Merge branch 'dev'

mesaport/Access/gyre_access.py

@@ -5,6 +5,9 @@
 from . import access_helper
 from .support.utils import cwd
 
+from threading import Lock
+file_operation_lock = Lock()
+
 """
 This module defines the `GyreAccess` class, which handles GYRE input file operations.
 
@@ -20,19 +23,15 @@
 """
 
 class GyreAccess:
-    def __init__(self, path, binary=False, target=''):
+    def __init__(self):
         """
         Args:
             path (str): The path to the GYRE input file.
             binary (str): The name of the binary file to be used.
             target (str): The target to be used.
         """
         self.check_env()
-        self.path = path
-        self.binary = binary
-        self.target = target
-        self.projectDir = os.path.abspath(path)
-        self.gyre_in = None
+        self.default_sections = self.gyreDefaults()
 
     def check_env(self):
         """
@@ -89,35 +88,36 @@ def writetoGyreFile(self, wdir, parameter, value, default_section=None, gyre_in=
             sections (list): A list with the sections of the inlist file.
         """   
         if default_section is None:
-            for section, values in self.gyreDefaults().items():
+            for section, values in self.default_sections.items():
                 if parameter in values:
                     default_section = section
             if default_section is None:
                 raise(f"Parameter {parameter} not found in any GYRE input files.")
         this_section = False
         with cwd(wdir):
-            with open(gyre_in, "r") as file:
-                lines = file.readlines()
-            with open(gyre_in, "w+") as f:
-                indent = "    "
-                for line in lines:
-                    edited = False
-                    if default_section in line:
-                        this_section = True
-                    if this_section:
-                        if parameter in line:
-                            if parameter == line.split("=")[0].strip():
-                                f.write(line.replace(line.split("=")[1], f" {value}    ! Changed\n"))
+            with file_operation_lock:
+                with open(gyre_in, "r") as file:
+                    lines = file.readlines()
+                with open(gyre_in, "w+") as f:
+                    indent = "    "
+                    for line in lines:
+                        edited = False
+                        if default_section in line:
+                            this_section = True
+                        if this_section:
+                            if parameter in line:
+                                if parameter == line.split("=")[0].strip():
+                                    f.write(line.replace(line.split("=")[1], f" {value}    ! Changed\n"))
+                                    edited = True
+                                    this_section = False
+                            elif line[0] == "/":
+                                f.write(indent)
+                                f.write(f"{parameter} = {value}    ! Added\n")
+                                f.write("/")
                                 edited = True
                                 this_section = False
-                        elif line[0] == "/":
-                            f.write(indent)
-                            f.write(f"{parameter} = {value}    ! Added\n")
-                            f.write("/")
-                            edited = True
-                            this_section = False
-                    if not edited:
-                        f.write(line)
+                        if not edited:
+                            f.write(line)
 
 
 
@@ -135,19 +135,19 @@ def modify_gyre_params(self, wdir, filename, data_format, gyre_in="gyre.in", dif
         self.writetoGyreFile(wdir, parameter="summary_file", value=f"'{filename.split('.')[0]}-freqs-nad.dat'", default_section="&nad_output", gyre_in=gyre_in)
 
 
-    def set(self, arg, gyre_in="gyre.in"):
+    def set(self, arg, wdir, gyre_in="gyre.in"):
         """Sets the value of a parameter in the inlist file.
 
         Args:
             arg (dict or list of dicts): A dictionary or a list of dictionaries with the parameters to be set.
         """    
         if isinstance(arg, dict):
             for key, value in arg.items():
-                self.writetoGyreFile(self.projectDir, key, access_helper.toFortranType(value), gyre_in=gyre_in)
+                self.writetoGyreFile(wdir, key, access_helper.toFortranType(value), gyre_in=gyre_in)
         elif isinstance(arg, list):
             for item in arg:
                 for key, value in item.items():
-                    self.writetoGyreFile(self.projectDir, key, access_helper.toFortranType(value), gyre_in=gyre_in)
+                    self.writetoGyreFile(wdir, key, access_helper.toFortranType(value), gyre_in=gyre_in)
         elif arg is None:
             pass
         else:

mesaport/ProjectOps/ops_helper.py

@@ -1,6 +1,7 @@
 import subprocess
 import shlex
-import sys, os, glob
+import sys, os, glob, time
+import numpy as np
 import shutil
 from rich import print
 
