diff --git a/bin/stack-config b/bin/stack-config
index 66496991..63c82bcc 100755
--- a/bin/stack-config
+++ b/bin/stack-config
@@ -4,7 +4,7 @@
 # dependencies = [
 #   "jinja2",
 #   "jsonschema",
-#   "pyYAML",
+#   "ruamel.yaml >=0.15.1"
 # ]
 # ///
 
diff --git a/pyproject.toml b/pyproject.toml
index 583f5d46..4a24915b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ requires-python = ">=3.12"
 dependencies = [
   "Jinja2",
   "jsonschema",
-  "PyYAML",
+  "ruamel.yaml >=0.15.1",
 ]
 classifiers = [
   "Development Status :: 5 - Production/Stable",
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000..79d70ed3
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,4 @@
+Jinja2
+jsonschema
+pytest
+ruamel.yaml >=0.15.1
diff --git a/stackinator/builder.py b/stackinator/builder.py
index ae4997a1..243c7391 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -9,10 +9,12 @@
 from datetime import datetime
 
 import jinja2
-import yaml
+from ruamel.yaml import YAML
 
 from . import VERSION, cache, root_logger, spack_util
 
+yaml = YAML()
+
 
 def install(src, dst, *, ignore=None, symlinks=False):
     """Call shutil.copytree or shutil.copy2. copy2 is used if `src` is not a directory.
@@ -139,7 +141,7 @@ def environment_meta(self, recipe):
               "root": /user-environment/env/default,
               "activate": /user-environment/env/default/activate.sh,
               "description": "simple devolpment env: compilers, MPI, python, cmake."
-              "env_vars": {
+              "recipe_variables": {
                 ...
               }
             },
@@ -307,17 +309,17 @@ def generate(self, recipe):
         # the packages.yaml configuration that will be used when building all environments
         # - the system packages.yaml with gcc removed
         # - plus additional packages provided by the recipe
-        global_packages_yaml = yaml.dump(recipe.packages["global"])
+
         global_packages_path = config_path / "packages.yaml"
         with global_packages_path.open("w") as fid:
-            fid.write(global_packages_yaml)
+            yaml.dump(recipe.packages["global"], fid)
 
         # generate a mirrors.yaml file if build caches have been configured
         if recipe.mirror:
             dst = config_path / "mirrors.yaml"
             self._logger.debug(f"generate the build cache mirror: {dst}")
             with dst.open("w") as fid:
-                fid.write(cache.generate_mirrors_yaml(recipe.mirror))
+                cache.generate_mirrors_yaml(recipe.mirror, fid)
 
         # Add custom spack package recipes, configured via Spack repos.
         # Step 1: copy Spack repos to store_path where they will be used to
@@ -346,7 +348,7 @@ def generate(self, recipe):
         if repo_yaml.exists() and repo_yaml.is_file():
             # open repos.yaml file and reat the list of repos
             with repo_yaml.open() as fid:
-                raw = yaml.load(fid, Loader=yaml.Loader)
+                raw = yaml.load(fid)
                 P = raw["repos"]
 
             self._logger.debug(f"the system configuration has a repo file {repo_yaml} refers to {P}")
@@ -438,7 +440,10 @@ def generate(self, recipe):
             compiler_config_path.mkdir(exist_ok=True)
             for file, raw in files.items():
                 with (compiler_config_path / file).open(mode="w") as f:
-                    f.write(raw)
+                    if type(raw) is str:
+                        f.write(raw)
+                    else:
+                        yaml.dump(raw, f)
 
         # generate the makefile and spack.yaml files that describe the environments
         environment_files = recipe.environment_files
@@ -477,7 +482,7 @@ def generate(self, recipe):
             generate_modules_path = self.path / "modules"
             generate_modules_path.mkdir(exist_ok=True)
             with (generate_modules_path / "modules.yaml").open("w") as f:
-                yaml.dump(recipe.modules, f)
+                yaml.dump(recipe.modules_yaml_data, f)
 
