From 6b27aebeb429d1f7c2bb450c49cd43270d1d007e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 23 Feb 2023 11:18:54 -0800
Subject: [PATCH 01/11] colify.py: get rid of **kwargs (#35641)

`colify` is an old module in Spack that still uses `**kwargs` liberally.

We should be more explicit. Doing this eliminates the need for many
checks (can't pass the wrong arg if it isn't allowed) and makes the
function documentation more clear.
---
 lib/spack/llnl/util/tty/colify.py | 95 +++++++++++++++++++------------
 1 file changed, 60 insertions(+), 35 deletions(-)

diff --git a/lib/spack/llnl/util/tty/colify.py b/lib/spack/llnl/util/tty/colify.py
index 3ab7d9978a3..d22be2a2e1f 100644
--- a/lib/spack/llnl/util/tty/colify.py
+++ b/lib/spack/llnl/util/tty/colify.py
@@ -11,6 +11,7 @@
 import io
 import os
 import sys
+from typing import IO, Any, List, Optional
 
 from llnl.util.tty import terminal_size
 from llnl.util.tty.color import cextra, clen
@@ -97,7 +98,16 @@ def config_uniform_cols(elts, console_width, padding, cols=0):
     return config
 
 
-def colify(elts, **options):
+def colify(
+    elts: List[Any],
+    cols: int = 0,
+    output: Optional[IO] = None,
+    indent: int = 0,
+    padding: int = 2,
+    tty: Optional[bool] = None,
+    method: str = "variable",
+    console_cols: Optional[int] = None,
+):
     """Takes a list of elements as input and finds a good columnization
     of them, similar to how gnu ls does. This supports both
     uniform-width and variable-width (tighter) columns.
@@ -106,31 +116,21 @@ def colify(elts, **options):
     using ``str()``.
 
     Keyword Arguments:
-        output (typing.IO): A file object to write to. Default is ``sys.stdout``
-        indent (int): Optionally indent all columns by some number of spaces
-        padding (int): Spaces between columns. Default is 2
-        width (int): Width of the output. Default is 80 if tty not detected
-        cols (int): Force number of columns. Default is to size to terminal, or
+        output: A file object to write to. Default is ``sys.stdout``
+        indent: Optionally indent all columns by some number of spaces
+        padding: Spaces between columns. Default is 2
+        width: Width of the output. Default is 80 if tty not detected
+        cols: Force number of columns. Default is to size to terminal, or
             single-column if no tty
-        tty (bool): Whether to attempt to write to a tty. Default is to autodetect a
+        tty: Whether to attempt to write to a tty. Default is to autodetect a
             tty. Set to False to force single-column output
-        method (str): Method to use to fit columns. Options are variable or uniform.
+        method: Method to use to fit columns. Options are variable or uniform.
             Variable-width columns are tighter, uniform columns are all the same width
             and fit less data on the screen
+        console_cols: number of columns on this console (default: autodetect)
     """
-    # Get keyword arguments or set defaults
-    cols = options.pop("cols", 0)
-    output = options.pop("output", sys.stdout)
-    indent = options.pop("indent", 0)
-    padding = options.pop("padding", 2)
-    tty = options.pop("tty", None)
-    method = options.pop("method", "variable")
-    console_cols = options.pop("width", None)
-
-    if options:
-        raise TypeError(
-            "'%s' is an invalid keyword argument for this function." % next(options.iterkeys())
-        )
+    if output is None:
+        output = sys.stdout
 
     # elts needs to be an array of strings so we can count the elements
     elts = [str(elt) for elt in elts]
@@ -153,10 +153,11 @@ def colify(elts, **options):
             cols = 1
 
     # Specify the number of character columns to use.
-    if not console_cols:
+    if console_cols is None:
         console_rows, console_cols = terminal_size()
-    elif type(console_cols) != int:
+    elif not isinstance(console_cols, int):
         raise ValueError("Number of columns must be an int")
+
     console_cols = max(1, console_cols - indent)
 
     # Choose a method.  Variable-width colums vs uniform-width.
@@ -192,7 +193,13 @@ def colify(elts, **options):
     return (config.cols, tuple(config.widths))
 
 
-def colify_table(table, **options):
+def colify_table(
+    table: List[List[Any]],
+    output: Optional[IO] = None,
+    indent: int = 0,
+    padding: int = 2,
+    console_cols: Optional[int] = None,
+):
     """Version of ``colify()`` for data expressed in rows, (list of lists).
 
     Same as regular colify but:
@@ -218,20 +225,38 @@ def transpose():
             for row in table:
                 yield row[i]
 
-    if "cols" in options:
-        raise ValueError("Cannot override columsn in colify_table.")
-    options["cols"] = columns
-
-    # don't reduce to 1 column for non-tty
-    options["tty"] = True
-
-    colify(transpose(), **options)
+    colify(
+        transpose(),
+        cols=columns,  # this is always the number of cols in the table
+        tty=True,  # don't reduce to 1 column for non-tty
+        output=output,
+        indent=indent,
+        padding=padding,
+        console_cols=console_cols,
+    )
 
 
-def colified(elts, **options):
+def colified(
+    elts: List[Any],
+    cols: int = 0,
+    output: Optional[IO] = None,
+    indent: int = 0,
+    padding: int = 2,
+    tty: Optional[bool] = None,
+    method: str = "variable",
+    console_cols: Optional[int] = None,
+):
     """Invokes the ``colify()`` function but returns the result as a string
     instead of writing it to an output string."""
     sio = io.StringIO()
-    options["output"] = sio
-    colify(elts, **options)
+    colify(
+        elts,
+        cols=cols,
+        output=sio,
+        indent=indent,
+        padding=padding,
+        tty=tty,
+        method=method,
+        console_cols=console_cols,
+    )
     return sio.getvalue()

From d286146c641ce826eeb67089bd3e24912406e51b Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Thu, 23 Feb 2023 17:09:28 -0800
Subject: [PATCH 02/11] WarpX 23.02 (#35633)

