merge develop

Author: Samuel Moors

RELEASE_NOTES

@@ -3,7 +3,67 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at https://docs.easybuild.io/release-notes .
 
-The latest version of easybuild-easyblocks provides 199 software-specific easyblocks and 45 generic easyblocks.
+The latest version of easybuild-easyblocks provides 200 software-specific easyblocks and 45 generic easyblocks.
+
+
+v5.1.1 (6 July 2025)
+--------------------
+
+update/bugfix release
+
+- new easyblocks:
+  - add custom easyblock for BLIS, which can also be used for AOCL-BLAS (#3773)
+- enhancements:
+  - add support for iterative build of OpenBLAS with 64-bit integers (#2753)
+  - add Kokkos mapping for AMD zen4 and NVIDIA Grace to LAMMPS easyblock (#3742)
+  - enhance LLVM easyblock to use `dlopen` for AMDGPU/CUDA libomptarget / offload target libraries (#3747)
+  - enhance Rust easyblock to allow specifying channel to use (stable vs nightly) (#3749)
+  - enhance `run_pip_check` function to respect EasyBuild configuration option to ignore unversioned (0.0.0) Python packages (#3753)
+  - enhance SuperLU easyblock to set configure options for ParMETIS (or disable it if ParMETIS is not a dependency) (#3767)
+  - symlink CUPTI files to standard locations in CUDA installation (#3791)
+  - enhance `PythonPackage` to allow specifying location to temporary installation used in test step + also update `$PATH` to pick up on binaries/scripts from it (#3797)
+  - add support for `UCX`, `CUDA` and `mpi_abi` directly in MPICH easyblock (#3807)
+  - refactor LLVM easyblock and install OpenMP library symlinks (#3815)
+  - enhance `Bundle` generic easyblock to also run test step for each bundle component (#3748, #3752, #3775)
+- updates:
+  - remove `2to3` file from sanity check in Anaconda easyblock (no longer there in recent versions) (#3761)
+  - update numpy easyblock to support installing numpy >= 2.0 (#3777)
+  - update Mesa easyblock to use not use removed `swrast` as gallium driver for Mesa versions >= 25.x (#3790)
+- bug fixes:
+  - bug fixes for custom easyblock for LLVM:
+    - ensure sysroot dynamic linker is used + add ignore patterns for failing tests that can be ignored in LLVM easyblock (#3741)
+    - fix configuration option for OpenMP offload target + logic in sanity check step in LLVM easyblock (#3755)
+    - use `self.start_dir` in LLVM easyblock (#3770)
+    - moved logic from the constructor to `configure_step` in LLVM easyblock (so it can be used to install bundle component) (#3781)
+    - fix LLVM easyblock to allow building with multiple versions at once (#3812)
+    - do not create compiler configs for LLVM < 19 (#3817)
+    - fix condition to ignore failed LLVM GPU tests (#3819)
+  - fix/simplify use of `self.cfg.dependencies()` in various easyblocks: `CMake` (#3810), `OpenFOAM` (#3814), `PETSc` (#3813), `SLEPc` (#3811), `Term::ReadLine::Gnu` (#3808)
+  - take into account that `f90wrap_version` may be `None` in MetalWalls easyblock (#3468)
+  - fix `enhance_sanity_check` for `PythonPackage` (#3477)
+  - improve reliability of PyTorch test reporting (#3723)
+  - also install OpenCOSMORS for ORCA versions >= 6.0 (#3726)
+  - fix missed f-string in `PythonPackage` easyblock (#3729)
+  - use `--enable-install-libiberty` to enable `libiberty` for `binutils` + move `libiberty.a` binutils library to `lib` subdirectory if it's the only file in `lib64` subdirectory (#3736, #3822)
+  - make sure RPATH wrappers shipped via `buildenv` are world executable (#3743)
+  - take into account that `$PYTHONPATH` and `$PATH` may be unset in configure step of custom easyblock for scipy (#3744)
+  - set `$HOME` to temporary folder for TensorFlow build and tests  (#3751)
+  - fix unbound variable `install_args` in Conda easyblock (#3763)
+  - set `$CARGO_NET_OFFLINE` to `true` in `set_cargo_vars` method of `Cargo` easyblock (only if `offline` mode is used), so it's set for every extension when `CargoPythonBundle` easyblock is used (#3764)
+  - fix test step for `CMakeNinja` easyblock by customizing `test_cmd` and `runtest` easyconfig parameters (#3771)
+  - use `parallel` property rather than value of (deprecated) `parallel` easyconfig parameter in ORCA easyblock (#3772)
+  - (re)set environment variables used by `cargo` in prepare step of `Cargo` easyblock (#3774)
+  - don't forcibly set `$LD_LIBRARY_PATH` in LAMMPS sanity check (#3776)
+  - add missing call to `make_module_step` for components in `Bundle` easyblock (#3801)
+  - add support for hwloc to MPICH easyblock (#3821)
+- enhancements and fixes for test suite:
+  - allow test case filtering and other `unittest` arguments (#3653)
+- other changes:
+  - disable trace output when unpacking crates in Cargo easyblock (#3750)
+  - update Rust easyblock to disable installations of docs via `--disable-docs` configure option (#3768)
+  - simplify remaining `super()` calls (#3780)
+  - handle `$PATH` environment variable with `module_load_environment` in init of `Binary` easyblock (#3787)
+  - change ABAQUS easyblock to use `LM_LICENSE_FILE` instead of `ABAQUSLM_LICENSE_FILE` (#3794)
 
