fix: Apptainer build mount points and SLURM resource limits

- Add %setup section to create mount points before container init
- Use --no-mount home,tmp during build to prevent bind errors
- Increase FDR computation time to 4h and memory to 32GB

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

apptainer.def

@@ -6,7 +6,19 @@ From: pytorch/pytorch:2.1.0-cuda12.1-cudnn8-runtime
     Version 1.0
     Description Conformal Protein Retrieval - Functional protein mining with statistical guarantees
 
+%setup
+    # Create mount points in the container rootfs BEFORE the container is created
+    # This runs on the host and $APPTAINER_ROOTFS points to the container's root
+    # Required because the system may try to bind mount these paths during build
+    mkdir -p ${APPTAINER_ROOTFS}/shared
+    mkdir -p ${APPTAINER_ROOTFS}/scratch
+    mkdir -p ${APPTAINER_ROOTFS}/groups
+    mkdir -p ${APPTAINER_ROOTFS}/home
+
 %post
+    # Ensure mount points exist (redundant but safe)
+    mkdir -p /shared /scratch /groups /home
+
     # Update and install system dependencies
     apt-get update && apt-get install -y \
         git \

scripts/slurm_build_apptainer.sh

@@ -31,7 +31,9 @@ echo "Temp dir: $APPTAINER_TMPDIR"
 echo ""
 
 # Build the container
-apptainer build --fakeroot cpr.sif apptainer.def
+# Use --no-mount to disable automatic bind mounts during build
+# This prevents "destination doesn't exist" errors from system-configured mounts
+apptainer build --fakeroot --no-mount home,tmp cpr.sif apptainer.def
 
 BUILD_STATUS=$?
 

scripts/slurm_compute_fdr_thresholds.sh

@@ -4,8 +4,8 @@
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=4
-#SBATCH --mem=16G
-#SBATCH --time=01:00:00
+#SBATCH --mem=32G
+#SBATCH --time=04:00:00
 #SBATCH --output=/groups/doudna/projects/ronb/conformal-protein-retrieval/logs/fdr_thresholds_%j.log
 #SBATCH --error=/groups/doudna/projects/ronb/conformal-protein-retrieval/logs/fdr_thresholds_%j.err