  - add RISC-V support to custom easyblocks for Clang (#3325), Java (#3323), Mesa (#3324)
+  - add a sanity check for OpenFOAM's 'wmake' to make sure it finds the compiler commands (#3328)
+  - always override the compiler version check for CUDA installations (#3329)
+  - allow version mismatchs between OpenSSL components in host system as long as they fulfill version requirements (#3340)
+  - allow external PRRTE in OpenMPI easyblock (#3347)
+- various bug fixes, including:
+  - don't manipulate setup.py for Python 3.12+ when using alternate sysroot (#3313)
+  - do not run unit tests on Python 3.5 (#3326)
+  - avoid sanity check on the software itself for CargoPythonBundle easyblock (#3341)
+  - fix malformed '$CPATH' for intel-compilers on Debian/Ubuntu (#3346)
+- other changes:
+  - Binary easyblock already adds top level directory to PATH, so no need to do it in the Stata easyblock (#3307)
 
 
 v4.9.1 (5 April 2024)

easybuild/easyblocks/c/cuda.py

@@ -156,6 +156,14 @@ def install_step(self):
         # Use C locale to avoid localized questions and crash on CUDA 10.1
         self.cfg.update('preinstallopts', "export LANG=C && ")
 
+        # As a CUDA recipe gets older and the OS gets updated, it is
+        # likely that the system GCC becomes too new for the CUDA version.
+        # Since in EasyBuild we know/expect that CUDA will only ever get used
+        # as a dependency within the context of a toolchain, we can override
+        # the compiler version check that would cause the installation to
+        # fail.
+        self.cfg.update('installopts', "--override")
+
         cmd = "%(preinstallopts)s %(interpreter)s %(script)s %(installopts)s" % {
             'preinstallopts': self.cfg['preinstallopts'],
             'interpreter': install_interpreter,

easybuild/easyblocks/e/easybuildmeta.py

@@ -112,7 +112,10 @@ def install_step(self):
         try:
             subdirs = os.listdir(self.builddir)
             for pkg in self.easybuild_pkgs:
-                seldirs = [x for x in subdirs if x.startswith(pkg)]
+                # also consider "normalized" package name, with dashes ('-') replaced by underscores ('_'),
+                # which is being enforced by recent versions of setuptools (>= 69.0.3?)
+                pkg_norm = pkg.replace('-', '_')
+                seldirs = [x for x in subdirs if x.startswith(pkg) or x.startswith(pkg_norm)]
                 if len(seldirs) != 1:
                     # setuptools is optional since it may be available in the OS;
                     # vsc-install and vsc-base sources are optional,

easybuild/easyblocks/generic/cargopythonbundle.py

@@ -53,6 +53,10 @@ def __init__(self, *args, **kwargs):
         self.check_for_sources = False  # make Bundle allow sources (as crates are treated as sources)
         super(CargoPythonBundle, self).__init__(*args, **kwargs)
 
+        # Cargo inherits from ExtensionEasyBlock, thus EB treats the software itself as an extension
+        # Setting modulename to False to ensure that sanity checks are performed on the extensions only
+        self.options = {'modulename': False}
+
     def extract_step(self):
         """Specifically use the overloaded variant from Cargo as is populates vendored sources with checksums."""
         return Cargo.extract_step(self)

easybuild/easyblocks/i/intel_compilers.py

@@ -177,7 +177,12 @@ def make_module_extra(self):
         res = run_shell_cmd("gcc -print-multiarch")
         multiarch_out = res.output.strip()
         if res.exit_code == 0 and multiarch_out:
-            res = run_shell_cmd("gcc -E -Wp,-v -xc /dev/null 2>&1 | grep %s$" % multiarch_out)
+            multi_arch_inc_dir_cmd = '|'.join([
+                "gcc -E -Wp,-v -xc /dev/null 2>&1",
+                "grep %s$" % multiarch_out,
+                "grep -v /include-fixed/",
+            ])
+            res = run_shell_cmd(multi_arch_inc_dir_cmd)
             multiarch_inc_dir = res.output.strip()
             if res.exit_code == 0 and multiarch_inc_dir:
                 self.log.info("Adding multiarch include path %s to $CPATH in generated module file", multiarch_inc_dir)

