Merge pull request #25 from molssi-seamm/dev

Updating for running from containers

HISTORY.rst

@@ -1,6 +1,9 @@
 =======
 History
 =======
+2024.1.11 -- Changes to allow running in containers.
+   * Moved to the new executor and ensured it still runs directly.
+   * Fixed bugs in printing the summary output.
 
 2023.8.23 -- Fix for installation of Psi4
    * Psi4 is now available on CondaForge, so install from there if requested.

devtools/conda-envs/test_env.yaml

@@ -11,7 +11,6 @@ dependencies:
   # Of the code
   - numpy
   - optking
-  - psutil
   - scipy
   - seamm
   - tabulate
@@ -29,5 +28,6 @@ dependencies:
 
   # Pip-only installs
   - pip:
-    # Documentation
-    - sphinx-copybutton
+      - seamm-exec
+      # Documentation
+      - sphinx-copybutton

psi4_step/data/references.bib

@@ -1,16 +1,16 @@
 @article{doi:10.1063/5.0006002,
-    author = {Smith,Daniel G. A.  and Burns,Lori A.  and Simmonett,Andrew C.  and
-              Parrish,Robert M.  and Schieber,Matthew C.  and Galvelis,Raimondas and
-              Kraus,Peter and Kruse,Holger and Di Remigio,Roberto and Alenaizan,Asem
-              and James,Andrew M.  and Lehtola,Susi and Misiewicz,Jonathon P.  and
-              Scheurer,Maximilian and Shaw,Robert A.  and Schriber,Jeffrey B.  and
-              Xie,Yi and Glick,Zachary L.  and Sirianni,Dominic A.  and
-              O’Brien,Joseph Senan and Waldrop,Jonathan M.  and Kumar,Ashutosh and
-              Hohenstein,Edward G.  and Pritchard,Benjamin P.  and Brooks,Bernard R.
-              and Schaefer,Henry F.  and Sokolov,Alexander Yu.  and Patkowski,Konrad
-              and DePrince,A. Eugene and Bozkaya,Uğur and King,Rollin A.  and
-              Evangelista,Francesco A.  and Turney,Justin M.  and Crawford,T. Daniel
-              and Sherrill,C. David },
+    author = {Smith, Daniel G. A. and Burns, Lori A. and Simmonett, Andrew C. and
+              Parrish, Robert M. and Schieber, Matthew C. and Galvelis, Raimondas and
+              Kraus, Peter and Kruse, Holger and Di Remigio, Roberto and Alenaizan, Asem and
+              James, Andrew M. and Lehtola, Susi and Misiewicz, Jonathon P. and
+              Scheurer, Maximilian and Shaw, Robert A. and Schriber, Jeffrey B. and
+              Xie, Yi and Glick, Zachary L. and Sirianni, Dominic A. and
+              O’Brien, Joseph Senan and Waldrop, Jonathan M. and Kumar, Ashutosh and
+              Hohenstein, Edward G. and Pritchard, Benjamin P. and Brooks, Bernard R. and
+              Schaefer, Henry F. and Sokolov, Alexander Yu. and Patkowski, Konrad and
+              DePrince, A. Eugene and Bozkaya, Uğur and King, Rollin A. and
+              Evangelista, Francesco A. and Turney, Justin M. and Crawford, T. Daniel and
+              Sherrill, C. David},
     title = {PSI4 1.4: Open-source software for high-throughput quantum chemistry},
     journal = {The Journal of Chemical Physics},
     volume = {152},
@@ -21,13 +21,13 @@ @article{doi:10.1063/5.0006002
     URL = {https://doi.org/10.1063/5.0006002},
     eprint = {https://doi.org/10.1063/5.0006002}
 }
-@Misc{packmol_step,
-	author = {Saxe, P.},
+@Misc{psi4_step,
+	author = {Paul Saxe},
 	title = {Psi4 plug-in for SEAMM},
-	month = {oct},
-	year = 2020,
+	month = {$month},
+	year = {$year},
 	organization = {Molecular Sciences Software Institute (MolSSI)},
 	url = {https://github.com/molssi-seamm/psi4_step},
 	address = {Blacksburg, VA, USA},
-	version = {2020.10.6}
+	version = {$version}
 }

psi4_step/energy.py

@@ -52,10 +52,15 @@ def git_revision(self):
         """The git version of this module."""
         return psi4_step.__git_revision__
 
-    def description_text(self, P=None, calculation_type="Single-point energy"):
+    def description_text(
+        self,
+        P=None,
+        calculation_type="Single-point energy",
+        configuration=None,
+    ):
         """Prepare information about what this node will do"""
 
