Merge pull request #2061 from easybuilders/4.2.x

release EasyBuild 4.2.1

Author: migueldiascosta

.gitignore

@@ -9,3 +9,4 @@ build/
 dist/
 *egg-info/
 *.swp
+.mypy_cache/

RELEASE_NOTES

@@ -3,7 +3,42 @@ 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 219 software-specific easyblocks and 36 generic easyblocks.
+The latest version of easybuild-easyblocks provides 219 software-specific easyblocks and 37 generic easyblocks.
+
+v4.2.1 (May 20th 2020)
+----------------------
+
+update/bugfix release
+
+- add generic easyblock for installing Go packages: GoPackage (#2042)
+- minor enhancements, including:
+  - update config.guess for all R packages, required installing R + extensions on Linux/POWER systems (#1949)
+  - add support for preinstallopts and install in subdirectory to Tarball generic easyblock (#1989, #2049)
+  - rewrite GROMACS easyblock to install all four variations (single/double precision, with/without MPI) in the same directory (#1991)
+  - add custom 'subdir_version' easyconfig parameter for FLUENT (#2021)
+  - use updated config.guess in GCC easyblock (#2033, #2059)
+  - add extra question pattern to support installing CPLEX 12.10 (#2038)
+  - add support for building NWChem on top of external GlobalArrays + also define $LAPACK_LIB (required for NWChem 7.x) (#2043)
+  - execute minimal test in sanity check commands in impi easyblock (#2045)
+  - update for MotionCor2 easyblock for v1.3.1 (#2046)
+  - fixes + enhancements for PETSc easyblock (#2048)
+- various bug fixes, including:
+  - use correct version in ELPA preprocessor flag used for QuantumESPRESSO v6.x (#2027)
+  - generically find the arch folder and add top-level bin/lib symlinks in PDT & TAU easyblocks (#2029)
+  - fix typo in LAMMPS easyblock preventing disabling the USER-INTEL package via configopts (#2031)
+  - let CMakeMake remove 'easybuild_obj' build directory if it already exists (#2032)
+  - include own lib dir in RPATH before system lib dirs in binutils easyblock (#2044)
+  - clean $CPATH before building ROOT to avoid clash between external LLVM loaded as a dependency and internal LLVM used by ROOT (#2047)
+  - don't let extract_file change directory in various easyblocks (#2051)
+  - make postinstallcmds available to Mathematica easyconfigs + add bin/Executables to $PATH (#2052)
+  - fix the extra dirs added to PATH in FreeSurfer easyblock (#2053)
+  - correct download url for test data in WPS easyblock (#2055)
+  - fix typo in warning in TensorFlow easyblock (#2057)
+  - fix failing sanity check under --module-only in GCC easyblock (#2059)
+- other changes:
+  - add configure options for CubeLib/CubeWriter dependencies in Score-P easyblock (#2030)
+  - remove local find_glob_pattern in Blender & ROOT easyblocks, use function provided by filetools instead (#2037)
+
 
 v4.2.0 (April 14th 2020)
 ------------------------

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('4.2.0')
+VERSION = LooseVersion('4.2.1')
 UNKNOWN = 'UNKNOWN'
 
 

easybuild/easyblocks/b/binutils.py

@@ -50,6 +50,7 @@ def extra_options(extra_vars=None):
         extra_vars = ConfigureMake.extra_options(extra_vars=extra_vars)
         extra_vars.update({
             'install_libiberty': [True, "Also install libiberty (implies building with -fPIC)", CUSTOM],
+            'use_debuginfod': [False, "Build with debuginfod (used from system)", CUSTOM],
         })
         return extra_vars
 