         # write the meta data
         meta_path = store_path / "meta"
diff --git a/stackinator/cache.py b/stackinator/cache.py
index 24177e33..2adb80ac 100644
--- a/stackinator/cache.py
+++ b/stackinator/cache.py
@@ -1,15 +1,17 @@
 import os
 import pathlib
 
-import yaml
+from ruamel.yaml import YAML
 
 from . import schema
 
+yaml = YAML()
+
 
 def configuration_from_file(file, mount):
     with file.open() as fid:
         # load the raw yaml input
-        raw = yaml.load(fid, Loader=yaml.Loader)
+        raw = yaml.load(fid)
 
         # validate the yaml
         schema.CacheValidator.validate(raw)
@@ -40,7 +42,7 @@ def configuration_from_file(file, mount):
         return raw
 
 
-def generate_mirrors_yaml(config):
+def generate_mirrors_yaml(config, out):
     path = config["path"].as_posix()
     mirrors = {
         "mirrors": {
@@ -55,4 +57,6 @@ def generate_mirrors_yaml(config):
         }
     }
 
-    return yaml.dump(mirrors, default_flow_style=False)
+    yaml = YAML()
+    yaml.default_flow_style = True
+    yaml.dump(mirrors, out)
diff --git a/stackinator/etc/envvars.py b/stackinator/etc/envvars.py
index 0f122057..7c63b6c8 100755
--- a/stackinator/etc/envvars.py
+++ b/stackinator/etc/envvars.py
@@ -7,8 +7,6 @@
 from enum import Enum
 from typing import List, Optional
 
-import yaml
-
 
 class EnvVarOp(Enum):
     PREPEND = 1
@@ -504,12 +502,8 @@ def view_impl(args):
     envvars.remove_root(args.build_path)
 
     if args.compilers is not None:
-        if not os.path.isfile(args.compilers):
-            print(f"error - compiler yaml file {args.compilers} does not exist")
-            exit(1)
-
         with open(args.compilers, "r") as file:
-            data = yaml.safe_load(file)
+            data = json.load(file)
 
         compilers = []
         for p in data["packages"].values():
diff --git a/stackinator/recipe.py b/stackinator/recipe.py
index 7850d036..3f9450de 100644
--- a/stackinator/recipe.py
+++ b/stackinator/recipe.py
@@ -3,11 +3,13 @@
 import re
 
 import jinja2
-import yaml
+from ruamel.yaml import YAML
 
 from . import cache, root_logger, schema, spack_util
 from .etc.envvars import EnvVarSet
 
+yaml = YAML()
+
 
 class Recipe:
     @property
@@ -58,7 +60,7 @@ def __init__(self, args):
             raise FileNotFoundError(f"The recipe path '{compiler_path}' does not contain compilers.yaml")
 
         with compiler_path.open() as fid:
-            raw = yaml.load(fid, Loader=yaml.Loader)
+            raw = yaml.load(fid)
             schema.CompilersValidator.validate(raw)
             self.generate_compiler_specs(raw)
 
@@ -68,7 +70,7 @@ def __init__(self, args):
         self._logger.debug(f"opening {modules_path}")
         if modules_path.is_file():
             with modules_path.open() as fid:
-                self.modules = yaml.load(fid, Loader=yaml.Loader)
+                self.modules = yaml.load(fid)
                 schema.ModulesValidator.validate(self.modules)
 
                 # Note:
@@ -94,7 +96,7 @@ def __init__(self, args):
         recipe_packages_path = self.path / "packages.yaml"
         if recipe_packages_path.is_file():
             with recipe_packages_path.open() as fid:
-                raw = yaml.load(fid, Loader=yaml.Loader)
+                raw = yaml.load(fid)
                 recipe_packages = raw["packages"]
 