Update `warpx` & `py-warpx` to the latest release.
---
 var/spack/repos/builtin/packages/py-warpx/package.py | 4 +++-
 var/spack/repos/builtin/packages/warpx/package.py    | 3 ++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-warpx/package.py b/var/spack/repos/builtin/packages/py-warpx/package.py
index fefdf2355e6..bb4782bbe59 100644
--- a/var/spack/repos/builtin/packages/py-warpx/package.py
+++ b/var/spack/repos/builtin/packages/py-warpx/package.py
@@ -18,7 +18,7 @@ class PyWarpx(PythonPackage):
     """
 
     homepage = "https://ecp-warpx.github.io"
-    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.01.tar.gz"
+    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.02.tar.gz"
     git = "https://github.com/ECP-WarpX/WarpX.git"
 
     maintainers("ax3l", "dpgrote", "RemiLehe")
@@ -27,6 +27,7 @@ class PyWarpx(PythonPackage):
 
     # NOTE: if you update the versions here, also see warpx
     version("develop", branch="development")
+    version("23.02", sha256="a6c63ebc38cbd224422259a814be501ac79a3b734dab7f59500b6957cddaaac1")
     version("23.01", sha256="e853d01c20ea00c8ddedfa82a31a11d9d91a7f418d37d7f064cf8a241ea4da0c")
     version("22.12", sha256="96019902cd6ea444a1ae515e8853048e9074822c168021e4ec1687adc72ef062")
     version("22.11", sha256="528f65958f2f9e60a094e54eede698e871ccefc89fa103fe2a6f22e4a059515e")
@@ -53,6 +54,7 @@ class PyWarpx(PythonPackage):
     variant("mpi", default=True, description="Enable MPI support")
 
     for v in [
+        "23.02",
         "23.01",
         "22.12",
         "22.11",
diff --git a/var/spack/repos/builtin/packages/warpx/package.py b/var/spack/repos/builtin/packages/warpx/package.py
index ae954da9bb7..850a37495ae 100644
--- a/var/spack/repos/builtin/packages/warpx/package.py
+++ b/var/spack/repos/builtin/packages/warpx/package.py
@@ -17,7 +17,7 @@ class Warpx(CMakePackage):
     """
 
     homepage = "https://ecp-warpx.github.io"
-    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.01.tar.gz"
+    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.02.tar.gz"
     git = "https://github.com/ECP-WarpX/WarpX.git"
 
     maintainers("ax3l", "dpgrote", "MaxThevenet", "RemiLehe")
@@ -25,6 +25,7 @@ class Warpx(CMakePackage):
 
     # NOTE: if you update the versions here, also see py-warpx
     version("develop", branch="development")
+    version("23.02", sha256="a6c63ebc38cbd224422259a814be501ac79a3b734dab7f59500b6957cddaaac1")
     version("23.01", sha256="e853d01c20ea00c8ddedfa82a31a11d9d91a7f418d37d7f064cf8a241ea4da0c")
     version("22.12", sha256="96019902cd6ea444a1ae515e8853048e9074822c168021e4ec1687adc72ef062")
     version("22.11", sha256="528f65958f2f9e60a094e54eede698e871ccefc89fa103fe2a6f22e4a059515e")

From 07897900ebb1278113a696675a158ae6d5b3e41b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vin=C3=ADcius?= <vgpinto@inf.ufrgs.br>
Date: Sat, 25 Feb 2023 02:22:17 -0300
Subject: [PATCH 03/11] ompss-2 dependencies (#35642)

---
 var/spack/repos/builtin/packages/ompss-2/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/ompss-2/package.py b/var/spack/repos/builtin/packages/ompss-2/package.py
index a786288b76e..55efe7633a4 100644
--- a/var/spack/repos/builtin/packages/ompss-2/package.py
+++ b/var/spack/repos/builtin/packages/ompss-2/package.py
@@ -31,6 +31,8 @@ class Ompss2(Package):
     depends_on("python", type="build")
     depends_on("cmake", type="build")
     depends_on("extrae", when="+extrae")
+    depends_on("boost@1.59.0:")
+    depends_on("numactl")
 
     resource(
         name="jemalloc",
@@ -105,6 +107,8 @@ def install_nanos6(self, spec, prefix):
             "--prefix=%s" % prefix,
             "--with-jemalloc=%s" % prefix,
             "--with-hwloc=%s" % spec["hwloc"].prefix,
+            "--with-boost=%s" % spec["boost"].prefix,
+            "--with-libnuma=%s" % spec["numactl"].prefix,
             "--disable-stats-instrumentation",
             "--disable-verbose-instrumentation",
             "--disable-lint-instrumentation",

From 4e13b5374fc48685dbe9ad6cac1d28839d83d8a2 Mon Sep 17 00:00:00 2001
From: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
Date: Sat, 25 Feb 2023 06:32:33 +0100
Subject: [PATCH 04/11] fix dump problem (#35673)

if dump file existed it was not truncating the file, resulting in
a file with unaltered filesize, with the new content at the beginning,
"padded" with the tail of the old content, since the new content was
not enough to overwrite it.
---
 lib/spack/spack/util/environment.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py
index c85b8822531..cad8552f7bd 100644
--- a/lib/spack/spack/util/environment.py
+++ b/lib/spack/spack/util/environment.py
@@ -138,7 +138,7 @@ def dump_environment(path, environment=None):
     use_env = environment or os.environ
     hidden_vars = set(["PS1", "PWD", "OLDPWD", "TERM_SESSION_ID"])
 
-    fd = os.open(path, os.O_WRONLY | os.O_CREAT, 0o600)
+    fd = os.open(path, os.O_WRONLY | os.O_CREAT | os.O_TRUNC, 0o600)
     with os.fdopen(fd, "w") as env_file:
         for var, val in sorted(use_env.items()):
             env_file.write(

From b0b4a05d44883260b82c0978a01494fdb968b7d3 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 26 Feb 2023 23:22:48 -0700
Subject: [PATCH 05/11] py-nbqa: add new package (#35707)

---
 .../repos/builtin/packages/py-nbqa/package.py | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-nbqa/package.py

diff --git a/var/spack/repos/builtin/packages/py-nbqa/package.py b/var/spack/repos/builtin/packages/py-nbqa/package.py
new file mode 100644
index 00000000000..0d9683b45b8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nbqa/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyNbqa(PythonPackage):
+    """Run any standard Python code quality tool on a Jupyter Notebook."""
+
+    homepage = "https://github.com/nbQA-dev/nbQA"
+    pypi = "nbqa/nbqa-1.6.3.tar.gz"
+
+    version("1.6.3", sha256="5394a29fc6d27b9a950c0a36d2d9de25de980be9acfe2a3f3aea0d27b5f7fec1")
+
+    depends_on("python@3.8:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-ipython@7.8:", type=("build", "run"))
+    depends_on("py-tokenize-rt@3.2:", type=("build", "run"))
+    depends_on("py-tomli", type=("build", "run"))