@@ -62,7 +63,11 @@ def configure_step(self):
             # determine list of 'lib' directories to use rpath for;
             # this should 'harden' the resulting binutils to bootstrap GCC
             # (no trouble when other libstdc++ is build etc)
-            libdirs = []
+
+            # The installed lib dir must come first though to avoid taking system libs over installed ones, see:
+            # https://github.com/easybuilders/easybuild-easyconfigs/issues/10056
+            # Escaping: Double $$ for Make, \$ for shell to get literal $ORIGIN in the file
+            libdirs = [r'\$\$ORIGIN/../lib']
             for libdir in ['/usr/lib', '/usr/lib64', '/usr/lib/x86_64-linux-gnu/']:
                 # also consider /lib, /lib64
                 alt_libdir = libdir.replace('usr/', '')
@@ -75,7 +80,8 @@ def configure_step(self):
                 elif os.path.exists(alt_libdir):
                     libdirs.append(alt_libdir)
 
-            libs += ' '.join('-Wl,-rpath=%s' % libdir for libdir in libdirs)
+            # Mind the single quotes
+            libs += ' '.join("-Wl,-rpath='%s'" % libdir for libdir in libdirs)
 
         # configure using `--with-system-zlib` if zlib is a (build) dependency
         zlibroot = get_software_root('zlib')
@@ -101,8 +107,9 @@ def configure_step(self):
                 else:
                     libs += ' ' + libz_path
 
-        self.cfg.update('preconfigopts', "env LIBS='%s'" % libs)
-        self.cfg.update('prebuildopts', "env LIBS='%s'" % libs)
+        # Using double quotes for LIBS to allow single quotes in libs
+        self.cfg.update('preconfigopts', 'LIBS="%s"' % libs)
+        self.cfg.update('prebuildopts', 'LIBS="%s"' % libs)
 
         # use correct sysroot, to make sure 'ld' also considers system libraries
         self.cfg.update('configopts', '--with-sysroot=/')
@@ -115,6 +122,12 @@ def configure_step(self):
         if LooseVersion(self.version) > LooseVersion('2.24'):
             self.cfg.update('configopts', "--enable-gold --enable-plugins --enable-ld=default")
 
+        if LooseVersion(self.version) >= LooseVersion('2.34'):
+            if self.cfg['use_debuginfod']:
+                self.cfg.update('configopts', '--with-debuginfod')
+            else:
+                self.cfg.update('configopts', '--without-debuginfod')
+
         # complete configuration with configure_method of parent
         super(EB_binutils, self).configure_step()
 

easybuild/easyblocks/b/blender.py

@@ -27,11 +27,11 @@
 
 @author: Samuel Moors (Vrije Universiteit Brussel)
 """
-import glob
 import os
 
 from easybuild.easyblocks.generic.cmakemake import CMakeMake
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import find_glob_pattern
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.systemtools import get_shared_lib_ext
 
@@ -45,15 +45,6 @@ def extra_options():
         extra_vars['separate_build_dir'][0] = True
         return extra_vars
 
-    def find_glob_pattern(self, glob_pattern):
-        """Find unique file/dir matching glob_pattern (raises error if more than one match is found)"""
-        if self.dry_run:
-            return glob_pattern
-        res = glob.glob(glob_pattern)
-        if len(res) != 1:
-            raise EasyBuildError("Was expecting exactly one match for '%s', found %d: %s", glob_pattern, len(res), res)
-        return res[0]
-
     def configure_step(self):
         """Set CMake options for Blender"""
 
@@ -81,12 +72,12 @@ def configure_step(self):
             site_packages = os.path.join(python_root, 'lib', 'python%s' % pyshortver, 'site-packages')
 