-        if not P:
+        if P is not None:
             P = self.parameters.values_to_dict()
 
         if P["level"] == "recommended":
@@ -75,7 +80,8 @@ def description_text(self, P=None, calculation_type="Single-point energy"):
             text = f"{calculation_type} using {method} with an "
             text += f"exchange-correlation potential of {functional}"
             if (
-                len(psi4_step.dft_functionals[functional]["dispersion"]) > 1
+                functional in psi4_step.dft_functionals
+                and len(psi4_step.dft_functionals[functional]["dispersion"]) > 1
                 and P["dispersion"] != "none"
             ):
                 text += f" with the {P['dispersion']} dispersion correction."
@@ -87,6 +93,17 @@ def description_text(self, P=None, calculation_type="Single-point energy"):
         # Spin
         if P["spin-restricted"] == "yes":
             text += " The spin will be restricted to a pure eigenstate."
+        elif P["spin-restricted"] == "default":
+            if configuration is not None:
+                if configuration.spin_multiplicity == 1:
+                    text += " The spin will be restricted to a pure eigenstate."
+                else:
+                    text += " The spin will not be restricted and may not be a "
+                    text += "proper eigenstate."
+            else:
+                text += " The spin will be restricted to a pure "
+                text += "eigenstate for singlet states. Otherwise it will not "
+                text += "be restricted and may not be a proper eigenstate."
         elif self.is_expr(P["spin-restricted"]):
             text += " Whether the spin will be restricted to a pure "
             text += "eigenstate will be determined by {P['spin-restricted']}"
@@ -95,11 +112,21 @@ def description_text(self, P=None, calculation_type="Single-point energy"):
             text += "proper eigenstate."
 
         # Plotting
-        if P["density"]:
-            if P["orbitals"]:
+        if isinstance(P["density"], str):
+            density = P["density"] != "no"
+        else:
+            density = P["density"]
+
+        if isinstance(P["orbitals"], str):
+            orbitals = P["orbitals"] != "no"
+        else:
+            orbitals = P["orbitals"]
+
+        if density:
+            if orbitals:
                 text += "\nThe alpha and beta electron, total, and spin densities, "
                 text += f"and orbitals {P['selected orbitals']} will be plotted."
-        elif P["orbitals"]:
+        elif orbitals:
             text += f"\nThe orbitals {P['selected orbitals']} will be plotted."
 
         return self.header + "\n" + __(text, **P, indent=4 * " ").__str__()
@@ -122,7 +149,13 @@ def get_input(self, calculation_type="energy", restart=None):
                 PP[key] = "{:~P}".format(PP[key])
 
         self.description = []
-        self.description.append(__(self.description_text(PP), **PP, indent=self.indent))
+        self.description.append(
+            __(
+                self.description_text(PP, configuration=configuration),
+                **PP,
+                indent=self.indent,
+            )
+        )
 
         lines = []
         if calculation_type == "energy":

psi4_step/optimization.py

@@ -38,15 +38,22 @@ def __init__(
 
         self.description = "A geometry optimization"
 
-    def description_text(self, P=None):
+    def description_text(
+        self,
+        P=None,
+        calculation_type="Geometry optimization",
+        configuration=None,
+    ):
         """Prepare information about what this node will do"""
 
         if not P:
             P = self.parameters.values_to_dict()
 
-        text = super().description_text(P=P, calculation_type="Geometry optimization")
+        text = super().description_text(
+            P=P, calculation_type=calculation_type, configuration=configuration
+        )
 
-        added = "The geometry optimization will use the {optimization method} "
+        added = "\nThe geometry optimization will use the {optimization method} "
         if P["max geometry steps"] == "default":
             added += "method, using the default maximum number of steps, which"
             added += " is based on the system size."
@@ -89,7 +96,13 @@ def get_input(self, calculation_type="optimize"):
                 PP[key] = "{:~P}".format(PP[key])
 
         self.description = []
-        self.description.append(__(self.description_text(PP), **PP, indent=self.indent))
+        self.description.append(
+            __(
+                self.description_text(PP, configuration=configuration),
+                **PP,
+                indent=self.indent,
+            )
+        )
 
         lines = []
         lines.append("")

psi4_step/psi4.py

@@ -3,16 +3,15 @@
 """Non-graphical part of the Psi4 step in a SEAMM flowchart
 """
 
+import configparser
 import json
 import logging
 from pathlib import Path
 import pprint
 
-import psutil
-
 import psi4_step
 import seamm
-from seamm_util import ureg, Q_  # noqa: F401
+import seamm_exec
 import seamm_util.printing as printing
 from seamm_util.printing import FormattedText as __
 
@@ -236,13 +235,6 @@ def create_parser(self):
             return result
 
         # Options for Psi4
-        parser.add_argument(
-            parser_name,
-            "--psi4-path",
-            default="",
-            help="the path to the Psi4 executable",
-        )
-
         parser.add_argument(
             parser_name,
             "--ncores",
@@ -324,7 +316,7 @@ def run(self):
         printer.important(self.header)
         printer.important("")
 
