Merge branch 'main' into 632-receiving-keyerror-3-during-arc-restart

arc/job/adapter.py

@@ -764,7 +764,7 @@ def set_cpu_and_mem(self):
             self.submit_script_memory = math.ceil(total_submit_script_memory)  # in MB
         if cluster_software in ['pbs']:
             # In PBS, "#PBS -l select=1:ncpus=8:mem=12000000" specifies the memory for all cores to be 12 MB.
-            self.submit_script_memory = math.ceil(total_submit_script_memory) * 1E6  # in Bytes
+            self.submit_script_memory = math.ceil(total_submit_script_memory) * 1E8  # in Bytes
         elif cluster_software in ['slurm']:
             # In Slurm, "#SBATCH --mem-per-cpu=2000" specifies the memory **per cpu/thread** to be 2000 MB.
             self.submit_script_memory = math.ceil(total_submit_script_memory / self.cpu_cores)  # in MB

arc/job/adapter_test.py

@@ -334,7 +334,7 @@ def test_set_cpu_and_mem(self):
         self.job_4.server = 'server3'
         self.job_4.cpu_cores = None
         self.job_4.set_cpu_and_mem()
-        expected_memory = math.ceil(14 * 1024 * 1.1) * 1E6
+        expected_memory = math.ceil(14 * 1024 * 1.1) * 1E8
         self.assertEqual(self.job_4.submit_script_memory, expected_memory)
         self.job_4.server = 'local'
 

arc/job/adapters/molpro.py

@@ -320,8 +320,13 @@ def set_input_file_memory(self) -> None:
         Set the input_file_memory attribute.
         """
         # Molpro's memory is per cpu core and in MW (mega word; 1 MW ~= 8 MB; 1 GB = 128 MW)
-        self.input_file_memory = math.ceil(self.job_memory_gb * 128 / self.cpu_cores)
-
+        # https://www.molpro.net/pipermail/molpro-user/2010-April/003723.html
+        # In the link, they describe the conversion of 100,000,000 Words (100Mword) is equivalent to
+        # 800,000,000 bytes (800 mb). 
+        # Formula - (100,000,000 [Words]/( 800,000,000 [Bytes] / (job mem in gb * 1000,000,000 [Bytes])))/ 1000,000 [Words -> MegaWords] 
+        # The division by 1E6 is for converting into MWords
+        self.input_file_memory = math.ceil((1E8/(8E8 /(self.job_memory_gb * 1E9)))/1E6)
+
     def execute_incore(self):
         """
         Execute a job incore.

arc/job/adapters/molpro_test.py

@@ -40,13 +40,13 @@ def test_set_cpu_and_mem(self):
         """Test assigning number of cpu's and memory"""
         self.job_1.cpu_cores = 48
         self.job_1.input_file_memory = None
-        self.job_1.submit_script_memory = None
+        self.job_1.submit_script_memory = 14
         self.job_1.set_cpu_and_mem()
         self.assertEqual(self.job_1.cpu_cores, 48)
 
     def test_set_input_file_memory(self):
         """Test setting the input_file_memory argument"""
-        expected_memory = math.ceil(14 * 128 / 48)
+        expected_memory = math.ceil((1E8/(8E8 /(14 * 1E9)))/1E6)
         self.assertEqual(self.job_1.input_file_memory, expected_memory)
 
     def test_write_input_file(self):
@@ -55,7 +55,7 @@ def test_write_input_file(self):
         with open(os.path.join(self.job_1.local_path, input_filenames[self.job_1.job_adapter]), 'r') as f:
             content_1 = f.read()
         job_1_expected_input_file = """***,spc1
-memory,38,m;
+memory,1750,m;
 file,1,file1.int    !allocate permanent integral file
 file,2,file2.wfu    !allocate permanent wave-function (dump) file
 

arc/job/trsh.py

@@ -8,6 +8,7 @@
 
 import numpy as np
 import pandas as pd
+import re
 
 from arc.common import (check_torsion_change,
                         determine_ess,
@@ -362,7 +363,12 @@ def determine_ess_status(output_path: str,
                     # e.g.: `A further 246.03 Mwords of memory are needed for the triples to run.
                     # Increase memory to 996.31 Mwords.` (w/o the line break)
                     keywords = ['Memory']
-                    error = f'Additional memory required: {line.split()[2]} MW'
+                    for line0 in reverse_lines:
+                        if ' For full I/O' in line0 and 'increase memory by' in line0 and 'Mwords to' in line0:
+                            memory_increase = re.findall(r"[\d.]+", line0)[0]
+                            error = f"Additional memory required: {memory_increase} MW"
+                            break
+                    error = f'Additional memory required: {line.split()[2]} MW' if 'error' not in locals() else error
                     break
                 elif 'insufficient memory available - require' in line:
                     # e.g.: `insufficient memory available - require              228765625  have

arc/job/trsh_test.py

@@ -344,6 +344,19 @@ def test_trsh_ess_job(self):
                                                                        num_heavy_atoms, cpu_cores, ess_trsh_methods)
         self.assertIn('memory', ess_trsh_methods)
         self.assertEqual(memory, 96.0)
+
+        # Molpro: Insuffienct Memory 3 Test
+        path = os.path.join(self.base_path['molpro'], 'insufficient_memory_3.out')
+        status, keywords, error, line = trsh.determine_ess_status(output_path=path,
+                                                                  species_label='TS',
+                                                                  job_type='sp')
+        job_status = {'keywords': keywords, 'error': error}
+        output_errors, ess_trsh_methods, remove_checkfile, level_of_theory, software, job_type, fine, trsh_keyword, \
+            memory, shift, cpu_cores, couldnt_trsh = trsh.trsh_ess_job(label, level_of_theory, server, job_status,
+                                                                       job_type, software, fine, memory_gb,
+                                                                       num_heavy_atoms, cpu_cores, ess_trsh_methods)
+        self.assertIn('memory', ess_trsh_methods)
+        self.assertEqual(memory, 62.0)
 
         # Test Orca
         # Orca: test 1