@@ -38,16 +39,26 @@ def run_subprocess(commands, wdir, silent=True, runlog='', status=None,
                 Pass os.environ.copy() to use the current environment. Or pass a dictionary with the environment variables to be used.
     """   
     if gyre_in is not None:
-        gyre_obj = GyreAccess(wdir)
-        if not os.path.exists(os.join(wdir, "gyre.in")):
-            gyre_obj.load(gyre_in=gyre_in, dest=wdir)
+        gyre_obj = GyreAccess()
         if parallel:
             num = filename.split(".")[0]
-            shutil.copy(gyre_in, os.path.join(wdir, f"gyre{num}.in"))
-            gyre_in = os.path.join(wdir, f"gyre{num}.in")
+            new_gyre_in = os.path.join(wdir, f"gyre{num}.in")
+            gyre_obj.modify_gyre_params(wdir, filename, data_format, gyre_in=new_gyre_in)
+            gyre_obj.set(arg=gyre_input_params, wdir=wdir, gyre_in=new_gyre_in)
+            time.sleep(1)
+
+            # Update gyre_in to the new file
+            gyre_in = new_gyre_in
             commands = commands.replace("gyre.in", f"gyre{num}.in")
-        gyre_obj.modify_gyre_params(wdir, filename, data_format, gyre_in=gyre_in)
-        gyre_obj.set(gyre_input_params)
+            runlog = runlog.replace("gyre.log", f"gyre{num}.log")
+        else:
+            new_gyre_in = os.path.join(wdir, "gyre.in")
+            shutil.copyfile(gyre_in, new_gyre_in)
+            gyre_in = new_gyre_in
+            gyre_obj.modify_gyre_params(wdir, filename, data_format, gyre_in=gyre_in)
+            gyre_obj.set(arg=gyre_input_params, wdir=wdir, gyre_in=gyre_in)
+
+
 
     evo_terminated = False
     termination_code = None
@@ -100,12 +111,6 @@ def run_subprocess(commands, wdir, silent=True, runlog='', status=None,
                 sys.stdout.write(errline)
             logfile.write( "\n\n"+("*"*100)+"\n\n" )
         _data, error = proc.communicate()
-    if gyre_in is not None:
-        working_dir = wdir.replace("LOGS", "")
-        with open(f'{working_dir}/gyre.log', 'a+') as f:
-            f.write(f"Done with {filename}.\n")
-        if parallel:
-            os.remove(gyre_in)
     if proc.returncode or error:
         print('The process raised an error:', proc.returncode, error)
         return False
@@ -121,6 +126,11 @@ def run_subprocess(commands, wdir, silent=True, runlog='', status=None,
                         age = age_
             return termination_code, age
         else:
+            working_dir = wdir.replace("LOGS", "")
+            with open(f'{working_dir}/gyre.log', 'a+') as f:
+                f.write(f"Done with {filename}.\n")
+            if parallel:
+                os.remove(gyre_in)
             return True
 
 def process_outline(outline):

mesaport/ProjectOps/project_ops.py

@@ -372,6 +372,11 @@ def runGyre(self, gyre_in, files='all', wdir=None, data_format="GYRE", silent=Tr
             if parallel:
                 gyre_input_params = gyre_input_params if gyre_input_params is not None else repeat(None)
                 os.environ['HDF5_USE_FILE_LOCKING'] = 'FALSE'
+                ## copy gyre.in to gyre1.in, gyre2.in, etc. for parallel runs
+                for i, file in enumerate(files):
+                    num = file.split(".")[0]
+                    new_gyre_in = os.path.join(wdir, f"gyre{num}.in")
+                    shutil.copyfile(gyre_in, new_gyre_in)
                 # commands, wdir, 
                 # silent=True, runlog='', 
                 # status=None, filename="", 
@@ -381,7 +386,7 @@ def runGyre(self, gyre_in, files='all', wdir=None, data_format="GYRE", silent=Tr
                         repeat(silent), repeat(runlog),
                         repeat(None), files, repeat(data_format),
                         repeat(True), repeat(gyre_in),
-                        gyre_input_params, repeat(None), repeat(env))
+                        gyre_input_params, repeat(None), repeat(os.environ.copy()))
                 if n_cores is None:
                     n_cores = psutil.cpu_count(logical=True) 
                     Pool = mp.Pool
@@ -401,7 +406,21 @@ def runGyre(self, gyre_in, files='all', wdir=None, data_format="GYRE", silent=Tr
                             executor.map(ops_helper.run_subprocess, *args)
 
                     except Exception as e:
+                        filenames = glob.glob(os.path.join(LOGS_dir, f"gyre*.log"))
+                        with open(runlog, 'a+') as outfile:
+                            for fname in filenames:
+                                with open(fname) as infile:
+                                    for line in infile:
+                                        outfile.write(line)
+                                os.remove(fname)
                         raise e
+                filenames = glob.glob(os.path.join(LOGS_dir, f"gyre*.log"))
+                with open(runlog, 'a+') as outfile:
+                    for fname in filenames:
+                        with open(fname) as infile:
+                            for line in infile:
+                                outfile.write(line)
+                        os.remove(fname)
                 res = True
             else:
                 for i, file in enumerate(files):