             # We assume that numpy/requests are included with the Python installation (no longer true for 2019a)
-            numpy_root = self.find_glob_pattern(
+            numpy_root = find_glob_pattern(
                 os.path.join(site_packages, 'numpy-*-py%s-linux-x86_64.egg' % pyshortver))
-            requests_root = self.find_glob_pattern(os.path.join(site_packages, 'requests-*-py%s.egg' % pyshortver))
-            python_lib = self.find_glob_pattern(
+            requests_root = find_glob_pattern(os.path.join(site_packages, 'requests-*-py%s.egg' % pyshortver))
+            python_lib = find_glob_pattern(
                 os.path.join(python_root, 'lib', 'libpython%s*.%s' % (pyshortver, shlib_ext)))
-            python_include_dir = self.find_glob_pattern(os.path.join(python_root, 'include', 'python%s*' % pyshortver))
+            python_include_dir = find_glob_pattern(os.path.join(python_root, 'include', 'python%s*' % pyshortver))
 
             self.cfg.update('configopts', '-DPYTHON_VERSION=%s' % pyshortver)
             self.cfg.update('configopts', '-DPYTHON_LIBRARY=%s' % python_lib)

easybuild/easyblocks/c/cplex.py

@@ -92,6 +92,8 @@ def install_step(self):
             "PRESS <ENTER> TO EXIT THE INSTALLER:": '',
             "CHOOSE LOCALE BY NUMBER:": '',
             "Choose Instance Management Option:": '',
+            "No model content or proprietary data will be sent.\n1- Yes\n2- No\n"
+            "ENTER THE NUMBER OF THE DESIRED CHOICE:": '2',
         }
         noqanda = [r'Installing\.\.\..*\n.*------.*\n\n.*============.*\n.*$']
 

easybuild/easyblocks/f/fluent.py

@@ -32,17 +32,29 @@
 from distutils.version import LooseVersion
 
 from easybuild.easyblocks.generic.packedbinary import PackedBinary
+from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.filetools import adjust_permissions
 from easybuild.tools.run import run_cmd
 
 
 class EB_FLUENT(PackedBinary):
     """Support for installing FLUENT."""
 
+    @staticmethod
+    def extra_options():
+        extra_vars = PackedBinary.extra_options()
+        extra_vars['subdir_version'] = [None, "Version to use to determine installation subdirectory", CUSTOM]
+        return extra_vars
+
     def __init__(self, *args, **kwargs):
         """Custom constructor for FLUENT easyblock, initialize/define class parameters."""
         super(EB_FLUENT, self).__init__(*args, **kwargs)
-        self.fluent_verdir = 'v%s' % ''.join(self.version.split('.')[:2])
+
+        subdir_version = self.cfg['subdir_version']
+        if subdir_version is None:
+            subdir_version = ''.join(self.version.split('.')[:2])
+
+        self.fluent_verdir = 'v%s' % subdir_version
 
     def install_step(self):
         """Custom install procedure for FLUENT."""

easybuild/easyblocks/f/freesurfer.py

@@ -44,18 +44,18 @@ def extra_options():
         extra_vars = {
             'license_text': ['', "Text for required license file.", MANDATORY],
         }
-        return EasyBlock.extra_options(extra_vars)
+        return Tarball.extra_options(extra_vars)
 
     def install_step(self):
         """Custom installation procedure for FreeSurfer, which includes installed the license file '.license'."""
         super(EB_FreeSurfer, self).install_step()
         write_file(os.path.join(self.installdir, '.license'), self.cfg['license_text'])
 
-    def make_module_guesses(self):
+    def make_module_req_guess(self):
         """Include correct subdirectories to $PATH for FreeSurfer."""
-        guesses = super(EB_FreeSurfer, self).make_module_guesses()
+        guesses = super(EB_FreeSurfer, self).make_module_req_guess()
 
-        guesses['PATH'] = ['bin', 'fsfast/bin', 'mni/bin', 'tktools']
+        guesses['PATH'].extend([os.path.join('fsfast', 'bin'), os.path.join('mni', 'bin'), 'tktools'])
 
         return guesses
 

easybuild/easyblocks/g/gcc.py

@@ -48,9 +48,10 @@
 from easybuild.tools.filetools import apply_regex_substitutions, symlink, 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, get_platform_name
+from easybuild.tools.systemtools import check_os_dependency, get_os_name, get_os_type
 from easybuild.tools.systemtools import get_gcc_version, get_shared_lib_ext
 from easybuild.tools.toolchain.compiler import OPTARCH_GENERIC
+from easybuild.tools.utilities import nub
 