-        # Add the main citation for DFTB+
+        # Add the main citation for Psi4
         self.references.cite(
             raw=self._bibliography["doi:10.1063/5.0006002"],
             alias="psi4",
@@ -344,41 +336,39 @@ def run(self):
         options = self.options
         seamm_options = self.global_options
 
-        # How many processors does this node have?
-        n_cores = psutil.cpu_count(logical=False)
-        self.logger.info("The number of cores is {}".format(n_cores))
+        # Get the computational environment and set limits
+        ce = seamm_exec.computational_environment()
 
-        # How many threads to use
+        # Maximum number of threads
+        n_threads = ce["NTASKS"]
         if options["ncores"] == "available":
-            n_threads = n_cores
+            pass
         else:
             n_threads = int(options["ncores"])
-        if n_threads > n_cores:
-            n_threads = n_cores
-        if n_threads < 1:
-            n_threads = 1
+            if n_threads < 1:
+                n_threads = 1
         if seamm_options["ncores"] != "available":
-            n_threads = min(n_threads, int(options["ncores"]))
-        self.logger.info(f"Psi4 will use {n_threads} threads.")
-
-        # How much memory to use
-        svmem = psutil.virtual_memory()
+            tmp = int(seamm_options["ncores"])
+            if tmp < n_threads:
+                n_threads = tmp
+        ce["NTASKS"] = n_threads
 
+        # And memory
         if seamm_options["memory"] == "all":
-            mem_limit = svmem.total
+            mem_limit = ce["MEM_PER_NODE"]
         elif seamm_options["memory"] == "available":
             # For the default, 'available', use in proportion to number of
             # cores used
-            mem_limit = svmem.total * (n_threads / n_cores)
+            mem_limit = n_threads * ce["MEM_PER_CPU"]
         else:
             mem_limit = dehumanize(seamm_options["memory"])
 
         if options["memory"] == "all":
-            memory = svmem.total
+            memory = ce["MEM_PER_NODE"]
         elif options["memory"] == "available":
             # For the default, 'available', use in proportion to number of
             # cores used
-            memory = svmem.total * (n_threads / n_cores)
+            memory = n_threads * ce["MEM_PER_CPU"]
         else:
             memory = dehumanize(options["memory"])
 
@@ -395,12 +385,9 @@ def run(self):
         min_memory = dehumanize("250 MiB")
         if min_memory > memory:
             memory = min_memory
+        ce["MEM_PER_NODE"] = memory
         memory = humanize(memory, kilo=1024)
 
-        printer.important(
-            self.indent + f"    Psi4 will use {n_threads} threads and {memory} memory\n"
-        )
-
         # Work through the subflowchart to find out what to do.
         self.subflowchart.root_directory = self.flowchart.root_directory
 
@@ -409,15 +396,6 @@ def run(self):
         # Get the first real node
         node0 = self.subflowchart.get_node("1").next()
 
-        # See if this is a normal or special run
-        # node = node0
-        # while node is not None:
-        #     if isinstance(node, psi4_step.AcceleratedOptimization):
-        #         node.run(node0, memory, n_threads)
-        #         return next_node
-
-        #     node = node.next()
-
         # Start the input data
         input_data = []
         input_data.append("import json")
@@ -474,24 +452,37 @@ def run(self):
             result["stderr"] = ""
             failed = False
         else:
-            exe_path = Path(options["psi4_path"])
-            env = {
-                "PSIPATH": str(exe_path),
-                "PATH": str(exe_path),
-            }
-
-            local = seamm.ExecLocal()
-            exe = exe_path / "psi4"
-            result = local.run(
-                cmd=[str(exe), f"-n {n_threads}"],
+            executor = self.flowchart.executor
+
+            # Read configuration file for Psi4
+            ini_dir = Path(seamm_options["root"]).expanduser()
+            full_config = configparser.ConfigParser()
+            full_config.read(ini_dir / "psi4.ini")
+            executor_type = executor.name
+            if executor_type not in full_config:
+                raise RuntimeError(
+                    f"No section for '{executor_type}' in Psi4 ini file "
+                    f"({ini_dir / 'psi4.ini'})"
+                )
+            config = dict(full_config.items(executor_type))
+
+            printer.important(
+                self.indent
+                + f"    Psi4 will use {ce['NTASKS']} threads and {memory} memory\n"
+            )
+
+            result = executor.run(
+                cmd=["{code}"],
+                config=config,
+                directory=self.directory,
                 files=files,
                 return_files=return_files,
-                env=env,
-                directory=directory,
                 in_situ=True,
-            )  # yapf: disable
+                shell=True,
+                ce=ce,
+            )
 
-            if result is None:
+            if not result:
                 self.logger.error("There was an error running Psi4")
                 raise RuntimeError("There was an error running Psi4")