From 313c7386c4ede8a3df7f698df49fde81367731a0 Mon Sep 17 00:00:00 2001
From: Alex Richert <82525672+AlexanderRichert-NOAA@users.noreply.github.com>
Date: Sun, 26 Feb 2023 22:26:50 -0800
Subject: [PATCH 06/11] go: set GOMAXPROCS to limit number of build processes
 (#35703)

---
 var/spack/repos/builtin/packages/go/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index 8f3647c06fa..9d798a7d8c7 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -116,6 +116,7 @@ def setup_build_environment(self, env):
         # internal Spack wrappers and fail.
         env.set("CC_FOR_TARGET", self.compiler.cc)
         env.set("CXX_FOR_TARGET", self.compiler.cxx)
+        env.set("GOMAXPROCS", make_jobs)
 
     def setup_dependent_package(self, module, dependent_spec):
         """Called before go modules' install() methods.

From 6ab792fb03226eb6d26a090de89573866c98b245 Mon Sep 17 00:00:00 2001
From: Larry Knox <lrknox@hdfgroup.org>
Date: Mon, 27 Feb 2023 00:35:30 -0600
Subject: [PATCH 07/11] hdf5-vol-cache: add v1.1 (#35685)

---
 var/spack/repos/builtin/packages/hdf5-vol-cache/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/hdf5-vol-cache/package.py b/var/spack/repos/builtin/packages/hdf5-vol-cache/package.py
index 62616e4de20..1010d540b1d 100644
--- a/var/spack/repos/builtin/packages/hdf5-vol-cache/package.py
+++ b/var/spack/repos/builtin/packages/hdf5-vol-cache/package.py
@@ -14,6 +14,7 @@ class Hdf5VolCache(CMakePackage):
     maintainers("hyoklee", "lrknox")
 
     version("default", branch="develop")
+    version("v1.1", tag="v1.1")
     version("v1.0", tag="v1.0")
 
     depends_on("hdf5-vol-async")

From a4b949492b09199a14424ed439c5105b8b8c9975 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Mon, 27 Feb 2023 00:38:27 -0600
Subject: [PATCH 08/11] r-twosamplemr: add new package and dependencies
 (#35683)

---
 .../packages/r-arrangements/package.py        | 27 ++++++++++
 .../builtin/packages/r-googleauthr/package.py | 28 ++++++++++
 .../builtin/packages/r-ieugwasr/package.py    | 26 ++++++++++
 .../builtin/packages/r-iterpc/package.py      | 29 +++++++++++
 .../r-mendelianrandomization/package.py       | 32 ++++++++++++
 .../repos/builtin/packages/r-meta/package.py  | 33 ++++++++++++
 .../builtin/packages/r-metadat/package.py     | 21 ++++++++
 .../builtin/packages/r-metafor/package.py     | 39 ++++++++++++++
 .../builtin/packages/r-mr-raps/package.py     | 24 +++++++++
 .../packages/r-mrinstruments/package.py       | 19 +++++++
 .../repos/builtin/packages/r-mrmix/package.py | 18 +++++++
 .../builtin/packages/r-mrpresso/package.py    | 21 ++++++++
 .../builtin/packages/r-radialmr/package.py    | 23 +++++++++
 .../builtin/packages/r-twosamplemr/package.py | 51 +++++++++++++++++++
 14 files changed, 391 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-arrangements/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-googleauthr/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-ieugwasr/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-iterpc/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-mendelianrandomization/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-meta/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-metadat/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-metafor/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-mr-raps/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-mrinstruments/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-mrmix/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-mrpresso/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-radialmr/package.py
 create mode 100644 var/spack/repos/builtin/packages/r-twosamplemr/package.py