         # load system/packages.yaml -> system_packages (if it exists)
@@ -103,7 +105,7 @@ def __init__(self, args):
         if system_packages_path.is_file():
             # load system yaml
             with system_packages_path.open() as fid:
-                raw = yaml.load(fid, Loader=yaml.Loader)
+                raw = yaml.load(fid)
                 system_packages = raw["packages"]
 
         # extract gcc packages from system packages
@@ -123,7 +125,7 @@ def __init__(self, args):
         if network_path.is_file():
             self._logger.debug(f"opening {network_path}")
             with network_path.open() as fid:
-                raw = yaml.load(fid, Loader=yaml.Loader)
+                raw = yaml.load(fid)
                 if "packages" in raw:
                     network_packages = raw["packages"]
                 if "mpi" in raw:
@@ -146,7 +148,7 @@ def __init__(self, args):
             raise FileNotFoundError(f"The recipe path '{environments_path}' does not contain environments.yaml")
 
         with environments_path.open() as fid:
-            raw = yaml.load(fid, Loader=yaml.Loader)
+            raw = yaml.load(fid)
             # add a special environment that installs tools required later in the build process.
             # currently we only need squashfs for creating the squashfs file.
             raw["uenv_tools"] = {
@@ -280,7 +282,7 @@ def config(self, config_path):
             raise FileNotFoundError(f"The recipe path '{config_path}' does not contain config.yaml")
 
         with config_path.open() as fid:
-            raw = yaml.load(fid, Loader=yaml.Loader)
+            raw = yaml.load(fid)
             schema.ConfigValidator.validate(raw)
             self._config = raw
 
@@ -324,6 +326,13 @@ def environment_view_meta(self):
 
         return view_meta
 
+    @property
+    def modules_yaml_data(self):
+        with self.modules.open() as fid:
+            raw = yaml.load(fid)
+            raw["modules"]["default"]["roots"]["tcl"] = (pathlib.Path(self.mount) / "modules").as_posix()
+            return raw
+
     # creates the self.environments field that describes the full specifications
     # for all of the environments sets, grouped in environments, from the raw
     # environments.yaml input.
@@ -411,6 +420,7 @@ def generate_environment_specs(self, raw):
                 # ["uenv"]["env_vars"] = {"set": [], "unset": [], "prepend_path": [], "append_path": []}
                 if view_config is None:
                     view_config = {}
+
                 view_config.setdefault("link", "roots")
                 view_config.setdefault("uenv", {})
                 view_config["uenv"].setdefault("add_compilers", True)
@@ -525,7 +535,7 @@ def compiler_files(self):
             files["config"][compiler]["spack.yaml"] = spack_yaml_template.render(config=config)
             # compilers/gcc/packages.yaml
             if compiler == "gcc":
-                files["config"][compiler]["packages.yaml"] = yaml.dump(self.packages["gcc"])
+                files["config"][compiler]["packages.yaml"] = self.packages["gcc"]
 
         return files
 
diff --git a/stackinator/schema.py b/stackinator/schema.py
index 3a2a9842..60335ae7 100644
--- a/stackinator/schema.py
+++ b/stackinator/schema.py
@@ -3,7 +3,7 @@
 from textwrap import dedent
 
 import jsonschema
-import yaml
+from ruamel.yaml import YAML
 
 from . import root_logger
 
@@ -11,7 +11,12 @@
 
 
 def py2yaml(data, indent):
-    dump = yaml.dump(data)
+    yaml = YAML()
+    from io import StringIO
+
+    buffer = StringIO()
+    yaml.dump(data, buffer)
+    dump = buffer.getvalue()
     lines = [ln for ln in dump.split("\n") if ln != ""]
     res = ("\n" + " " * indent).join(lines)
     return res
diff --git a/stackinator/templates/Make.user b/stackinator/templates/Make.user
index cb8acb03..68c8f154 100644
--- a/stackinator/templates/Make.user
+++ b/stackinator/templates/Make.user
@@ -2,6 +2,8 @@
 
