Merge pull request #2785 from easybuilders/4.6.x

release EasyBuild 4.6.1

.github/workflows/linting.yml

@@ -2,7 +2,7 @@ name: Static Analysis
 on: [push, pull_request]
 jobs:
   python-linting:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
     - uses: actions/checkout@v2
 

.github/workflows/unit_tests.yml

@@ -2,7 +2,7 @@ name: easyblocks unit tests
 on: [push, pull_request]
 jobs:
   build:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
         python: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9, '3.10']

RELEASE_NOTES

@@ -6,6 +6,33 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en
 The latest version of easybuild-easyblocks provides 246 software-specific easyblocks and 37 generic easyblocks.
 
 
+v4.6.1 (September 12th 2022)
+----------------------------
+
+update/bugfix release
+
+- minor enhancements and updates, including:
+  - update LAMMPS easyblock for LAMMPS/23Jun22 (#2213)
+  - reduce the number of command line options for 'cmake' command in CMakeMake generic easyblock (#2514)
+  - update libQGLViewer easyblock to take into account changes in the shared library names depending on Qt versions they are compiled with (#2730)
+  - improve PLUMED detection in GROMACS easyblock (#2749)
+  - make `$LD_LIBRARY_PATH` detection more robust for LAMMPS (#2765)
+  - enhance NVHPC easyblock to avoid superfluous warning (#2767)
+  - enhance PyTorch easyblock to also capture tests failing with signal (#2768)
+  - enhance PythonPackage easyblock to make sure all test command output makes it to the EasyBuild log, also when return_output_ec=True (#2770)
+  - set $NVHPC_CUDA_HOME for NVHPC 22.7+ (#2776)
+- various bug fixes, including:
+  - make Amber easyblock aware of FlexiBLAS (#2720)
+  - update PyTorch easyblock to configure without breakpad support on POWER (#2763)
+  - use lib* in post_install step of FFTW.MPI easyblock to fix paths not being found on Linux distros favouring lib64 (like Suse/SLES) (#2771)
+  - use det_cmake_version function to determine CMake version in CMakeMake generic easyblock (#2772)
+  - don't enable building of ld.gold when installing binutils on a RISC-V system + don't configure GCC to use gold as default linker on a RISC-V system (#2780)
+  - tweak Amber(Tools) easyblock to run tests from top-level directory (#2781)
+  - fix version check for NVPTX library in sanity check of Clang easyblock (#2783)
+- other changes:
+  - update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (#2779)
+
+
 v4.6.0 (July 8th 2022)
 ----------------------
 

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('4.6.0')
+VERSION = LooseVersion('4.6.1')
 UNKNOWN = 'UNKNOWN'
 
 

easybuild/easyblocks/a/amber.py

@@ -141,6 +141,17 @@ def configure_step(self):
         if self.toolchain.options.get('openmp', None):
             self.cfg.update('configopts', '-DOPENMP=TRUE')
 
+        # note: for Amber 20, a patch is required to fix the CMake scripts so they're aware of FlexiBLAS:
+        # - cmake/patched-cmake-modules/FindBLASFixed.cmake
+        # - cmake/patched-cmake-modules/FindLAPACKFixed.cmake
+        flexiblas_root = get_software_root('FlexiBLAS')
+        if flexiblas_root:
+            self.cfg.update('configopts', '-DBLA_VENDOR=FlexiBLAS')
+        else:
+            openblas_root = get_software_root('OpenBLAS')
+            if openblas_root:
+                self.cfg.update('configopts', '-DBLA_VENDOR=OpenBLAS')
+
         cudaroot = get_software_root('CUDA')
         if cudaroot:
             self.with_cuda = True
@@ -213,13 +224,14 @@ def configuremake_install_step(self):
 
         # define environment variables for MPI, BLAS/LAPACK & dependencies
         mklroot = get_software_root('imkl')
-        openblasroot = get_software_root('OpenBLAS')
+        flexiblas_root = get_software_root('FlexiBLAS')
+        openblas_root = get_software_root('OpenBLAS')
         if mklroot:
             env.setvar('MKL_HOME', os.getenv('MKLROOT'))
-        elif openblasroot:
+        elif flexiblas_root or openblas_root:
             lapack = os.getenv('LIBLAPACK')
             if lapack is None:
-                raise EasyBuildError("LIBLAPACK (from OpenBLAS) not found in environment.")
+                raise EasyBuildError("$LIBLAPACK for OpenBLAS or FlexiBLAS not defined in build environment!")
             else:
                 env.setvar('GOTO', lapack)
 