diff --git a/var/spack/repos/builtin/packages/r-arrangements/package.py b/var/spack/repos/builtin/packages/r-arrangements/package.py
new file mode 100644
index 00000000000..d8138743722
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-arrangements/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RArrangements(RPackage):
+    """Fast Generators and Iterators for Permutations, Combinations, Integer
+    Partitions and Compositions.
+
+    Fast generators and iterators for permutations, combinations, integer
+    partitions and compositions. The arrangements are in lexicographical order
+    and generated iteratively in a memory efficient manner. It has been
+    demonstrated that 'arrangements' outperforms most existing packages of
+    similar kind. Benchmarks could be found at
+    <https://randy3k.github.io/arrangements/articles/benchmark.html>."""
+
+    cran = "arrangements"
+
+    version("1.1.9", sha256="e9b5dcb185ec9b28201b196384b04a8d5a15f4ddb9e0b0b2a0c718635ff7345b")
+
+    depends_on("r@3.4.0:", type=("build", "run"))
+    depends_on("r-gmp", type=("build", "run"))
+    depends_on("r-r6", type=("build", "run"))
+    depends_on("gmp@4.2.3:")
diff --git a/var/spack/repos/builtin/packages/r-googleauthr/package.py b/var/spack/repos/builtin/packages/r-googleauthr/package.py
new file mode 100644
index 00000000000..d31fd7f0c19
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-googleauthr/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RGoogleauthr(RPackage):
+    """Authenticate and Create Google APIs.
+
+    Create R functions that interact with OAuth2 Google APIs
+    <https://developers.google.com/apis-explorer/> easily, with auto-refresh
+    and Shiny compatibility."""
+
+    cran = "googleAuthR"
+
+    version("2.0.0", sha256="ba504baf3bde2e1b3e988bee7602df5765cc6ca542cf0ab76a782c4e60966feb")
+
+    depends_on("r@3.3.0:", type=("build", "run"))
+    depends_on("r-assertthat", type=("build", "run"))
+    depends_on("r-cli", type=("build", "run"))
+    depends_on("r-digest", type=("build", "run"))
+    depends_on("r-gargle@1.2.0:", type=("build", "run"))
+    depends_on("r-httr@1.4.0:", type=("build", "run"))
+    depends_on("r-jsonlite@1.6:", type=("build", "run"))
+    depends_on("r-memoise@1.1.0:", type=("build", "run"))
+    depends_on("r-rlang", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-ieugwasr/package.py b/var/spack/repos/builtin/packages/r-ieugwasr/package.py
new file mode 100644
index 00000000000..bce36046bba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ieugwasr/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RIeugwasr(RPackage):
+    """R Interface to the OpenGWAS Database API.
+
+    R interface to the OpenGWAS database API. Includes a wrapper
+    to make generic calls to the API, plus convenience functions for
+    specific queries."""
+
+    homepage = "https://github.com/MRCIEU/ieugwasr"
+    url = "https://github.com/MRCIEU/ieugwasr/archive/refs/tags/0.1.5.tar.gz"
+
+    version("0.1.5", sha256="8d900d5a780f23836c80191f9635fbf48a0ca94f828452948c0f445e3217f422")
+
+    depends_on("r@3.6.0:", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-googleauthr", type=("build", "run"))
+    depends_on("r-dplyr", type=("build", "run"))
+    depends_on("r-httr", type=("build", "run"))
+    depends_on("r-jsonlite", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-iterpc/package.py b/var/spack/repos/builtin/packages/r-iterpc/package.py
new file mode 100644
index 00000000000..f038fe32492
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-iterpc/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RIterpc(RPackage):
+    """Efficient Iterator for Permutations and Combinations.
+
+    Iterator for generating permutations and combinations. They can be either
+    drawn with or without replacement, or with distinct/ non-distinct items
+    (multiset). The generated sequences are in lexicographical order
+    (dictionary order). The algorithms to generate permutations and
+    combinations are memory efficient. These iterative algorithms enable users
+    to process all sequences without putting all results in the memory at the
+    same time. The algorithms are written in C/C++ for faster performance.
+    Note: 'iterpc' is no longer being maintained. Users are recommended to
+    switch to 'arrangements'."""
+
+    cran = "iterpc"
+
+    version("0.4.2", sha256="38bd464042a27536f676e889263eb2c257a431b59083f58cb54473f42ba2071b")
+
+    depends_on("r@3.0.0:", type=("build", "run"))
+    depends_on("r-iterators", type=("build", "run"))
+    depends_on("r-gmp@0.5-12:", type=("build", "run"))
+    depends_on("r-arrangements@1.0.0:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-mendelianrandomization/package.py b/var/spack/repos/builtin/packages/r-mendelianrandomization/package.py
new file mode 100644
index 00000000000..ed7b9a905b3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mendelianrandomization/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMendelianrandomization(RPackage):
+    """Mendelian Randomization Package.
+
+    Encodes several methods for performing Mendelian randomization analyses
+    with summarized data. Summarized data on genetic associations with the
+    exposure and with the outcome can be obtained from large consortia. These
+    data can be used for obtaining causal estimates using instrumental variable
+    methods."""
+
+    cran = "MendelianRandomization"
+
+    version("0.7.0", sha256="cad7cc1b6964fc7d299864378694c5fd947caa83796a1958e581299796b854c7")
+
+    depends_on("r@3.0.1:", type=("build", "run"))
+    depends_on("r-knitr", type=("build", "run"))
+    depends_on("r-rmarkdown", type=("build", "run"))
+    depends_on("r-plotly@3.6.0:", type=("build", "run"))
+    depends_on("r-ggplot2@1.0.1:", type=("build", "run"))
+    depends_on("r-robustbase@0.92-6:", type=("build", "run"))
+    depends_on("r-matrix@1.2:", type=("build", "run"))
+    depends_on("r-iterpc@0.3:", type=("build", "run"))
+    depends_on("r-quantreg@5.01:", type=("build", "run"))
+    depends_on("r-rjson", type=("build", "run"))
+    depends_on("r-glmnet", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-meta/package.py b/var/spack/repos/builtin/packages/r-meta/package.py
new file mode 100644
index 00000000000..b82dce10896
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-meta/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMeta(RPackage):
+    """General Package for Meta-Analysis.
+
+    User-friendly general package providing standard methods for meta-analysis
+    and supporting Schwarzer, Carpenter, and Rücker
+    <doi:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - common
+    effect and random effects meta-analysis; - several plots (forest, funnel,
+    Galbraith / radial, L'Abbe, Baujat, bubble); - three-level meta-analysis
+    model; - generalised linear mixed model; - Hartung-Knapp method for random
+    effects model; - Kenward-Roger method for random effects model; -
+    prediction interval; - statistical tests for funnel plot asymmetry; -
+    trim-and-fill method to evaluate bias in meta-analysis; - meta-regression;
+    - cumulative meta-analysis and leave-one-out meta-analysis; - import data
+    from 'RevMan 5'; - produce forest plot summarising several (subgroup)
+    meta-analyses."""
+
+    cran = "meta"
+
+    version("6.2-0", sha256="8ec8fb412996bbe17d3ca073f15c191a77bad486b08f39d7b8c2d07360ad5781")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-metafor@3.0-0:", type=("build", "run"))
+    depends_on("r-lme4", type=("build", "run"))
+    depends_on("r-compquadform", type=("build", "run"))
+    depends_on("r-xml2", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-metadat/package.py b/var/spack/repos/builtin/packages/r-metadat/package.py
new file mode 100644
index 00000000000..71e24954181
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-metadat/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMetadat(RPackage):
+    """Meta-Analysis Datasets.
+
+    A collection of meta-analysis datasets for teaching purposes,
+    illustrating/testing meta-analytic methods, and validating published
+    analyses."""
+
+    cran = "metadat"
+
+    version("1.2-0", sha256="f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-mathjaxr", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-metafor/package.py b/var/spack/repos/builtin/packages/r-metafor/package.py
