fix+enhance NWChem easyblock

easybuilders · Dec 8, 2023 · e0bfdab · e0bfdab
1 parent eda2199
commit e0bfdab
Showing 1 changed file with 20 additions and 34 deletions.
diff --git a/easybuild/easyblocks/n/nwchem.py b/easybuild/easyblocks/n/nwchem.py
@@ -29,7 +29,6 @@
 """
 import os
 import re
-import shutil
 import stat
 import tempfile
 
@@ -40,7 +39,8 @@
 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 adjust_permissions, change_dir, mkdir, remove_file, symlink, write_file
+from easybuild.tools.filetools import (adjust_permissions, change_dir, copy_dir, copy_file, mkdir, remove_file,
+                                       remove_dir, symlink, write_file)
 from easybuild.tools.modules import get_software_libdir, get_software_root, get_software_version
 from easybuild.tools.run import run_cmd
 
@@ -325,16 +325,19 @@ def install_step(self):
             # binary
             bindir = os.path.join(self.installdir, 'bin')
             mkdir(bindir)
-            shutil.copy(os.path.join(self.cfg['start_dir'], 'bin', self.cfg['target'], 'nwchem'),
-                        bindir)
+            copy_file(os.path.join(self.cfg['start_dir'], 'bin', self.cfg['target'], 'nwchem'),
+                      os.path.join(bindir, 'nwchem'))
 
             # data
-            shutil.copytree(os.path.join(self.cfg['start_dir'], 'src', 'data'),
-                            os.path.join(self.installdir, 'data'))
-            shutil.copytree(os.path.join(self.cfg['start_dir'], 'src', 'basis', 'libraries'),
-                            os.path.join(self.installdir, 'data', 'libraries'))
-            shutil.copytree(os.path.join(self.cfg['start_dir'], 'src', 'nwpw', 'libraryps'),
-                            os.path.join(self.installdir, 'data', 'libraryps'))
+            copy_dir(os.path.join(self.cfg['start_dir'], 'src', 'data'),
+                     os.path.join(self.installdir, 'data'))
+            copy_dir(os.path.join(self.cfg['start_dir'], 'src', 'basis', 'libraries'),
+                     os.path.join(self.installdir, 'data', 'libraries'))
+            copy_dir(os.path.join(self.cfg['start_dir'], 'src', 'nwpw', 'libraryps'),
+                     os.path.join(self.installdir, 'data', 'libraryps'))
+            # examples (needed for the test_cases_step)
+            copy_dir(os.path.join(self.cfg['start_dir'], 'examples'),
+                     os.path.join(self.installdir, 'examples'))
 
         except OSError as err:
             raise EasyBuildError("Failed to install NWChem: %s", err)
@@ -388,23 +391,6 @@ def make_module_extra(self):
 
         return txt
 
-    def cleanup_step(self):
-        """Copy stuff from build directory we still need, if any."""
-
-        try:
-            exs_dir = os.path.join(self.cfg['start_dir'], 'examples')
-
-            self.examples_dir = os.path.join(tempfile.mkdtemp(), 'examples')
-
-            shutil.copytree(exs_dir, self.examples_dir)
-
-            self.log.info("Copied %s to %s." % (exs_dir, self.examples_dir))
-
-        except OSError as err:
-            raise EasyBuildError("Failed to copy examples: %s", err)
-
-        super(EB_NWChem, self).cleanup_step()
-
     def test_cases_step(self):
         """Run provided list of test cases, or provided examples is no test cases were specified."""
 
@@ -438,7 +424,7 @@ def test_cases_step(self):
                 ('md/benzene', ['benzene.nw'])
             ]
 
-            self.cfg['tests'] = [(os.path.join(self.examples_dir, d), l) for (d, l) in examples]
+            self.cfg['tests'] = [(os.path.join(self.installdir, 'examples', d), l) for (d, l) in examples]
             self.log.info("List of examples to be run as test cases: %s" % self.cfg['tests'])
 
         try:
@@ -452,7 +438,7 @@ def test_cases_step(self):
                 local_nwchemrc_dir = os.path.dirname(self.local_nwchemrc)
                 if not os.path.exists(local_nwchemrc_dir):
                     os.makedirs(local_nwchemrc_dir)
-                shutil.copy2(default_nwchemrc, self.local_nwchemrc)
+                copy_file(default_nwchemrc, self.local_nwchemrc)
 
                 # only try to create symlink if it's not there yet
                 # we've verified earlier that the symlink is what we expect it to be if it's there
@@ -483,11 +469,12 @@ def test_cases_step(self):
                     test_file = os.path.join(testdir, item)
                     if os.path.isfile(test_file):
                         self.log.debug("Copying %s to %s" % (test_file, tmpdir))
-                        shutil.copy2(test_file, tmpdir)
+                        copy_file(test_file, tmpdir)
 
                 # run tests
+                n_mpi_ranks = min(self.cfg['parallel'], 4)
                 for testx in tests:
-                    cmd = "nwchem %s" % testx
+                    cmd = '%s %s' % (self.toolchain.mpi_cmd_for('nwchem', n_mpi_ranks), testx)
                     msg = "Running test '%s' (from %s) in %s..." % (cmd, testdir, tmpdir)
                     self.log.info(msg)
                     test_cases_log.write("\n%s\n" % msg)
@@ -516,7 +503,7 @@ def test_cases_step(self):
 
                 # go back
                 change_dir(cwd)
-                shutil.rmtree(tmpdir)
+                remove_dir(tmpdir)
 
             fail_ratio = fail / tot
             fail_pcnt = fail_ratio * 100
@@ -534,8 +521,7 @@ def test_cases_step(self):
 
             # cleanup
             try:
-                shutil.rmtree(self.examples_dir)
-                shutil.rmtree(local_nwchemrc_dir)
+                remove_dir(local_nwchemrc_dir)
             except OSError as err:
                 raise EasyBuildError("Cleanup failed: %s", err)