@@ -317,12 +329,12 @@ def install_step(self):
 
         # Run the tests located in the build directory
         if self.cfg['runtest']:
-            pretestcommands = 'source %s/amber.sh && cd %s/test' % (self.installdir, self.builddir)
+            pretestcommands = 'source %s/amber.sh && cd %s' % (self.installdir, self.builddir)
 
             # serial tests
-            run_cmd("%s && make test" % pretestcommands, log_all=True, simple=True)
+            run_cmd("%s && make test.serial" % pretestcommands, log_all=True, simple=True)
             if self.with_cuda:
-                (out, ec) = run_cmd("%s && make test.cuda.serial" % pretestcommands, log_all=True, simple=False)
+                (out, ec) = run_cmd("%s && make test.cuda_serial" % pretestcommands, log_all=True, simple=False)
                 if ec > 0:
                     self.log.warning("Check the output of the Amber cuda tests for possible failures")
 

easybuild/easyblocks/b/binutils.py

@@ -39,7 +39,7 @@
 from easybuild.tools.filetools import apply_regex_substitutions, copy_file
 from easybuild.tools.modules import get_software_libdir, get_software_root
 from easybuild.tools.run import run_cmd
-from easybuild.tools.systemtools import get_shared_lib_ext
+from easybuild.tools.systemtools import RISCV, get_cpu_family, get_shared_lib_ext
 from easybuild.tools.utilities import nub
 
 
@@ -56,6 +56,13 @@ def extra_options(extra_vars=None):
         })
         return extra_vars
 
+    def __init__(self, *args, **kwargs):
+        """Easyblock constructor"""
+        super(EB_binutils, self).__init__(*args, **kwargs)
+
+        # ld.gold linker is not supported on RISC-V
+        self.use_gold = get_cpu_family() != RISCV
+
     def determine_used_library_paths(self):
         """Check which paths are used to search for libraries"""
 
@@ -158,7 +165,9 @@ def configure_step(self):
 
         # enable gold linker with plugin support, use ld as default linker (for recent versions of binutils)
         if LooseVersion(self.version) > LooseVersion('2.24'):
-            self.cfg.update('configopts', "--enable-gold --enable-plugins --enable-ld=default")
+            self.cfg.update('configopts', "--enable-plugins --enable-ld=default")
+            if self.use_gold:
+                self.cfg.update('configopts', '--enable-gold')
 
         if LooseVersion(self.version) >= LooseVersion('2.34'):
             if self.cfg['use_debuginfod']:
@@ -221,8 +230,9 @@ def sanity_check_step(self):
         shlib_ext = get_shared_lib_ext()
 
         if LooseVersion(self.version) > LooseVersion('2.24'):
-            binaries.append('ld.gold')
             lib_exts.append(shlib_ext)
+            if self.use_gold:
+                binaries.append('ld.gold')
 
         bin_paths = [os.path.join('bin', b) for b in binaries]
         inc_paths = [os.path.join('include', h) for h in headers]

easybuild/easyblocks/c/clang.py

@@ -554,7 +554,7 @@ def sanity_check_step(self):
             cuda_cc = cfg_cuda_cc or ec_cuda_cc or []
             # We need the CUDA capability in the form of '75' and not '7.5'
             cuda_cc = [cc.replace('.', '') for cc in cuda_cc]
-            if LooseVersion('11.0') < LooseVersion(self.version) < LooseVersion('13.0'):
+            if LooseVersion('12.0') < LooseVersion(self.version) < LooseVersion('13.0'):
                 custom_paths['files'].extend(["lib/libomptarget-nvptx-cuda_%s-sm_%s.bc" % (x, y)
                                              for x in CUDA_TOOLKIT_SUPPORT for y in cuda_cc])
             else:

easybuild/easyblocks/f/fftwmpi.py

@@ -63,9 +63,11 @@ def post_install_step(self):
         """Custom post install step for FFTW.MPI"""
 
