Merge branch 'main' into aspect_ratio_plot

before-notebook.d/43_start-hq.sh

@@ -10,34 +10,51 @@ set -x
 # But for developers, please update your cgroup version to v2.
 # See: https://kubernetes.io/docs/concepts/architecture/cgroups/#using-cgroupv2
 
-# computer memory from runtime
-MEMORY_LIMIT=$(cat /sys/fs/cgroup/memory.max)
+# Default to cgroupv1 paths
+CPU_QUOTA_PATH="/sys/fs/cgroup/cpu/cpu.cfs_quota_us"
+CPU_PERIOD_PATH="/sys/fs/cgroup/cpu/cpu.cfs_period_us"
+MEMORY_LIMIT_PATH="/sys/fs/cgroup/memory/memory.limit_in_bytes"
 
-if [ "$MEMORY_LIMIT" = "max" ]; then
-  MEMORY_LIMIT=4096
-  echo "No memory limit set, use 4GiB"
-else
-  MEMORY_LIMIT=$(echo "scale=0; $MEMORY_LIMIT / (1024 * 1024)" | bc)
-  echo "Memory Limit: ${MEMORY_LIMIT} MiB"
+# Fallback if cgroupv2 paths exist
+if [ -f /sys/fs/cgroup/cpu.max ]; then
+  CPU_QUOTA_PATH="/sys/fs/cgroup/cpu.max"
+  CPU_PERIOD_PATH="/sys/fs/cgroup/cpu.max"
+fi
+
+if [ -f /sys/fs/cgroup/memory.max ]; then
+  MEMORY_LIMIT_PATH="/sys/fs/cgroup/memory.max"
 fi
 
-# Compute number of cpus allocated to the container
-CPU_LIMIT=$(awk '{print $1}' /sys/fs/cgroup/cpu.max)
-CPU_PERIOD=$(awk '{print $2}' /sys/fs/cgroup/cpu.max)
+# Compute memory limit
+if [ -f "$MEMORY_LIMIT_PATH" ]; then
+  MEMORY_LIMIT=$(cat "$MEMORY_LIMIT_PATH")
+  if [ "$MEMORY_LIMIT" = "max" ] || [ "$MEMORY_LIMIT" -eq -1 ]; then
+    MEMORY_LIMIT=4096
+  else
+    MEMORY_LIMIT=$(echo "scale=0; $MEMORY_LIMIT / (1024 * 1024)" | bc)
+  fi
+else
+  MEMORY_LIMIT=4096
+fi
+echo "Memory Limit: ${MEMORY_LIMIT} MiB"
 
-if [ "$CPU_PERIOD" -ne 0 ]; then
-  CPU_NUMBER=$(echo "scale=2; $CPU_LIMIT / $CPU_PERIOD" | bc)
-  echo "Number of CPUs allocated: $CPU_NUMBER"
+# Compute CPU limit
+if [ -f "$CPU_QUOTA_PATH" ] && [ -f "$CPU_PERIOD_PATH" ]; then
+  CPU_LIMIT=$(cat "$CPU_QUOTA_PATH")
+  CPU_PERIOD=$(cat "$CPU_PERIOD_PATH")
 
-  # for HQ setting round to integer number of CPUs, the left are for system tasks
-  CPU_LIMIT=$(echo "scale=0; $CPU_LIMIT / $CPU_PERIOD" | bc)
+  if [ "$CPU_LIMIT" != "max" ] && [ "$CPU_PERIOD" -ne 0 ]; then
+    CPU_NUMBER=$(echo "scale=2; $CPU_LIMIT / $CPU_PERIOD" | bc)
+    CPU_LIMIT=$(echo "$CPU_NUMBER / 1" | bc)  # Round down to integer
+  else
+    CPU_LIMIT=$(nproc)
+  fi
 else
-  # if no limit (with local OCI without setting cpu limit, use all CPUs)
   CPU_LIMIT=$(nproc)
-  echo "No CPU limit set"
 fi
+echo "Number of CPUs allocated: $CPU_LIMIT"
 
-# Start hq server with a worker
+# Start HQ server and worker
 run-one-constantly hq server start 1>$HOME/.hq-stdout 2>$HOME/.hq-stderr &
 run-one-constantly hq worker start --cpus=${CPU_LIMIT} --resource "mem=sum(${MEMORY_LIMIT})" --no-detect-resources &
 

docs/source/conf.py

@@ -13,7 +13,7 @@
 
 # -- Project information -----------------------------------------------------
 
-version = "v24.10.0a6"
+version = "v24.10.0a7"
 release = f"{version}-dev"
 project = "Quantum ESPRESSO App"
 copyright_first_year = "2023"

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = aiidalab_qe
-version = 24.10.0a6
+version = 24.10.0a7
 description = Package for the AiiDAlab QE app
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -54,6 +54,7 @@ aiidalab_qe.app.parameters = qeapp.yaml
 aiidalab_qe.app.static.styles = *.css
 aiidalab_qe.app.static.templates = *.jinja
 aiidalab_qe.app.structure.examples = *
+aiidalab_qe.app.result.components.summary = schema.json
 aiidalab_qe.plugins.xas = pseudo_toc.yaml
 aiidalab_qe.plugins.xps.structure_examples = *
 aiidalab_qe.plugins.xas.structure_examples = *
@@ -76,7 +77,7 @@ categories =
     quantum
 
 [bumpver]
-current_version = "v24.10.0a6"
+current_version = "v24.10.0a7"
 version_pattern = "v0Y.0M.PATCH[PYTAGNUM]"
 commit_message = "Bump version {old_version} -> {new_version}"
 commit = True

src/aiidalab_qe/setup/codes.py

@@ -1,3 +1,4 @@
+import json
 import subprocess
 from pathlib import Path
 from shutil import which
@@ -44,18 +45,45 @@ def get_qe_env():
 
 
 def qe_installed():
-    import json
+    """Check if Quantum Espresso (QE) is installed in the specified conda environment.
 
-    env_exist = get_qe_env().exists()
-    proc = subprocess.run(
-        ["conda", "list", "-n", f"{get_qe_env().name}", "--json", "--full-name", "qe"],
-        check=True,
-        capture_output=True,
-    )
+    Returns:
+        bool: True if the environment exists and QE is installed; False otherwise.
+    """
+    try:
+        # Verify if the specified conda environment exists
+        env_exist = get_qe_env().exists()
+
+        if not env_exist:
+            return False
+
+        # Run the conda list command to check for the QE package
+        proc = subprocess.run(
+            [
+                "conda",
+                "list",
+                "-n",
+                f"{get_qe_env().name}",
+                "--json",
+                "--full-name",
+                "qe",
+            ],
+            check=True,
+            capture_output=True,
+        )
 
-    info = json.loads(str(proc.stdout.decode()))[0]
+        # Load and interpret the JSON output
+        info = json.loads(proc.stdout.decode())
 
-    return env_exist and "qe" == info["name"]
+        # Check if 'qe' is listed in the environment
+        for package in info:
+            if package.get("name") == "qe":
+                return True
+        return False  # noqa: TRY300
+    except Exception as error:
+        raise RuntimeError(
+            "Failed to check if Quantum Espresso is installed."
+        ) from error
 
 
 def install_qe():

src/aiidalab_qe/version.py

@@ -2,4 +2,4 @@
 
 """This module contains project version information for both the app and the workflow."""
 
-__version__ = "v24.10.0a6"
+__version__ = "v24.10.0a7"