easybuild/easyblocks/o/openfoam.py

@@ -41,14 +41,15 @@
 import shutil
 import stat
 import tempfile
+import textwrap
 from easybuild.tools import LooseVersion
 
 import easybuild.tools.environment as env
 import easybuild.tools.toolchain as toolchain
 from easybuild.easyblocks.generic.cmakemake import setup_cmake_env
 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.filetools import adjust_permissions, apply_regex_substitutions, mkdir, write_file
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import get_shared_lib_ext, get_cpu_architecture, AARCH64, POWER
@@ -293,6 +294,23 @@ def configure_step(self):
                     else:
                         env.setvar("%s_ROOT" % depend.upper(), dependloc)
 
+            if get_software_root('CGAL') and LooseVersion(get_software_version('CGAL')) >= LooseVersion('5.0'):
+                # CGAL >= 5.x is header-only, but when using it OpenFOAM still needs MPFR.
+                # It may fail to find it, so inject the right settings and paths into the "have_cgal" script.
+                have_cgal_script = os.path.join(self.builddir, self.openfoamdir, 'wmake', 'scripts', 'have_cgal')
+                if get_software_root('MPFR') and os.path.exists(have_cgal_script):
+                    eb_cgal_config = textwrap.dedent('''
+                    # Injected by EasyBuild
+                    HAVE_CGAL=true
+                    HAVE_MPFR=true
+                    CGAL_FLAVOUR=header
+                    CGAL_INC_DIR=${EBROOTCGAL}/include
+                    CGAL_LIB_DIR=${EBROOTCGAL}/lib
+                    MPFR_INC_DIR=${EBROOTMPFR}/include
+                    MPFR_LIB_DIR=${EBROOTMPFR}/lib
+                    ''')
+                    write_file(have_cgal_script, eb_cgal_config, append=True)
+
     def build_step(self):
         """Build OpenFOAM using make after sourcing script to set environment."""
 
@@ -486,6 +504,11 @@ def sanity_check_step(self):
             test_foammonitor = "! foamMonitor -h 2>&1 | grep 'not installed'"
             custom_commands.append(' && '.join([load_openfoam_env, test_foammonitor]))
 
+        if self.is_dot_com and self.looseversion >= LooseVersion("2012"):
+            # Make sure that wmake can see the compilers
+            test_wmake_compilers = ["command -V $(wmake -show-cxx)", "command -V $(wmake -show-c)"]
+            custom_commands.append(' && '.join([load_openfoam_env] + test_wmake_compilers))
+
         custom_paths = {
             'files': [os.path.join(self.openfoamdir, 'etc', x) for x in ["bashrc", "cshrc"]] + bins + libs,
             'dirs': dirs,

easybuild/easyblocks/o/openmpi.py

@@ -243,7 +243,11 @@ def sanity_check_step(self):
                 if build_option('mpi_tests'):
                     params.update({'nr_ranks': ranks, 'cmd': test_exe})
                     # Allow oversubscription for this test (in case of hyperthreading)
-                    custom_commands.append("OMPI_MCA_rmaps_base_oversubscribe=1 " + mpi_cmd_tmpl % params)
+                    if LooseVersion(self.version) >= '5.0':
+                        extra_env = "PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe"
+                    else:
+                        extra_env = "OMPI_MCA_rmaps_base_oversubscribe=1"
+                    custom_commands.append(extra_env + " " + mpi_cmd_tmpl % params)
                     # Run with 1 process which may trigger other bugs
                     # See https://github.com/easybuilders/easybuild-easyconfigs/issues/12978
                     params['nr_ranks'] = 1