new file mode 100644
index 00000000000..534c80fa478
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-metafor/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMetafor(RPackage):
+    """Meta-Analysis Package for R.
+
+    A comprehensive collection of functions for conducting meta-analyses in R.
+    The package includes functions to calculate various effect sizes or outcome
+    measures, fit equal-, fixed-, random-, and mixed-effects models to such
+    data, carry out moderator and meta-regression analyses, and create various
+    types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe,
+    Baujat, bubble, and GOSH plots). For meta-analyses of binomial and
+    person-time data, the package also provides functions that implement
+    specialized methods, including the Mantel-Haenszel method, Peto's method,
+    and a variety of suitable generalized linear (mixed-effects) models (i.e.,
+    mixed-effects logistic and Poisson regression models). Finally, the package
+    provides functionality for fitting meta-analytic multivariate/multilevel
+    models that account for non-independent sampling errors and/or true effects
+    (e.g., due to the inclusion of multiple treatment studies, multiple
+    endpoints, or other forms of clustering). Network meta-analyses and
+    meta-analyses accounting for known correlation structures (e.g., due to
+    phylogenetic relatedness) can also be conducted. An introduction to the
+    package can be found in Viechtbauer (2010) <doi:10.18637/jss.v036.i03>."""
+
+    cran = "metafor"
+
+    version("3.8-1", sha256="d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-matrix", type=("build", "run"))
+    depends_on("r-metadat", type=("build", "run"))
+    depends_on("r-nlme", type=("build", "run"))
+    depends_on("r-mathjaxr", type=("build", "run"))
+    depends_on("r-pbapply", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-mr-raps/package.py b/var/spack/repos/builtin/packages/r-mr-raps/package.py
new file mode 100644
index 00000000000..496756f9164
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mr-raps/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMrRaps(RPackage):
+    """Two Sample Mendelian Randomization using Robust Adjusted Profile Score.
+
+    Mendelian randomization is a method of identifying and estimating a
+    confounded causal effect using genetic instrumental variables. This
+    packages implements methods for two-sample Mendelian randomization with
+    summary statistics by using Robust Adjusted Profile Score (RAPS).
+    References: Qingyuan Zhao, Jingshu Wang, Jack Bowden, Dylan S. Small.
+    Statistical inference in two-sample summary-data Mendelian randomization
+    using robust adjusted profile score. <arXiv:1801.09652>."""
+
+    cran = "mr.raps"
+
+    version("0.2", sha256="c899f6143dac99e1232ff0a8d9f5fe099d4f69960782e6843db5b0d7f4f63b19")
+
+    depends_on("r-nortest", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-mrinstruments/package.py b/var/spack/repos/builtin/packages/r-mrinstruments/package.py
new file mode 100644
index 00000000000..d80922c1cab
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mrinstruments/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMrinstruments(RPackage):
+    """Data sources for genetic instruments to be used in MR.
+
+    Datasets of eQTLs, GWAS catalogs, etc."""
+
+    homepage = "https://github.com/MRCIEU/MRInstruments"
+    url = "https://github.com/MRCIEU/MRInstruments/archive/refs/tags/0.3.3.tar.gz"
+
+    version("0.3.3", sha256="4ddbaf6335133e8f7baef469d6bc1f89212462b9f4062c9e4ddda37b12eb3486")
+
+    depends_on("r@2.10:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-mrmix/package.py b/var/spack/repos/builtin/packages/r-mrmix/package.py
new file mode 100644
index 00000000000..d6c51a75416
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mrmix/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMrmix(RPackage):
+    """Mendelian Randomization Analysis Using Mixture Models (MRMix).
+
+    This package gives robust estimation of causal effects by conducting
+    Mendelian randomization analysis using a mixture model approach."""
+
+    homepage = "https://github.com/gqi/MRMix"
+    git = "https://github.com/gqi/MRMix"
+
+    version("0.1.0", commit="56afdb2bc96760842405396f5d3f02e60e305039")
diff --git a/var/spack/repos/builtin/packages/r-mrpresso/package.py b/var/spack/repos/builtin/packages/r-mrpresso/package.py
new file mode 100644
index 00000000000..7d4ab68341d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mrpresso/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMrpresso(RPackage):
+    """Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier
+    (MR-PRESSO) test.
+
+    MR-PRESSO (Mendelian Randomization Pleiotropy RESidual Sum and Outlier) is
+    a framework that allows for the evaluation of pleiotropy in
+    multi-instrument Mendelian Randomization utilizing genome-wide summary
+    association statistics."""
+
+    homepage = "https://github.com/rondolab/MR-PRESSO"
+    git = "https://github.com/rondolab/MR-PRESSO"
+
+    version("1.0", commit="cece763b47e59763a7916974de43c7cb93843e41")
diff --git a/var/spack/repos/builtin/packages/r-radialmr/package.py b/var/spack/repos/builtin/packages/r-radialmr/package.py
new file mode 100644
index 00000000000..301bd60fc17
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-radialmr/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RRadialmr(RPackage):
+    """RadialMR.
+
+    A package for implementing radial inverse variance weighted and MR-Egger
+    methods."""
+
+    homepage = "https://github.com/WSpiller/RadialMR"
+    git = "https://github.com/WSpiller/RadialMR"
+
+    version("1.0", commit="d63d3fc8270836ab441b9e14a5ba3eeb2795d7cb")
+
+    depends_on("r@3.5.0:", type=("build", "run"))
+    depends_on("r-ggplot2", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-plotly", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-twosamplemr/package.py b/var/spack/repos/builtin/packages/r-twosamplemr/package.py
new file mode 100644
index 00000000000..7ca1bc9a221
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-twosamplemr/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RTwosamplemr(RPackage):
+    """Two Sample MR functions and interface to MR Base database.
+
+    A package for performing Mendelian randomization using GWAS summary data.
+    It uses the IEU GWAS database to obtain data automatically, and a wide
+    range of methods to run the analysis. You can use the MR-Base web app to
+    try out a limited range of the functionality in this package, but for any
+    serious work we strongly recommend using this R package."""
+
+    homepage = "https://mrcieu.github.io/TwoSampleMR/"
+    url = "https://github.com/MRCIEU/TwoSampleMR/archive/refs/tags/v0.5.6.tar.gz"
+
+    version("0.5.6", sha256="c63eb008ab7ed08a6f30ccbf0c299beb31b2f5835e5e2aa1b59c5e4fe284a30c")
+
+    depends_on("r@3.6.0:", type=("build", "run"))
+    depends_on("r-ieugwasr@0.1.5:", type=("build", "run"))
+    depends_on("r-ggplot2", type=("build", "run"))
+    depends_on("r-gridextra", type=("build", "run"))
+    depends_on("r-cowplot", type=("build", "run"))
+    depends_on("r-plyr", type=("build", "run"))
+    depends_on("r-reshape2", type=("build", "run"))
+    depends_on("r-stringr", type=("build", "run"))
+    depends_on("r-knitr", type=("build", "run"))
+    depends_on("r-markdown", type=("build", "run"))
+    depends_on("r-gtable", type=("build", "run"))
+    depends_on("r-rmarkdown", type=("build", "run"))
+    depends_on("r-mendelianrandomization", type=("build", "run"))
+    depends_on("r-dplyr", type=("build", "run"))
+    depends_on("r-mr-raps", type=("build", "run"))
+    depends_on("r-psych", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-car", type=("build", "run"))
+    depends_on("r-randomforest", type=("build", "run"))
+    depends_on("r-meta", type=("build", "run"))
+    depends_on("r-data-table", type=("build", "run"))
+    depends_on("r-mrpresso", type=("build", "run"))
+    depends_on("r-mrinstruments", type=("build", "run"))
+    depends_on("r-radialmr", type=("build", "run"))
+    depends_on("r-mrmix", type=("build", "run"))
+    depends_on("r-glmnet", type=("build", "run"))
+    depends_on("r-lattice", type=("build", "run"))
+    depends_on("r-pbapply", type=("build", "run"))
+    depends_on("r-mass", type=("build", "run"))