         # remove everything except include files that are already in non-MPI FFTW dependency.
-        remove(glob.glob(os.path.join(self.installdir, 'lib', 'libfftw.*')) +
-               glob.glob(os.path.join(self.installdir, 'lib', 'libfftw[lf].*')) +
-               [os.path.join(self.installdir, p) for p in ['bin', 'lib/pkgconfig', 'lib/cmake', 'share']])
+        remove(glob.glob(os.path.join(self.installdir, 'lib*', 'libfftw.*')) +
+               glob.glob(os.path.join(self.installdir, 'lib*', 'libfftw[lf].*')) +
+               glob.glob(os.path.join(self.installdir, 'lib*/pkgconfig')) +
+               glob.glob(os.path.join(self.installdir, 'lib*/cmake')) +
+               [os.path.join(self.installdir, p) for p in ['bin', 'share']])
         super(EB_FFTW_period_MPI, self).post_install_step()
 
     def sanity_check_step(self):

easybuild/easyblocks/g/gcc.py

@@ -51,8 +51,8 @@
 from easybuild.tools.filetools import which, write_file
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_cmd
-from easybuild.tools.systemtools import check_os_dependency, get_os_name, get_os_type
-from easybuild.tools.systemtools import get_cpu_architecture, get_gcc_version, get_shared_lib_ext
+from easybuild.tools.systemtools import RISCV, check_os_dependency, get_cpu_architecture, get_cpu_family
+from easybuild.tools.systemtools import get_gcc_version, get_shared_lib_ext, get_os_name, get_os_type
 from easybuild.tools.toolchain.compiler import OPTARCH_GENERIC
 from easybuild.tools.utilities import nub
 
@@ -90,7 +90,7 @@ def extra_options():
             'prefer_lib_subdir': [False, "Configure GCC to prefer 'lib' subdirs over 'lib64' when linking", CUSTOM],
             'profiled': [False, "Bootstrap GCC with profile-guided optimizations", CUSTOM],
             'use_gold_linker': [None, "Configure GCC to use GOLD as default linker "
-                                      "(default: True for GCC < 11.3.0)", CUSTOM],
+                                      "(default: enable automatically for GCC < 11.3.0, except on RISC-V)", CUSTOM],
             'withcloog': [False, "Build GCC with CLooG support", CUSTOM],
             'withisl': [False, "Build GCC with ISL support", CUSTOM],
             'withlibiberty': [False, "Enable installing of libiberty", CUSTOM],
@@ -526,8 +526,10 @@ def configure_step(self):
         # enable plugin support
         self.configopts += " --enable-plugins "
 
-        # use GOLD as default linker
-        if self.cfg['use_gold_linker']:
+        # use GOLD as default linker, except on RISC-V (since it's not supported there)
+        if get_cpu_family() == RISCV:
+            self.configopts += " --disable-gold --enable-ld=default"
+        elif self.cfg['use_gold_linker']:
             self.configopts += " --enable-gold=default --enable-ld --with-plugin-ld=ld.gold"
         else:
             self.configopts += " --enable-gold --enable-ld=default"

easybuild/easyblocks/g/gromacs.py

@@ -68,6 +68,8 @@ def extra_options():
             'mpiexec_numproc_flag': ['-np', "Flag to introduce the number of MPI tasks when running tests", CUSTOM],
             'mpi_numprocs': [0, "Number of MPI tasks to use when running tests", CUSTOM],
             'ignore_plumed_version_check': [False, "Ignore the version compatibility check for PLUMED", CUSTOM],
+            'plumed': [None, "Try to apply PLUMED patches. None (default) is auto-detect. " +
+                       "True or False forces behaviour.", CUSTOM],
         })
         extra_vars['separate_build_dir'][0] = True
         return extra_vars
@@ -201,9 +203,20 @@ def configure_step(self):
                 # to avoid that GROMACS finds and uses a system-wide CUDA compiler
                 self.cfg.update('configopts', "-DGMX_GPU=OFF")
 
-        # check whether PLUMED is loaded as a dependency
+        # PLUMED detection
+        # enable PLUMED support if PLUMED is listed as a dependency
+        # and PLUMED support is either explicitly enabled (plumed = True) or unspecified ('plumed' not defined)
         plumed_root = get_software_root('PLUMED')
+        if self.cfg['plumed'] and not plumed_root:
+            msg = "PLUMED support has been requested but PLUMED is not listed as a dependency."
+            raise EasyBuildError(msg)
+        elif plumed_root and self.cfg['plumed'] is False:
+            self.log.info('PLUMED was found, but compilation without PLUMED has been requested.')
+            plumed_root = None
+
         if plumed_root:
+            self.log.info('PLUMED support has been enabled.')
+
             # Need to check if PLUMED has an engine for this version
             engine = 'gromacs-%s' % self.version