[GROMACS] Support PLUMED for versions 2025 and newer

easybuild/easyblocks/g/gromacs.py

@@ -76,6 +76,9 @@ def extra_options():
             '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],
+            'parallel_test': [None, "Number of tests to run in parallel. Can help with hanging tests caused by " +
+                              "oversubscribed MPI processes. With None (default) the value of the parallel value " +
+                              "is used.", CUSTOM],
         })
         return extra_vars
 
@@ -155,6 +158,73 @@ def is_double_precision_cuda_build(self):
         cuda = get_software_root('CUDA')
         return cuda and self.double_prec_pattern in self.cfg['configopts']
 
+    def is_using_plumed_kernel(self):
+        gromacs_version = LooseVersion(self.version)
+
+        return not gromacs_version < '2025'
+
+    def is_cmake_shared_lib_plumed_patch_supported(self):
+        gromacs_version = LooseVersion(self.version)
+
+        return gromacs_version >= '5.1'
+
+    def configure_runtime_loading_of_plumed(self):
+        # Since 2025.0 GROMACS can use a subset of PLUMED interface by loading the PLUMED kernel library at runtime
+
+        # 1. Enable building with the nativelly supported PLUMED functions:
+        # https://manual.gromacs.org/documentation/2025.0/install-guide/index.html#building-with-plumed-support
+        self.cfg.update('configopts', "-DGMX_USE_PLUMED=ON")
+
+        # 2. Set the location of the runtime loaded PLUMED library:
+        # https://manual.gromacs.org/documentation/2025.0/reference-manual/special/plumed.html
+        self.cfg.update('modextrapaths', {
+            'PLUMED_KERNEL': {
+                'paths': '$EBROOTPLUMED/lib/libplumedKernel.so',
+                'prepend': False
+            }
+        })
+
+    def check_plumed_version_supports_patching_gromacs_engine(self, engine):
+        res = run_shell_cmd("plumed-patch -l")
+        if not re.search(engine, res.output):
+            plumed_ver = get_software_version('PLUMED')
+            msg = "There is no support in PLUMED version %s for GROMACS %s: %s" % (plumed_ver, self.version,
+                                                                                   res.output)
+            if self.cfg['ignore_plumed_version_check']:
+                self.log.warning(msg)
+            else:
+                raise EasyBuildError(msg)
+
+    def set_plumed_cmd(self):
+        if self.is_using_plumed_kernel():
+            self.configure_runtime_loading_of_plumed()
+            return
+
+        engine = 'gromacs-%s' % self.version
+
+        self.check_plumed_version_supports_patching_gromacs_engine(engine)
+
+        # PLUMED patching must be done at different stages depending on
+        # version of GROMACS. Just prepare first part of cmd here
+        plumed_cmd = "plumed-patch -p -e %s" % engine
+
+        if self.is_cmake_shared_lib_plumed_patch_supported():
+            # Use shared or static patch depending on
+            # setting of self.cfg['build_shared_libs']
+            # and adapt cmake flags accordingly as per instructions
+            # from "plumed patch -i"
+            if self.cfg['build_shared_libs']:
+                mode = 'shared'
+            else:
+                mode = 'static'
+            plumed_cmd = plumed_cmd + ' -m %s' % mode
+
+        self.plumed_cmd = plumed_cmd
+
+    def run_plumed_cmd(self):
+        if self.plumed_cmd:
+            run_shell_cmd(self.plumed_cmd)
+
     def prepare_step(self, *args, **kwargs):
         """Custom prepare step for GROMACS."""
 
@@ -229,23 +299,7 @@ def configure_step(self):
 
         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
-
-            res = run_shell_cmd("plumed-patch -l")
-            if not re.search(engine, res.output):
-                plumed_ver = get_software_version('PLUMED')
-                msg = "There is no support in PLUMED version %s for GROMACS %s: %s" % (plumed_ver, self.version,
-                                                                                       res.output)
-                if self.cfg['ignore_plumed_version_check']:
-                    self.log.warning(msg)
-                else:
-                    raise EasyBuildError(msg)
-
-            # PLUMED patching must be done at different stages depending on
-            # version of GROMACS. Just prepare first part of cmd here
-            plumed_cmd = "plumed-patch -p -e %s" % engine
+            self.set_plumed_cmd()
 
         # Ensure that the GROMACS log files report how the code was patched
         # during the build, so that any problems are easier to diagnose.
@@ -294,7 +348,7 @@ def configure_step(self):
 
             # Now patch GROMACS for PLUMED between configure and build
             if plumed_root:
-                run_shell_cmd(plumed_cmd)
+                self.run_plumed_cmd()
 
         else:
             if '-DGMX_MPI=ON' in self.cfg['configopts']:
@@ -354,18 +408,7 @@ def configure_step(self):
 
             # Now patch GROMACS for PLUMED before cmake
             if plumed_root:
-                if gromacs_version >= '5.1':
-                    # Use shared or static patch depending on
-                    # setting of self.cfg['build_shared_libs']
-                    # and adapt cmake flags accordingly as per instructions
-                    # from "plumed patch -i"
-                    if self.cfg['build_shared_libs']:
-                        mode = 'shared'
-                    else:
-                        mode = 'static'
-                    plumed_cmd = plumed_cmd + ' -m %s' % mode
-
-                run_shell_cmd(plumed_cmd)
+                self.run_plumed_cmd()
 
             # prefer static libraries, if available
             if self.cfg['build_shared_libs']:
@@ -524,7 +567,10 @@ def test_step(self):
 
                 # run 'make check' or whatever the easyconfig specifies
                 # in parallel since it involves more compilation
-                self.cfg.update('runtest', f"-j {self.cfg.parallel}")
+                if self.parallel_test:
+                    self.cfg.update('runtest', f"-j {self.parallel_test}")
+                else:
+                    self.cfg.update('runtest', f"-j {self.cfg.parallel}")
                 super().test_step()
 
                 if build_option('rpath'):