From f00431161131757bf69b992660a552bf38531907 Mon Sep 17 00:00:00 2001
From: Howard Pritchard <howardp@lanl.gov>
Date: Mon, 27 Feb 2023 01:57:36 -0700
Subject: [PATCH 09/11] OpenMPI:  add the 4.1.5 release (#35677)

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
---
 var/spack/repos/builtin/packages/openmpi/package.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index d9112884c32..f2d4640742b 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -42,10 +42,13 @@ class Openmpi(AutotoolsPackage, CudaPackage):
 
     # Current
     version(
-        "4.1.4", sha256="92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d"
-    )  # libmpi.so.40.30.4
+        "4.1.5", sha256="a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3"
+    )  # libmpi.so.40.30.5
 
     # Still supported
+    version(
+        "4.1.4", sha256="92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d"
+    )  # libmpi.so.40.30.4
     version(
         "4.1.3", sha256="3d81d04c54efb55d3871a465ffb098d8d72c1f48ff1cbaf2580eb058567c0a3b"
     )  # libmpi.so.40.30.3

From 9b46e92e13f94f5a165adc1abd4a7e6fffe3d650 Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Mon, 27 Feb 2023 04:36:28 -0500
Subject: [PATCH 10/11] Celeritas: new versions 0.2.1 and 0.1.5 (#35704)

* celeritas: new versions 0.1.5 and 0.2.1

* celeritas: deprecate old versions
---
 .../builtin/packages/celeritas/package.py     | 42 +++++++++++++++----
 1 file changed, 35 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/celeritas/package.py b/var/spack/repos/builtin/packages/celeritas/package.py
index 188cf554ff2..8ca11349e61 100644
--- a/var/spack/repos/builtin/packages/celeritas/package.py
+++ b/var/spack/repos/builtin/packages/celeritas/package.py
@@ -17,12 +17,38 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
 
     maintainers("sethrj")
 
-    version("0.2.0", sha256="12af28fda0e482a9eba89781b4ead445cf6f170bc1b8d88cc814e49b1ec09e9f")
-    version("0.1.4", sha256="ea82a03fc750a2a805f87afd9ac944109dd7537edb5c0c370f93d332d4cd47db")
-    version("0.1.3", sha256="992c49a48adba884fe3933c9624da5bf480ef0694809430ae98903f2c28cc881")
-    version("0.1.2", sha256="d123ea2e34267adba387d46bae8c9a1146a2e047f87f2ea5f823878c1684678d")
-    version("0.1.1", sha256="a1d58e29226e89a2330d69c40049d61e7c885cf991824e60ff8c9ccc95fc5ec6")
-    version("0.1.0", sha256="46692977b9b31d73662252cc122d7f016f94139475788bca7fdcb97279b93af8")
+    version("0.2.1", sha256="b3717b43f70dd0da848139da4171ca7a887bb6777908845b6d953d47b1f4db41")
+    version(
+        "0.2.0",
+        sha256="12af28fda0e482a9eba89781b4ead445cf6f170bc1b8d88cc814e49b1ec09e9f",
+        deprecated=True,
+    )
+    version("0.1.5", sha256="5e63b9ce7fcfe34a8938565b84453bce51fa6639d1ede13bb59d41de6431cef4")
+    version(
+        "0.1.4",
+        sha256="ea82a03fc750a2a805f87afd9ac944109dd7537edb5c0c370f93d332d4cd47db",
+        deprecated=True,
+    )
+    version(
+        "0.1.3",
+        sha256="992c49a48adba884fe3933c9624da5bf480ef0694809430ae98903f2c28cc881",
+        deprecated=True,
+    )
+    version(
+        "0.1.2",
+        sha256="d123ea2e34267adba387d46bae8c9a1146a2e047f87f2ea5f823878c1684678d",
+        deprecated=True,
+    )
+    version(
+        "0.1.1",
+        sha256="a1d58e29226e89a2330d69c40049d61e7c885cf991824e60ff8c9ccc95fc5ec6",
+        deprecated=True,
+    )
+    version(
+        "0.1.0",
+        sha256="46692977b9b31d73662252cc122d7f016f94139475788bca7fdcb97279b93af8",
+        deprecated=True,
+    )
 
     _cxxstd_values = ("14", "17")
 
@@ -49,7 +75,8 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("cmake@3.22:", type="build", when="+rocm")
 
     depends_on("nlohmann-json")
-    depends_on("geant4@10.6:", when="+geant4")
+    depends_on("geant4@10.7:11.0", when="@:0.2.0 +geant4")
+    depends_on("geant4@10.6:11.0", when="@0.2.1: +geant4")
     depends_on("hepmc3", when="+hepmc3")
     depends_on("root", when="+root")
     depends_on("swig", when="+swig")
@@ -68,6 +95,7 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("vecgeom +gdml@1.1.17:", when="+vecgeom")
     depends_on("vecgeom +cuda", when="+vecgeom +cuda")
 
+    conflicts("cxxstd=14", when="@0.3:")
     conflicts("+rocm", when="+cuda", msg="AMD and NVIDIA accelerators are incompatible")
     conflicts("+rocm", when="+vecgeom", msg="HIP support is only available with ORANGE")
     conflicts("^vecgeom+shared@1.2.0", when="+vecgeom +cuda")

From 773fd5ad849f90620508a34dc9eab52ddf55ca6d Mon Sep 17 00:00:00 2001
From: Harmen Stoppels <harmenstoppels@gmail.com>
Date: Mon, 27 Feb 2023 10:50:48 +0100
Subject: [PATCH 11/11] hpctoolkit: fix broken patches (#35711)

