Merge pull request easybuilders#829 from boegel/DL_POLY_Plumed

modify DL_POLY_Classic easyblock to support building with Plumed support (REVIEW)

easybuild/easyblocks/d/dl_poly_classic.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2013 Ghent University
+# Copyright 2013-2016 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -26,27 +26,87 @@
 EasyBuild support for DL_POLY Classic, implemented as an easyblock
 
 @author: Jens Timmerman (Ghent University)
+@author: Kenneth Hoste (Ghent University)
 """
+import glob
 import os
 import shutil
 
-from easybuild.tools.filetools import copytree
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import copy_file, copytree
+from easybuild.tools.run import run_cmd
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 
 
 class EB_DL_underscore_POLY_underscore_Classic(ConfigureMake):
     """Support for building and installing DL_POLY Classic."""
 
+    def __init__(self, *args, **kwargs):
+        """Easyblock constructor; initialize class variables."""
+        super(EB_DL_underscore_POLY_underscore_Classic, self).__init__(*args, **kwargs)
+
+        # check whether PLUMED is listed as a dependency
+        self.with_plumed = 'PLUMED' in [dep['name'] for dep in self.cfg['dependencies']]
+
+    # create PLUMED patch in prepare_step rather than patch_step,
+    # so we can rely on being in the unpacked source directory
+    def prepare_step(self):
+        """Generate PLUMED patch if PLUMED is listed as a dependency."""
+        super(EB_DL_underscore_POLY_underscore_Classic, self).prepare_step()
+
+        if self.with_plumed:
+            # see https://groups.google.com/d/msg/plumed-users/cWaIDU5F6Bw/bZUW3J9cCAAJ
+            diff_pat = 'dlpoly-*.diff'
+            try:
+                diff_hits = glob.glob(os.path.join(self.builddir, diff_pat))
+            except OSError as err:
+                raise EasyBuildError("Failed to find list of files/dirs that match '%s': %s", diff_pat, err)
+
+            if len(diff_hits) == 1:
+                plumed_patch = diff_hits[0]
+            elif not self.dry_run:
+                raise EasyBuildError("Expected to find exactly one match for '%s' in %s, found: %s",
+                                     diff_pat, self.builddir, diff_hits)
+
+            if not self.dry_run:
+                try:
+                    os.rename('source', 'srcmod')
+                except OSError as err:
+                    raise EasyBuildError("Failed to move 'source' directory to 'srcmod': %s", err)
+
+            engine = os.path.splitext(os.path.basename(plumed_patch))[0]
+            cmd = "plumed-patch -p --runtime -e %s -d %s" % (engine, plumed_patch)
+            run_cmd(cmd, log_all=True, simple=True)
+
     def configure_step(self):
         """Copy the makefile to the source directory and use MPIF90 to do a parrallel build"""
-        shutil.copy("build/MakePAR", "source/Makefile")
-        os.chdir("source")
+
         self.cfg.update('buildopts', 'LD="$MPIF90 -o" FC="$MPIF90 -c" par')
 
+        if self.with_plumed:
+            source_dir = 'srcmod'
+            self.cfg.update('buildopts', 'LDFLAGS="${LDFLAGS} -lplumed -ldl"')
+        else:
+            source_dir = 'source'
+
+        copy_file(os.path.join('build', 'MakePAR'), os.path.join(source_dir, 'Makefile'))
+        try:
+            os.chdir(source_dir)
+        except OSError as err:
+            raise EasyBuildError("Failed to change to %s: %s", source_dir, err)
+
     def install_step(self):
         """Copy the executables to the installation directory"""
         self.log.debug("copying %s/execute to %s, (from %s)", self.cfg['start_dir'], self.installdir, os.getcwd())
-        # create a /bin, this way we also get the PATH to be set correctly automatically
-        bin_path = os.path.join(self.installdir, "bin")
+        # create a 'bin' subdir, this way we also get $PATH to be set correctly automatically
         install_path = os.path.join(self.cfg['start_dir'], 'execute')
+        bin_path = os.path.join(self.installdir, 'bin')
         copytree(install_path, bin_path)
+
+    def sanity_check_step(self):
+        """Custom sanity check step for DL_POLY Classic"""
+        custom_paths = {
+            'files': ['bin/DLPOLY.X'],
+            'dirs': [],
+        }
+        super(EB_DL_underscore_POLY_underscore_Classic, self).sanity_check_step(custom_paths=custom_paths)