Update pm-cpu and pm-gpu spack templates with latest modules

docs/users_guide/spack/build.md

@@ -116,7 +116,6 @@ spack_script = get_spack_script(
     config_file=machine_config,
     include_e3sm_lapack=include_e3sm_lapack,
     include_e3sm_hdf5_netcdf=e3sm_hdf5_netcdf,
-    yaml_template=yaml_template
 )
 ```
 
@@ -161,7 +160,6 @@ mpicc, mpicxx, mpifc, mod_env_commands = get_modules_env_vars_and_mpi_compilers(
     shell='sh',  # or 'csh'
     include_e3sm_lapack=include_e3sm_lapack,
     include_e3sm_hdf5_netcdf=e3sm_hdf5_netcdf,
-    yaml_template=yaml_template
 )
 ```
 

mache/cime_machine_config/config_machines.xml

@@ -219,35 +219,35 @@
 
       <modules compiler="gnu">
         <command name="load">PrgEnv-gnu/8.5.0</command>
-        <command name="load">gcc-native/12.3</command>
-        <command name="load">cray-libsci/23.12.5</command>
+        <command name="load">gcc-native/13.2</command>
+        <command name="load">cray-libsci/24.07.0</command>
       </modules>
 
       <modules compiler="intel">
         <command name="load">PrgEnv-intel/8.5.0</command>
-        <command name="load">intel/2023.2.0</command>
+        <command name="load">intel/2024.1.0</command>
       </modules>
 
       <modules compiler="nvidia">
         <command name="load">PrgEnv-nvidia</command>
-        <command name="load">nvidia/24.5</command>
-        <command name="load">cray-libsci/23.12.5</command>
+        <command name="load">nvidia/25.5</command>
+        <command name="load">cray-libsci/24.07.0</command>
       </modules>
 
       <modules compiler="amdclang">
         <command name="load">PrgEnv-aocc</command>
         <command name="load">aocc/4.1.0</command>
-        <command name="load">cray-libsci/23.12.5</command>
+        <command name="load">cray-libsci/24.07.0</command>
       </modules>
 
       <modules>
         <command name="load">craype-accel-host</command>
-        <command name="load">craype/2.7.30</command>
-        <command name="load">cray-mpich/8.1.28</command>
+        <command name="load">craype/2.7.32</command>
+        <command name="load">cray-mpich/8.1.30</command>
         <command name="load">cray-hdf5-parallel/1.12.2.9</command>
         <command name="load">cray-netcdf-hdf5parallel/4.9.0.9</command>
-        <command name="load">cray-parallel-netcdf/1.12.3.9</command>
-        <command name="load">cmake/3.24.3</command>
+        <command name="load">cray-parallel-netcdf/1.12.3.13</command>
+        <command name="load">cmake/3.30.2</command>
       </modules>
     </module_system>
 
@@ -406,23 +406,23 @@
 
       <modules compiler="gnu.*">
         <command name="load">PrgEnv-gnu/8.5.0</command>
-        <command name="load">gcc-native/12.3</command>
+        <command name="load">gcc-native/13.2</command>
       </modules>
 
       <modules compiler="nvidia.*">
         <command name="load">PrgEnv-nvidia</command>
-        <command name="load">nvidia/24.5</command>
+        <command name="load">nvidia/25.5</command>
       </modules>
 
       <modules compiler="gnugpu">
-        <command name="load">cudatoolkit/12.4</command>
+        <command name="load">cudatoolkit/12.9</command>
         <command name="load">craype-accel-nvidia80</command>
       </modules>
 
       <modules compiler="nvidiagpu">
-        <command name="load">cudatoolkit/12.4</command>
+        <command name="load">cudatoolkit/12.9</command>
         <command name="load">craype-accel-nvidia80</command>
-        <command name="load">gcc-native-mixed/12.3</command>
+        <command name="load">gcc-native-mixed/13.2</command>
       </modules>
 
       <modules compiler="gnu">
@@ -434,13 +434,13 @@
       </modules>
 
       <modules>
-        <command name="load">cray-libsci/23.12.5</command>
-        <command name="load">craype/2.7.30</command>
-        <command name="load">cray-mpich/8.1.28</command>
-        <command name="load">cray-hdf5-parallel/1.12.2.9</command>
-        <command name="load">cray-netcdf-hdf5parallel/4.9.0.9</command>
-        <command name="load">cray-parallel-netcdf/1.12.3.9</command>
-        <command name="load">cmake/3.24.3</command>
+        <command name="load">cray-libsci/24.07.0</command>
+        <command name="load">craype/2.7.32</command>
+        <command name="load">cray-mpich/8.1.30</command>
+        <command name="load">cray-hdf5-parallel/1.14.3.1</command>
+        <command name="load">cray-netcdf-hdf5parallel/4.9.0.13</command>
+        <command name="load">cray-parallel-netcdf/1.12.3.13</command>
+        <command name="load">cmake/3.30.2</command>
       </modules>
     </module_system>
 

mache/machines/anvil.cfg

@@ -63,18 +63,6 @@ partitions = acme-small, acme-medium, acme-large
 qos = regular, acme_high
 
 
-# Config options related to spack environments
-[spack]
-
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = False
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = False
-
-
 # config options related to synchronizing files
 [sync]
 

mache/machines/aurora.cfg

@@ -49,18 +49,6 @@ account = E3SM_Dec
 # queues (default is the first)
 queues = prod, debug
 