 # Copy this file to Make.user and set some variables.
 
+SHELL := bash
+
 # This is the root of the software stack directory.
 BUILD_ROOT := {{ build_path }}
 
diff --git a/stackinator/templates/Makefile.environments b/stackinator/templates/Makefile.environments
index 5a530232..01929d9c 100644
--- a/stackinator/templates/Makefile.environments
+++ b/stackinator/templates/Makefile.environments
@@ -34,7 +34,7 @@ all:{% for env in environments %} {{ env }}/generated/build_cache{% endfor %}
 {{ env }}/generated/view_config: {{ env }}/generated/env
 {% for view in config.views %}
 	$(SPACK) env activate --with-view {{ view.name }} --sh ./{{ env }} > $(STORE)/env/{{ view.name }}/activate.sh
-	$(BUILD_ROOT)/envvars.py view {% if view.extra.add_compilers %}--compilers=./{{ env }}/packages.yaml {% endif %} --prefix_paths="{{ view.extra.prefix_string }}" $(STORE)/env/{{ view.name }} $(BUILD_ROOT)
+	$(BUILD_ROOT)/envvars.py view {% if view.extra.add_compilers %}--compilers=<(yq read -j -p v ./{{ env }}/packages.yaml) {% endif %} --prefix_paths="{{ view.extra.prefix_string }}" $(STORE)/env/{{ view.name }} $(BUILD_ROOT)
 {% endfor %}
 	touch $@
 
diff --git a/unittests/test_schema.py b/unittests/test_schema.py
index b30f73da..8b85cb57 100644
--- a/unittests/test_schema.py
+++ b/unittests/test_schema.py
@@ -5,10 +5,12 @@
 
 import jsonschema
 import pytest
-import yaml
+from ruamel.yaml import YAML
 
 import stackinator.schema as schema
 
+yaml = YAML()
+
 
 @pytest.fixture
 def test_path():
@@ -38,7 +40,7 @@ def recipe_paths(test_path, recipes):
 def test_config_yaml(yaml_path):
     # test that the defaults are set as expected
     with open(yaml_path / "config.defaults.yaml") as fid:
-        raw = yaml.load(fid, Loader=yaml.Loader)
+        raw = yaml.load(fid)
         schema.ConfigValidator.validate(raw)
         assert raw["store"] == "/user-environment"
         assert raw["spack"]["commit"] is None
@@ -55,10 +57,7 @@ def test_config_yaml(yaml_path):
             repo: https://github.com/spack/spack.git
             commit: develop-packages
     """)
-    raw = yaml.load(
-        config,
-        Loader=yaml.Loader,
-    )
+    raw = yaml.load(config)
     schema.ConfigValidator.validate(raw)
     assert raw["spack"]["commit"] is None
     assert raw["spack"]["packages"]["commit"] is not None
@@ -74,10 +73,7 @@ def test_config_yaml(yaml_path):
         packages:
             repo: https://github.com/spack/spack.git
     """)
-    raw = yaml.load(
-        config,
-        Loader=yaml.Loader,
-    )
+    raw = yaml.load(config)
     schema.ConfigValidator.validate(raw)
     assert raw["spack"]["commit"] == "develop"
     assert raw["spack"]["packages"]["commit"] is None
@@ -85,7 +81,7 @@ def test_config_yaml(yaml_path):
 
     # full config
     with open(yaml_path / "config.full.yaml") as fid:
-        raw = yaml.load(fid, Loader=yaml.Loader)
+        raw = yaml.load(fid)
         schema.ConfigValidator.validate(raw)
         assert raw["store"] == "/alternative-point"
         assert raw["spack"]["commit"] == "6408b51"
@@ -100,7 +96,7 @@ def test_config_yaml(yaml_path):
         spack:
             repo: https://github.com/spack/spack.git
         """)
-        raw = yaml.load(config, Loader=yaml.Loader)
+        raw = yaml.load(config)
         schema.ConfigValidator.validate(raw)
 