The patches don't have a stable checksum.
---
 ...62544717873432c49ef45c7cb99cc5de2fb8.patch |  91 ++++++++++++
 ...fd95b01d743edc5940c84e0079f462b2c23e.patch | 130 ++++++++++++++++++
 .../builtin/packages/hpctoolkit/package.py    |  10 +-
 3 files changed, 223 insertions(+), 8 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/hpctoolkit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch
 create mode 100644 var/spack/repos/builtin/packages/hpctoolkit/511afd95b01d743edc5940c84e0079f462b2c23e.patch

diff --git a/var/spack/repos/builtin/packages/hpctoolkit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch b/var/spack/repos/builtin/packages/hpctoolkit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch
new file mode 100644
index 00000000000..7cc956ac6b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpctoolkit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch
@@ -0,0 +1,91 @@
+From 411d62544717873432c49ef45c7cb99cc5de2fb8 Mon Sep 17 00:00:00 2001
+From: "Mark W. Krentel" <krentel@rice.edu>
+Date: Thu, 15 Dec 2022 16:43:43 -0600
+Subject: [PATCH] Add a temporary hack to allow both ROCM 5.2/5.3 to build
+ cleanly.
+
+There were some corner cases (build 5.3 pieces from spack and feed
+into autotools) that didn't work.  After the next release, I will want
+to rework ROCM configure more extensively.
+---
+ configure    | 21 +++++++++++++--------
+ configure.ac | 17 +++++++++++------
+ 2 files changed, 24 insertions(+), 14 deletions(-)
+
+diff --git a/configure b/configure
+index 1760e678e8..814376b3bd 100755
+--- a/configure
++++ b/configure
+@@ -23891,10 +23891,13 @@ $as_echo "$as_me: found $ROCM/rocprofiler/lib/librocprofiler64.so" >&6;}
+     fi
+ 
+     # HSA
+-    if test -f "$ROCM/include/hsa/hsa.h" ; then
+-      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM/include/hsa/hsa.h" >&5
+-$as_echo "$as_me: found $ROCM/include/hsa/hsa.h" >&6;}
+-      ROCM_HSA_IFLAGS="-I$ROCM/include/hsa"
++    # FIXME: as of rocm 5.2/5.3, this was not fully switched over,
++    # so temporarily use both paths.
++    if test -f "$ROCM/include/hsa/hsa.h" || test -f "$ROCM/include/hsa.h"
++    then
++      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM: hsa.h" >&5
++$as_echo "$as_me: found $ROCM: hsa.h" >&6;}
++      ROCM_HSA_IFLAGS="-I$ROCM/include -I$ROCM/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM/hsa"
+       found=yes
+     fi
+@@ -24020,10 +24023,12 @@ case "$ROCM_HSA" in
+     require_rocm=yes
+     found=no
+ 
+-    if test -f "$ROCM_HSA/include/hsa/hsa.h" ; then
+-      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM_HSA/include/hsa/hsa.h" >&5
+-$as_echo "$as_me: found $ROCM_HSA/include/hsa/hsa.h" >&6;}
+-      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include/hsa"
++    # FIXME: again, temporarily use both paths
++    if test -f "$ROCM_HSA/include/hsa/hsa.h" || test -f "$ROCM_HSA/include/hsa.h"
++    then
++      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM_HSA: hsa.h" >&5
++$as_echo "$as_me: found $ROCM_HSA: hsa.h" >&6;}
++      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include -I$ROCM_HSA/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM_HSA"
+       found=yes
+     fi
+diff --git a/configure.ac b/configure.ac
+index a14b15835f..9d5ed46134 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -4885,9 +4885,12 @@ case "$ROCM" in
+     fi
+ 
+     # HSA
+-    if test -f "$ROCM/include/hsa/hsa.h" ; then
+-      AC_MSG_NOTICE([found $ROCM/include/hsa/hsa.h])
+-      ROCM_HSA_IFLAGS="-I$ROCM/include/hsa"
++    # FIXME: as of rocm 5.2/5.3, this was not fully switched over,
++    # so temporarily use both paths.
++    if test -f "$ROCM/include/hsa/hsa.h" || test -f "$ROCM/include/hsa.h"
++    then
++      AC_MSG_NOTICE([found $ROCM: hsa.h])
++      ROCM_HSA_IFLAGS="-I$ROCM/include -I$ROCM/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM/hsa"
+       found=yes
+     fi
+@@ -5002,9 +5005,11 @@ case "$ROCM_HSA" in
+     require_rocm=yes
+     found=no
+ 
+-    if test -f "$ROCM_HSA/include/hsa/hsa.h" ; then
+-      AC_MSG_NOTICE([found $ROCM_HSA/include/hsa/hsa.h])
+-      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include/hsa"
++    # FIXME: again, temporarily use both paths
++    if test -f "$ROCM_HSA/include/hsa/hsa.h" || test -f "$ROCM_HSA/include/hsa.h"
++    then
++      AC_MSG_NOTICE([found $ROCM_HSA: hsa.h])
++      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include -I$ROCM_HSA/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM_HSA"
+       found=yes
+     fi
+-- 
+GitLab
+
diff --git a/var/spack/repos/builtin/packages/hpctoolkit/511afd95b01d743edc5940c84e0079f462b2c23e.patch b/var/spack/repos/builtin/packages/hpctoolkit/511afd95b01d743edc5940c84e0079f462b2c23e.patch
new file mode 100644
index 00000000000..03bdd0aedf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpctoolkit/511afd95b01d743edc5940c84e0079f462b2c23e.patch
@@ -0,0 +1,130 @@
+From 511afd95b01d743edc5940c84e0079f462b2c23e Mon Sep 17 00:00:00 2001
+From: "Mark W. Krentel" <krentel@rice.edu>
+Date: Tue, 18 May 2021 14:54:41 -0500
+Subject: [PATCH] Cleanup some usage for gcc/g++ 11.x (#413)
+
+1. Change epsilon to hpc_epsilon in prof/Metric header files.  This