 
 COMP_CMD_SYMLINKS = {
@@ -113,8 +114,6 @@ def __init__(self, *args, **kwargs):
         if get_os_name() not in ['ubuntu', 'debian']:
             self.cfg.update('unwanted_env_vars', ['LIBRARY_PATH'])
 
-        self.platform_lib = get_platform_name(withversion=True)
-
     def create_dir(self, dirname):
         """
         Create a dir to build in.
@@ -383,15 +382,17 @@ def configure_step(self):
         else:
             objdir = self.create_dir("obj")
 
+        # note: this also triggers the use of an updated config.guess script
+        # (unless both the 'build_type' and 'host_type' easyconfig parameters are specified)
+        build_type, host_type = self.determine_build_and_host_type()
+        if build_type:
+            configopts += ' --build=' + build_type
+        if host_type:
+            configopts += ' --host=' + host_type
+
         # IV) actual configure, but not on default path
         cmd = "../configure  %s %s" % (self.configopts, configopts)
 
-        # instead of relying on uname, we run the same command GCC uses to
-        # determine the platform
-        out, ec = run_cmd("../config.guess", simple=False)
-        if ec == 0:
-            self.platform_lib = out.rstrip()
-
         self.run_configure_cmd(cmd)
 
         self.disable_lto_mpfr_old_gcc(objdir)
@@ -624,7 +625,26 @@ def sanity_check_step(self):
 
         os_type = get_os_type()
         sharedlib_ext = get_shared_lib_ext()
-        common_infix = os.path.join('gcc', self.platform_lib, self.version)
+
+        # determine "configuration name" directory, see https://sourceware.org/autobook/autobook/autobook_17.html
+        # this differs across GCC versions;
+        # x86_64-unknown-linux-gnu was common for old GCC versions,
+        # x86_64-pc-linux-gnu is more likely with an updated config.guess script;
+        # since this is internal to GCC, we don't really care how it is named exactly,
+        # we only care that it's actually there
+
+        # we may get multiple hits (libexec/, lib/), which is fine,
+        # but we expect the same configuration name subdirectory in each of them
+        glob_pattern = os.path.join(self.installdir, 'lib*', 'gcc', '*-linux-gnu', self.version)
+        matches = glob.glob(glob_pattern)
+        if matches:
+            cands = nub([os.path.basename(os.path.dirname(x)) for x in matches])
+            if len(cands) == 1:
+                config_name_subdir = cands[0]
+            else:
+                raise EasyBuildError("Found multiple candidates for configuration name: %s", ', '.join(cands))
+        else:
+            raise EasyBuildError("Failed to determine configuration name: no matches for '%s'", glob_pattern)
 
         bin_files = ["gcov"]
         lib_files = []
@@ -639,7 +659,7 @@ def sanity_check_step(self):
             else:
                 lib_files.extend(["libasan.%s" % sharedlib_ext, "libasan.a"])
         libexec_files = []
-        dirs = ['lib/%s' % common_infix]
+        dirs = [os.path.join('lib', 'gcc', config_name_subdir, self.version)]
 
         if not self.cfg['languages']:
             # default languages are c, c++, fortran
@@ -678,7 +698,8 @@ def sanity_check_step(self):
             lib_files = [tuple([os.path.join(libdir, x) for libdir in libdirs]) for x in lib_files]
         # lib on SuSE, libexec otherwise
         libdirs = ['libexec', 'lib']
-        libexec_files = [tuple([os.path.join(libdir, common_infix, x) for libdir in libdirs]) for x in libexec_files]
+        common_infix = os.path.join('gcc', config_name_subdir, self.version)
+        libexec_files = [tuple([os.path.join(d, common_infix, x) for d in libdirs]) for x in libexec_files]
 
         old_cmds = [os.path.join('bin', x) for x in COMP_CMD_SYMLINKS.keys()]