easybuild/easyblocks/o/openssl_wrapper.py

@@ -30,7 +30,11 @@
 import os
 import re
 
-from urllib.parse import urlparse
+try:
+    from urllib.parse import urlparse
+except ImportError:
+    # fallback for Python 2.7, should be removed for EasyBuild >= 5.0
+    from urlparse import urlparse
 
 from easybuild.tools import LooseVersion
 

easybuild/easyblocks/p/python.py

@@ -197,8 +197,9 @@ def patch_step(self, *args, **kwargs):
         # if we're installing Python with an alternate sysroot,
         # we need to patch setup.py which includes hardcoded paths like /usr/include and /lib64;
         # this fixes problems like not being able to build the _ssl module ("Could not build the ssl module")
+        # Python 3.12 doesn't have setup.py any more
         sysroot = build_option('sysroot')
-        if sysroot:
+        if sysroot and LooseVersion(self.version) < LooseVersion('3.12'):
             sysroot_inc_dirs, sysroot_lib_dirs = [], []
 
             for pattern in ['include*', os.path.join('usr', 'include*')]:

easybuild/easyblocks/t/torchvision.py

@@ -28,10 +28,12 @@
 @author: Alexander Grund (TU Dresden)
 @author: Kenneth Hoste (HPC-UGent)
 """
+import os
+
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage, det_pylibdir
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.modules import get_software_version
+from easybuild.tools.modules import get_software_version, get_software_root
 import easybuild.tools.environment as env
 
 
@@ -69,18 +71,30 @@ def configure_step(self):
             if cuda_cc:
                 env.setvar('TORCH_CUDA_ARCH_LIST', ';'.join(cuda_cc))
 
+        libjpeg_root = get_software_root('libjpeg-turbo')
+        if libjpeg_root and 'TORCHVISION_INCLUDE' not in self.cfg['preinstallopts']:
+            env.setvar('TORCHVISION_INCLUDE', os.path.join(libjpeg_root, 'include'))
+
         super(EB_torchvision, self).configure_step()
 
     def sanity_check_step(self):
         """Custom sanity check for torchvision."""
-        custom_commands = None
-        custom_paths = None
+
+        # load module early ourselves rather than letting parent sanity_check_step method do so,
+        # so the correct 'python' command is used to by det_pylibdir() below;
+        if hasattr(self, 'sanity_check_module_loaded') and not self.sanity_check_module_loaded:
+            self.fake_mod_data = self.sanity_check_load_module(extension=self.is_extension)
+
+        custom_commands = []
+        custom_paths = {
+            'files': [],
+            'dirs': [det_pylibdir()],
+        }
 
         # check whether torchvision was indeed built with CUDA support,
         # cfr. https://discuss.pytorch.org/t/notimplementederror-could-not-run-torchvision-nms-with-arguments-from-\
         #      the-cuda-backend-this-could-be-because-the-operator-doesnt-exist-for-this-backend/132352/4
         if self.with_cuda:
-            custom_commands = []
             python_code = '\n'.join([
                 "import torch, torchvision",
                 "if torch.cuda.device_count():",
@@ -89,9 +103,15 @@ def sanity_check_step(self):
                 "    print(torchvision.ops.nms(boxes, scores, 0.5))",
             ])
             custom_commands.append('python -c "%s"' % python_code)
-            custom_paths = {
-                'files': [],
-                'dirs': [det_pylibdir()],
-            }
+
+        if get_software_root('libjpeg-turbo'):
+            # check if torchvision was built with libjpeg support
+            # if not, will show error "RuntimeError: encode_jpeg: torchvision not compiled with libjpeg support"
+            python_code = '\n'.join([
+                "import torch, torchvision",
+                "image_tensor = torch.zeros(1, 1, 1, dtype=torch.uint8)",
+                "print(torchvision.io.image.encode_jpeg(image_tensor))",
+            ])
+            custom_commands.append('python -c "%s"' % python_code)
 
         return super(EB_torchvision, self).sanity_check_step(custom_commands=custom_commands, custom_paths=custom_paths)