+ conflicted with using epsilon in some STL template libraries.
+
+ 2. Add const to some comparison operators that are used in some STL
+ maps.
+---
+ src/lib/banal/Struct-Inline.hpp   | 6 +++---
+ src/lib/prof/Metric-AExpr.cpp     | 4 ++--
+ src/lib/prof/Metric-AExpr.hpp     | 2 +-
+ src/lib/prof/Metric-AExprIncr.hpp | 6 +++---
+ src/lib/support/StringTable.hpp   | 2 +-
+ 5 files changed, 10 insertions(+), 10 deletions(-)
+
+diff --git a/src/lib/banal/Struct-Inline.hpp b/src/lib/banal/Struct-Inline.hpp
+index ffb93355fd..0099ad112d 100644
+--- a/src/lib/banal/Struct-Inline.hpp
++++ b/src/lib/banal/Struct-Inline.hpp
+@@ -150,14 +150,14 @@ public:
+     pretty_index = strTab.str2index(node.getPrettyName());
+   }
+ 
+-  bool operator == (const FLPIndex rhs)
++  bool operator == (const FLPIndex rhs) const
+   {
+     return file_index == rhs.file_index
+       && line_num == rhs.line_num
+       && pretty_index == rhs.pretty_index;
+   }
+ 
+-  bool operator != (const FLPIndex rhs)
++  bool operator != (const FLPIndex rhs) const
+   {
+     return ! (*this == rhs);
+   }
+@@ -167,7 +167,7 @@ public:
+ // Compare (file, line, proc) indices lexigraphically.
+ class FLPCompare {
+ public:
+-  bool operator() (const FLPIndex t1, const FLPIndex t2)
++  bool operator() (const FLPIndex t1, const FLPIndex t2) const
+   {
+     if (t1.file_index < t2.file_index) { return true; }
+     if (t1.file_index > t2.file_index) { return false; }
+diff --git a/src/lib/prof/Metric-AExpr.cpp b/src/lib/prof/Metric-AExpr.cpp
+index 2ce43e6d39..5b32ff67d1 100644
+--- a/src/lib/prof/Metric-AExpr.cpp
++++ b/src/lib/prof/Metric-AExpr.cpp
+@@ -483,7 +483,7 @@ CoefVar::eval(const Metric::IData& mdata) const
+   double sdev = sqrt(v_m.first); // always non-negative
+   double mean = v_m.second;
+   double z = 0.0;
+-  if (mean > epsilon) {
++  if (mean > hpc_epsilon) {
+     z = sdev / mean;
+   }
+ 
+@@ -522,7 +522,7 @@ RStdDev::eval(const Metric::IData& mdata) const
+   double sdev = sqrt(v_m.first); // always non-negative
+   double mean = v_m.second;
+   double z = 0.0;
+-  if (mean > epsilon) {
++  if (mean > hpc_epsilon) {
+     z = (sdev / mean) * 100;
+   }
+ 
+diff --git a/src/lib/prof/Metric-AExpr.hpp b/src/lib/prof/Metric-AExpr.hpp
+index 56359cc9df..d75189f763 100644
+--- a/src/lib/prof/Metric-AExpr.hpp
++++ b/src/lib/prof/Metric-AExpr.hpp
+@@ -97,7 +97,7 @@
+ 
+ //****************************************************************************
+ 
+-#define epsilon  (0.000001)
++#define hpc_epsilon  (0.000001)
+ 
+ namespace Prof {
+ 
+diff --git a/src/lib/prof/Metric-AExprIncr.hpp b/src/lib/prof/Metric-AExprIncr.hpp
+index f1b38d7f74..d0c0feb7e6 100644
+--- a/src/lib/prof/Metric-AExprIncr.hpp
++++ b/src/lib/prof/Metric-AExprIncr.hpp
+@@ -97,7 +97,7 @@
+ 
+ //****************************************************************************
+ 
+-#define epsilon  (0.000001)
++#define hpc_epsilon  (0.000001)
+ 
+ namespace Prof {
+ 
+@@ -841,7 +841,7 @@ public:
+     double sdev = finalizeStdDev(mdata);
+     double mean = accumVar(1, mdata);
+     double z = 0.0;
+-    if (mean > epsilon) {
++    if (mean > hpc_epsilon) {
+       z = sdev / mean;
+     }
+     accumVar(0, mdata) = z;
+@@ -927,7 +927,7 @@ public:
+     double sdev = finalizeStdDev(mdata);
+     double mean = accumVar(1, mdata);
+     double z = 0.0;
+-    if (mean > epsilon) {
++    if (mean > hpc_epsilon) {
+       z = (sdev / mean) * 100;
+     }
+     accumVar(0, mdata) = z;
+diff --git a/src/lib/support/StringTable.hpp b/src/lib/support/StringTable.hpp
+index 9930bc5649..36ce5b7fa9 100644
+--- a/src/lib/support/StringTable.hpp
++++ b/src/lib/support/StringTable.hpp
+@@ -75,7 +75,7 @@ namespace HPC {
+ // compare the strings, not the pointers
+ class StringCompare {
+ public:
+-  bool operator() (const std::string *s1, const std::string *s2)
++  bool operator() (const std::string *s1, const std::string *s2) const
+   {
+     return *s1 < *s2;
+   }
+-- 
+GitLab
+
diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py
index bb87c841af8..66972f39388 100644
--- a/var/spack/repos/builtin/packages/hpctoolkit/package.py
+++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py
@@ -162,17 +162,11 @@ class Hpctoolkit(AutotoolsPackage):
     # Fix the build for old revs with gcc 10.x.
     patch("gcc10-enum.patch", when="@2020.01.01:2020.08 %gcc@10.0:")
 
-    patch(
-        "https://gitlab.com/hpctoolkit/hpctoolkit/-/commit/511afd95b01d743edc5940c84e0079f462b2c23e.patch",
-        sha256="8da18df88a80847c092da8d0892de51ea2bf2523124148b6305ab8717707d897",
-        when="@2019.08.01:2021.03 %gcc@11.0:",
-    )
+    patch("511afd95b01d743edc5940c84e0079f462b2c23e.patch", when="@2019.08.01:2021.03 %gcc@11.0:")
 
     # Update configure for rocm 5.3.0
     patch(
-        "https://gitlab.com/hpctoolkit/hpctoolkit/-/commit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch",
-        sha256="484045891a665cdba3b0f141540c89f0d691ed32c5912ef62a93670d44c2786c",
-        when="@2022.04:2022.10 +rocm ^hip@5.3.0:",
+        "411d62544717873432c49ef45c7cb99cc5de2fb8.patch", when="@2022.04:2022.10 +rocm ^hip@5.3.0:"
     )
 
     # Change python to python3 for some old revs that use a script