-# Config options related to spack environments
-[spack]
-
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = False
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = False
-
-
 # config options related to synchronizing files
 [sync]
 

mache/machines/chicoma-cpu.cfg

@@ -40,18 +40,6 @@ partitions = standard, gpu
 qos = standard, debug
 
 
-# Config options related to spack environments
-[spack]
-
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = False
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = False
-
-
 # config options related to synchronizing files
 [sync]
 

mache/machines/chrysalis.cfg

@@ -56,19 +56,6 @@ cores_per_node = 128
 # available partition(s) (default is the first)
 partitions = compute, debug, Shigh
 
-
-# Config options related to spack environments
-[spack]
-
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = False
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = True
-
-
 # config options related to synchronizing files
 [sync]
 

mache/machines/compy.cfg

@@ -63,18 +63,6 @@ partitions = slurm
 qos = regular
 
 
-# Config options related to spack environments
-[spack]
-
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = True
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = False
-
-
 # config options related to synchronizing files
 [sync]
 

mache/machines/dane.cfg

@@ -53,18 +53,6 @@ cores_per_node = 112
 partitions = pbatch, pdebug
 
 
-# Config options related to spack environments
-[spack]
-
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = True
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = False
-
-
 # config options related to synchronizing files
 [sync]
 

mache/machines/frontier.cfg

@@ -56,14 +56,6 @@ partitions = batch
 # Config options related to spack environments
 [spack]
 
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = False
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = False
-
 # whether the machine uses cray compilers
 cray_compilers = True
 

mache/machines/pm-cpu.cfg

@@ -62,17 +62,10 @@ constraints = cpu
 # quality of service (default is the first)
 qos = regular, debug, premium
 
+
 # Config options related to spack environments
 [spack]
 
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = False
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = False
-
 # whether the machine uses cray compilers
 cray_compilers = True
 

mache/machines/pm-gpu.cfg

@@ -65,17 +65,10 @@ constraints = gpu
 # quality of service (default is the first)
 qos = regular, debug, premium
 
+
 # Config options related to spack environments
 [spack]
 
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = False
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = False
-
 # whether the machine uses cray compilers
 cray_compilers = True
 

mache/machines/ruby.cfg

@@ -53,18 +53,6 @@ cores_per_node = 56
 partitions = pbatch, pdebug
 
 
-# Config options related to spack environments
-[spack]
-
-# whether to load modules from the spack yaml file before loading the spack
-# environment
-modules_before = True
-
-# whether to load modules from the spack yaml file after loading the spack
-# environment
-modules_after = False
-
-
 # config options related to synchronizing files
 [sync]
 

mache/spack/config_machines.py

@@ -1,5 +1,6 @@
 import re
 from collections import defaultdict
+from importlib import resources as importlib_resources
 
 from lxml import etree
 
@@ -104,13 +105,13 @@ def config_to_shell_script(config, shell_type):
     script_lines.append('')
 
     if e3sm_hdf5_netcdf_modules:
-        script_lines.append('{% if e3sm_hdf5_netcdf %}')
+        script_lines.append('{%- if e3sm_hdf5_netcdf %}')
         script_lines.extend(
             _convert_module_commands_to_script_lines(
                 e3sm_hdf5_netcdf_modules, shell_type
             )
         )
-        script_lines.append('{% endif %}')
+        script_lines.append('{%- endif %}')
         script_lines.append('')
 
     script_lines.extend(_convert_env_vars_to_script_lines(config, shell_type))
@@ -121,7 +122,7 @@ def config_to_shell_script(config, shell_type):
 
 
 def extract_spack_from_config_machines(
-    machine, compiler, mpilib, shell, output
+    machine, compiler, mpilib, shell, output=None
 ):
     """
     Extract machine configuration from XML and write it to a shell script.
@@ -136,10 +137,18 @@ def extract_spack_from_config_machines(
         MPI library name.
     shell : str
         Shell script type ('sh' or 'csh').
-    output : str
+    output : str, optional
         Output file to write the shell script.
+
+    Returns
+    -------
+    script: str
+        The generated shell script as a string.
     """
-    config_filename = 'mache/cime_machine_config/config_machines.xml'
+    config_filename = (
+        importlib_resources.files('mache.cime_machine_config')
+        / 'config_machines.xml'
+    )
 
     config = extract_machine_config(config_filename, machine, compiler, mpilib)
     if config is None:
@@ -149,8 +158,11 @@ def extract_spack_from_config_machines(
         )
 
     script = config_to_shell_script(config, shell)
-    with open(output, 'w') as f:
-        f.write(script)
+    if output is not None:
+        with open(output, 'w') as f:
+            f.write(script)
+
+    return script
 
 
 def _convert_module_commands_to_script_lines(module_commands, shell_type):
@@ -249,12 +261,12 @@ def _convert_env_vars_to_script_lines(config, shell_type):
     script_lines.append('')
 
     if e3sm_hdf5_netcdf_env_vars:
-        script_lines.append('{% if e3sm_hdf5_netcdf %}')
+        script_lines.append('{%- if e3sm_hdf5_netcdf %}')
         for name, value in e3sm_hdf5_netcdf_env_vars:
             if shell_type == 'sh':
                 script_lines.append(f'export {name}="{value}"')
             elif shell_type == 'csh':
                 script_lines.append(f'setenv {name} "{value}"')
-        script_lines.append('{% endif %}')
+        script_lines.append('{%- endif %}')
 
     return script_lines