 
 v5.1.0 (26 May 2025)

easybuild/easyblocks/__init__.py

@@ -42,7 +42,7 @@
 # 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 = '5.1.1.dev0'
+VERSION = '5.1.2.dev0'
 UNKNOWN = 'UNKNOWN'
 
 

easybuild/easyblocks/a/abaqus.py

@@ -366,6 +366,6 @@ def make_module_extra(self):
         txt = super().make_module_extra()
         license_file = os.getenv('EB_ABAQUS_LICENSE_FILE', None)
         if license_file is not None:
-            txt += self.module_generator.prepend_paths('ABAQUSLM_LICENSE_FILE', [license_file], allow_abs=True)
+            txt += self.module_generator.prepend_paths('LM_LICENSE_FILE', [license_file], allow_abs=True)
 
         return txt

easybuild/easyblocks/a/amber.py

@@ -328,10 +328,13 @@ def install_step(self):
 
         super().install_step()
 
-        # Run the tests located in the build directory
+        # Run the tests
         if self.cfg['runtest']:
             if LooseVersion(self.version) >= LooseVersion('24'):
-                testdir = os.path.join(self.builddir, 'test')
+                if self.name == 'AmberTools':
+                    testdir = os.path.join(self.builddir, 'AmberTools', 'test')
+                elif self.name == 'Amber':
+                    testdir = os.path.join(self.builddir, 'test')
                 testname_cs = 'test.cuda.serial'
                 testname_cp = 'test.cuda.parallel'
             else:
@@ -341,12 +344,16 @@ def install_step(self):
             pretestcommands = 'source %s/amber.sh && cd %s' % (self.installdir, testdir)
 
             # serial tests
-            run_shell_cmd("%s && make test.serial" % pretestcommands)
+            if LooseVersion(self.version) >= LooseVersion('24'):
+                run_shell_cmd("%s && make test" % pretestcommands)
+            else:
+                run_shell_cmd("%s && make test.serial" % pretestcommands)
             if self.with_cuda:
                 res = run_shell_cmd(f"{pretestcommands} && make {testname_cs}")
                 if res.exit_code > 0:
                     self.log.warning("Check the output of the Amber cuda tests for possible failures")
 
+            # parallel tests
             if self.with_mpi:
                 # Hard-code parallel tests to use 4 threads
                 env.setvar("DO_PARALLEL", self.toolchain.mpi_cmd_for('', 4))
@@ -373,11 +380,15 @@ def sanity_check_step(self):
                         binaries.append('pmemd.cuda.MPI')
                     else:
                         binaries.append('pmemd.cuda_DPFP.MPI')
+        if self.name == 'AmberTools':
+            binaries.append('gem.pmemd')
 
         if self.with_mpi:
             binaries.extend(['sander.MPI'])
             if self.name == 'Amber':
                 binaries.append('pmemd.MPI')
+            if self.name == 'AmberTools':
+                binaries.append('gem.pmemd.MPI')
 
         custom_paths = {
             'files': [os.path.join(self.installdir, 'bin', binary) for binary in binaries],

easybuild/easyblocks/a/anaconda.py

@@ -33,7 +33,6 @@
 import stat
 
 from easybuild.easyblocks.generic.binary import Binary
-from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.filetools import adjust_permissions, clean_dir
 from easybuild.tools.modules import MODULE_LOAD_ENV_HEADERS
 from easybuild.tools.run import run_shell_cmd
@@ -42,16 +41,6 @@
 class EB_Anaconda(Binary):
     """Support for building/installing Anaconda and Miniconda."""
 