 
@@ -108,20 +104,20 @@ def test_recipe_config_yaml(recipe_paths):
     # validate the config.yaml in the test recipes
     for p in recipe_paths:
         with open(p / "config.yaml") as fid:
-            raw = yaml.load(fid, Loader=yaml.Loader)
+            raw = yaml.load(fid)
             schema.ConfigValidator.validate(raw)
 
 
 def test_compilers_yaml(yaml_path):
     # test that the defaults are set as expected
     with open(yaml_path / "compilers.defaults.yaml") as fid:
-        raw = yaml.load(fid, Loader=yaml.Loader)
+        raw = yaml.load(fid)
         schema.CompilersValidator.validate(raw)
         assert raw["gcc"] == {"version": "10.2"}
         assert raw["llvm"] is None
 
     with open(yaml_path / "compilers.full.yaml") as fid:
-        raw = yaml.load(fid, Loader=yaml.Loader)
+        raw = yaml.load(fid)
         schema.CompilersValidator.validate(raw)
         assert raw["gcc"] == {"version": "11"}
         assert raw["llvm"] == {"version": "13"}
@@ -132,13 +128,13 @@ def test_recipe_compilers_yaml(recipe_paths):
     # validate the compilers.yaml in the test recipes
     for p in recipe_paths:
         with open(p / "compilers.yaml") as fid:
-            raw = yaml.load(fid, Loader=yaml.Loader)
+            raw = yaml.load(fid)
             schema.CompilersValidator.validate(raw)
 
 
 def test_environments_yaml(yaml_path):
     with open(yaml_path / "environments.full.yaml") as fid:
-        raw = yaml.load(fid, Loader=yaml.Loader)
+        raw = yaml.load(fid)
         schema.EnvironmentsValidator.validate(raw)
 
         # the defaults-env does not set fields
@@ -181,7 +177,7 @@ def test_environments_yaml(yaml_path):
     # check that only allowed fields are accepted
     # from an example that was silently validated
     with open(yaml_path / "environments.err-providers.yaml") as fid:
-        raw = yaml.load(fid, Loader=yaml.Loader)
+        raw = yaml.load(fid)
         with pytest.raises(
             jsonschema.exceptions.ValidationError,
             match=r"Additional properties are not allowed \('providers' was unexpected",
@@ -193,7 +189,7 @@ def test_recipe_environments_yaml(recipe_paths):
     # validate the environments.yaml in the test recipes
     for p in recipe_paths:
         with open(p / "environments.yaml") as fid:
-            raw = yaml.load(fid, Loader=yaml.Loader)
+            raw = yaml.load(fid)
             schema.EnvironmentsValidator.validate(raw)
 
 
@@ -248,7 +244,7 @@ def test_recipe_environments_yaml(recipe_paths):
     ],
 )
 def test_valid_modules_yaml(recipe):
-    instance = yaml.load(recipe, Loader=yaml.Loader)
+    instance = yaml.load(recipe)
     schema.ModulesValidator.validate(instance)
     assert not instance["modules"]["default"]["arch_folder"]
 
@@ -267,4 +263,18 @@ def test_valid_modules_yaml(recipe):
 )
 def test_invalid_modules_yaml(recipe):
     with pytest.raises(Exception):
-        schema.ModulesValidator.validate(yaml.load(recipe, Loader=yaml.Loader))
+        schema.ModulesValidator.validate(yaml.load(recipe))
+
+
+def test_unique_properties():
+    invalid_config = dedent(
+        """
+        name: invalid-config
+        name: duplicate-name
+        """
+    )
+
+    from ruamel.yaml.constructor import DuplicateKeyError
+
+    with pytest.raises(DuplicateKeyError):
+        yaml.load(invalid_config)