diff --git a/.github/container/nsys_jax/nsys_jax/scripts/nsys_jax.py b/.github/container/nsys_jax/nsys_jax/scripts/nsys_jax.py
index dfd6b29d1..e5287c823 100644
--- a/.github/container/nsys_jax/nsys_jax/scripts/nsys_jax.py
+++ b/.github/container/nsys_jax/nsys_jax/scripts/nsys_jax.py
@@ -18,6 +18,7 @@
 import tempfile
 import time
 import traceback
+from typing import Optional
 import zipfile
 
 from .utils import execute_analysis_script, shuffle_analysis_arg
@@ -259,21 +260,22 @@ def override_nsys_default(arg, value):
     if "JAX_ENABLE_COMPILATION_CACHE" not in env:
         env["JAX_ENABLE_COMPILATION_CACHE"] = "false"
 
+    def format_flag(tup):
+        n, v = tup
+        return f"--{n}" if v is None else f"--{n}={v}"
+
     # Get the existing XLA_FLAGS and parse them into a dictionary.
-    xla_flag_list = shlex.split(env.get("XLA_FLAGS", ""))
-    xla_flags = {}
-    for flag in xla_flag_list:
+    xla_flags: dict[str, Optional[str]] = {}
+    for flag in shlex.split(env.get("XLA_FLAGS", "")):
         assert flag.startswith("--")
         bits = flag[2:].split("=", maxsplit=1)
         name, value = bits[0], bits[1] if len(bits) > 1 else None
-        assert name not in xla_flags
+        if name in xla_flags:
+            print(
+                f"WARNING: {format_flag((name, xla_flags[name]))} being overriden by {flag}"
+            )
         xla_flags[name] = value
 
-    def as_list(flags):
-        return [f"--{n}" if v is None else f"--{n}={v}" for n, v in flags.items()]
-
-    assert xla_flag_list == as_list(xla_flags)
-
     def as_bool(s):
         """String -> bool conversion following XLA's semantics."""
         if s.lower() == "true" or s == "1":
@@ -298,7 +300,7 @@ def as_bool(s):
 
     # Serialise the modified XLA flags. shlex.join is tempting, but doesn't seem to
     # get the right result for --xla_dump_hlo_pass_re=.*, as it adds extra quotes.
-    env["XLA_FLAGS"] = " ".join(as_list(xla_flags))
+    env["XLA_FLAGS"] = " ".join(map(format_flag, xla_flags.items()))
 
     # Run the application in nsys
     # TODO: consider being more fault-tolerant?
diff --git a/.github/container/nsys_jax/nsys_jax/scripts/patch_nsys.py b/.github/container/nsys_jax/nsys_jax/scripts/patch_nsys.py
index 44496e99a..bbf364560 100644
--- a/.github/container/nsys_jax/nsys_jax/scripts/patch_nsys.py
+++ b/.github/container/nsys_jax/nsys_jax/scripts/patch_nsys.py
@@ -1,4 +1,3 @@
-import os
 import re
 import shutil
 import subprocess
@@ -1372,11 +1371,20 @@ def main():
             patch_content = None
     if patch_content is not None:
         print(f"Patching Nsight Systems version {m.group(1)}")
-        # e.g. /opt/nvidia/nsight-systems-cli/2024.7.1/target-linux-x64
-        tdir = os.path.dirname(os.path.realpath(nsys))
+        nsys_recipe_help = subprocess.check_output(
+            [nsys, "recipe", "--help"], text=True
+        )
+        m = re.search(
+            r"List of required Python packages: '(.*?)/nsys_recipe/requirements/common.txt'",
+            nsys_recipe_help,
+        )
+        assert m is not None, (
+            f"Could not determine target directory from: {nsys_recipe_help}"
+        )
+        # e.g. /opt/nvidia/nsight-systems-cli/2024.7.1/target-linux-x64/python/packages
         subprocess.run(
             [shutil.which("git"), "apply"],
-            cwd=os.path.join(tdir, "python", "packages"),
+            cwd=m.group(1),
             input=patch_content,
             check=True,
             text=True,
diff --git a/.github/workflows/nsys-jax.yaml b/.github/workflows/nsys-jax.yaml
index e15cd557f..6e8fbfaf5 100644
--- a/.github/workflows/nsys-jax.yaml
+++ b/.github/workflows/nsys-jax.yaml
@@ -1,4 +1,4 @@
-name: nsys-jax pure-Python CI
+name: nsys-jax non-GPU CI
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
@@ -274,3 +274,22 @@ jobs:
           if [[ $format_status != 0 || $check_status != 0 ]]; then
             exit 1
           fi
+  installation:
+    strategy:
+      matrix:
+        include:
+          - container: "nvidia/cuda:12.6.3-base-ubuntu24.04"
+            nsys_package: "cuda-nsight-systems-12-6"
+          - container: "nvidia/cuda:12.8.0-base-ubuntu24.04"
+            nsys_package: "cuda-nsight-systems-12-8"
+    runs-on: ubuntu-latest
+    container: "${{ matrix.container }}"
+    steps:
+      - name: Install ${{ matrix.nsys_package }}
+        run: |
+          apt-get update
+          apt-get install -y git python3-pip ${{ matrix.nsys_package }}
+      - name: Install nsys-jax
+        run: pip install --break-system-packages git+https://github.com/NVIDIA/JAX-Toolbox.git@${{ github.head_ref || github.sha }}#subdirectory=.github/container/nsys_jax
+      - name: Run nsys-jax-patch-nsys
+        run: nsys-jax-patch-nsys