-    @staticmethod
-    def extra_options():
-        """Add extra config options specific to Python."""
-        extra_vars = {
-            'fix_python_shebang_for': [['bin/*'], "List of files for which Python shebang should be fixed "
-                                                  "to '#!/usr/bin/env python' (glob patterns supported) "
-                                                  "(default: ['bin/*'])", CUSTOM],
-        }
-        return Binary.extra_options(extra_vars)
-
     def __init__(self, *args, **kwargs):
         """Initialize class variables."""
         super().__init__(*args, **kwargs)
@@ -85,7 +74,7 @@ def sanity_check_step(self):
         Custom sanity check for Anaconda and Miniconda
         """
         custom_paths = {
-            'files': [os.path.join('bin', x) for x in ['2to3', 'conda', 'pydoc', 'python', 'sqlite3']],
+            'files': [os.path.join('bin', x) for x in ['conda', 'pydoc', 'python', 'sqlite3']],
             'dirs': ['bin', 'etc', 'lib', 'pkgs'],
         }
         super().sanity_check_step(custom_paths=custom_paths)

easybuild/easyblocks/a/armadillo.py

@@ -38,13 +38,6 @@
 class EB_Armadillo(CMakeMake):
     """Support for building Armadillo."""
 
-    @staticmethod
-    def extra_options():
-        """Extra easyconfig parameters for Armadillo."""
-        extra_vars = CMakeMake.extra_options()
-        extra_vars['separate_build_dir'][0] = True
-        return extra_vars
-
     def configure_step(self):
         """Set some extra environment variables before configuring."""
 

easybuild/easyblocks/b/binutils.py

@@ -37,7 +37,7 @@
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import apply_regex_substitutions, copy_file, symlink
+from easybuild.tools.filetools import apply_regex_substitutions, copy_file, move_file, remove_dir, symlink
 from easybuild.tools.modules import get_software_libdir, get_software_root
 from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import RISCV, get_cpu_family, get_gcc_version, get_shared_lib_ext
@@ -225,6 +225,20 @@ def install_step(self):
                 copy_file(os.path.join(self.cfg['start_dir'], 'libiberty', 'libiberty.texi'),
                           os.path.join(self.installdir, 'info', 'libiberty.texi'))
 
+            # if only libiberty.a is installed in 'lib64' subdirectory,
+            # move it to 'lib' subdirectory and remove empty 'lib64' subdirectory,
+            # so 'lib64' will be symlinked to 'lib' (by EasyBlock.post_processing_step)
+            lib64_path = os.path.join(self.installdir, 'lib64')
+            libiberty_static_lib = 'libiberty.a'
+            if os.path.exists(lib64_path) and os.listdir(lib64_path) == [libiberty_static_lib]:
+                lib_path = os.path.join(self.installdir, 'lib')
+                self.log.info(f"Found only {libiberty_static_lib} in {lib64_path}, moving it to {lib_path}")
+                src_path = os.path.join(lib64_path, libiberty_static_lib)
+                target_path = os.path.join(lib_path, libiberty_static_lib)
+                move_file(src_path, target_path)
+                self.log.info(f"Removing (now empty) {lib64_path} directory")
+                remove_dir(lib64_path)
+
     def sanity_check_step(self):
         """Custom sanity check for binutils."""
 

easybuild/easyblocks/b/blat.py

@@ -42,10 +42,10 @@ def configure_step(self):
         """Configure build: just create a 'bin' directory."""
         mkdir("bin")
 
-    def build_step(self, verbose=False):
+    def build_step(self, *args, **kwargs):
         """Build BLAT using make and the appropriate options (e.g. BINDIR=)."""
         self.cfg.update('prebuildopts', "MACHTYPE=x86_64")
         bindir = os.path.join(os.getcwd(), "bin")
         self.cfg.update('buildopts', "BINDIR=%s" % bindir)
 
-        return super().build_step(verbose=verbose)
+        return super().build_step(*args, **kwargs)

easybuild/easyblocks/c/cgal.py

@@ -42,12 +42,6 @@
 class EB_CGAL(CMakeMake):
     """Support for building CGAL."""
 
-    @staticmethod
-    def extra_options():
-        extra_vars = CMakeMake.extra_options()
-        extra_vars['separate_build_dir'][0] = True
-        return extra_vars
-
     def configure_step(self):
         """Set some extra environment variables before configuring."""
 

easybuild/easyblocks/c/clang.py

@@ -120,6 +120,14 @@ def __init__(self, *args, **kwargs):
         """Initialize custom class variables for Clang."""
 
         super().__init__(*args, **kwargs)
+
+        if LooseVersion(self.version) >= LooseVersion('18.1.6'):
+            raise EasyBuildError(
+                "The Clang EasyBlock has been deprecated and does not support LLVM versions >= 18.1.6. "
+                "Please use the 'LLVM' EasyBlock instead, which supports building Clang as well "
+                "as other LLVM projects."
+            )
+
         self.llvm_src_dir = None
         self.llvm_obj_dir_stage1 = None
         self.llvm_obj_dir_stage2 = None