Add one line installer and pulsatile case

README.md

@@ -4,7 +4,22 @@
 [arXiv:2404.14187](https://arxiv.org/abs/2404.14187)
 
 ## Quickstart
-1. Install docker and pull the svMultiphyiscs image from 
+
+### One-Line Install (Recommended)
+
+Install FSGe on a new machine with a single command:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Eleven7825/svFSGe/master/scripts/install.sh | bash
+```
+
+This will clone the repository, set up the Docker environment, and drop you into an interactive shell ready to run simulations.
+
+**Prerequisites**: Docker and git must be installed and Docker must be running.
+
+### Manual Setup
+
+1. Install docker and pull the svMultiphyiscs image from
 ```bash
 docker pull simvascular/solver:latest
 ```
@@ -54,19 +69,52 @@ python3 ./fsg.py in_sim/partitioned_full.json
 
 ## Quick Setup Script
 
-For convenience, use the provided setup script to automate Docker environment setup:
+If you've already cloned the repository, use the setup script to create a persistent Docker environment:
 
 ```bash
 # From the svFSGe directory
 ./scripts/setup_docker.sh
 ```
 
 This script will:
-- Create necessary directories
-- Start Docker container with proper mounts
+- Create a persistent Docker container named `fsg-dev`
+- Start the container with proper volume mounts
 - Clone and build svFSIplus
 - Install Python dependencies
-- Provide an interactive shell ready to run simulations 
+- Provide an interactive shell ready to run simulations
+
+The container persists after you exit. Run the script again to reconnect, or use:
+```bash
+docker exec -it fsg-dev /bin/bash
+```
+
+## HPC / Singularity Installation
+
+For HPC environments where Docker is not available, use Singularity/Apptainer:
+
+```bash
+git clone https://github.com/Eleven7825/svFSGe.git ~/svFSGe
+cd ~/svFSGe
+./scripts/setup_singularity.sh
+```
+
+**Run test simulation:**
+```bash
+./scripts/run_simulation.sh in_sim/partitioned_test.json
+```
+
+**Or manually with Singularity:**
+```bash
+singularity exec \
+  --bind ~/svfsi:/svfsi \
+  --bind ~/svFSGe:/svFSGe \
+  ~/svFSGe/singularity_images/simvascular-solver.sif \
+  python3 /svFSGe/fsg.py /svFSGe/in_sim/partitioned_test.json
+```
+
+**Note**: Adjust the number of cores in your configuration files to match your HPC allocation.
+
+**Prerequisites**: Singularity/Apptainer and git. See [README_SINGULARITY.md](README_SINGULARITY.md) for complete documentation.
 
 ## Continuous Integration
 

copy_latest_partitioned.sh

@@ -0,0 +1,129 @@
+#!/bin/bash
+
+# Script to copy latest partitioned_* folder with selective VTU/BIN file handling
+# Configuration
+SOURCE_BASE="${SOURCE_BASE:-bouchet:~/svFSGe}"  # Remote source on bouchet (sc3544)
+DEST_DIR="${DEST_DIR:-.}"  # Current directory by default
+KEEP_LAST_N_PULSATILE=400  # Keep last N pulsatile VTU files (ignore .bin files)
+KEEP_LAST_N_STEADY=10      # Keep last N steady VTU files (ignore .bin files)
+
+set -e  # Exit on error
+
+# Optional argument: folder name to copy (defaults to latest)
+FOLDER_ARG="${1:-}"
+
+# SSH ControlMaster settings - authenticate once, reuse connection
+SSH_HOST="${SOURCE_BASE%%:*}"
+CONTROL_PATH="/tmp/ssh_control_${SSH_HOST}_%h_%p_%r"
+SSH_OPTS="-o ControlMaster=auto -o ControlPath=$CONTROL_PATH -o ControlPersist=600"
+
+echo "=== Partitioned Folder Copy Script ==="
+echo "Source: $SOURCE_BASE"
+echo "Destination: $DEST_DIR"
+echo ""
+
+# Establish master connection (one-time authentication)
+if [[ $SOURCE_BASE == *:* ]]; then
+    echo "Establishing SSH connection (you'll authenticate once here)..."
+    ssh $SSH_OPTS -t "$SSH_HOST" "echo 'Connected'" > /dev/null 2>&1
+    echo ""
+fi
+
+# Find the target partitioned_* directory (use argument if provided, else latest)
+if [ -n "$FOLDER_ARG" ]; then
+    FOLDER_NAME="$FOLDER_ARG"
+    if [[ $SOURCE_BASE == *:* ]]; then
+        REMOTE_HOST="${SOURCE_BASE%%:*}"
+        LATEST_DIR="$REMOTE_HOST:~/svFSGe/$FOLDER_NAME"
+    else
+        LATEST_DIR="$SOURCE_BASE/$FOLDER_NAME"
+    fi
+elif [[ $SOURCE_BASE == *:* ]]; then
+    # Remote source - get just the folder name
+    REMOTE_HOST="${SOURCE_BASE%%:*}"
+    FOLDER_NAME=$(ssh $SSH_OPTS "$REMOTE_HOST" "ls -td ~/svFSGe/partitioned_* 2>/dev/null | head -1 | xargs basename" 2>/dev/null | tr -d '\r')
+    LATEST_DIR="$REMOTE_HOST:~/svFSGe/$FOLDER_NAME"
+else
+    # Local source
+    LATEST_DIR=$(ls -td "$SOURCE_BASE"/partitioned_* 2>/dev/null | head -1)
+    FOLDER_NAME=$(basename "$LATEST_DIR")
+fi
+
+if [ -z "$FOLDER_NAME" ]; then
+    echo "Error: No partitioned_* directory found in $SOURCE_BASE"
+    exit 1
+fi
+echo "Found latest folder: $FOLDER_NAME"
+
+# Create destination directory
+mkdir -p "$DEST_DIR/$FOLDER_NAME"
+
+# Step 1: Copy everything EXCEPT .vtu and .bin files
+echo "Step 1: Copying folder structure and other files (excluding VTU/BIN)..."
+if [[ $SOURCE_BASE == *:* ]]; then
+    rsync -av -e "ssh $SSH_OPTS" \
+        --exclude='pulsatile/*.vtu' \
+        --exclude='pulsatile/*.bin' \
+        --exclude='steady/*.vtu' \
+        --exclude='steady/*.bin' \
+        --exclude='gr_restart/*.vtu' \
+        "$LATEST_DIR/" "$DEST_DIR/$FOLDER_NAME/"
+else
+    rsync -av \
+        --exclude='pulsatile/*.vtu' \
+        --exclude='pulsatile/*.bin' \
+        --exclude='steady/*.vtu' \
+        --exclude='steady/*.bin' \
+        --exclude='gr_restart/*.vtu' \
+        "$LATEST_DIR/" "$DEST_DIR/$FOLDER_NAME/"
+fi
+
+# Step 2: Copy only last N VTU and BIN files
+echo "Step 2: Copying VTU and BIN files (last N timesteps)..."
+for dir in pulsatile steady; do
+    # Determine how many files to keep for this directory
+    if [ "$dir" = "pulsatile" ]; then
+        KEEP_LAST_N=$KEEP_LAST_N_PULSATILE
+    else
+        KEEP_LAST_N=$KEEP_LAST_N_STEADY
+    fi
+
+    echo "  Processing $dir (keeping last $KEEP_LAST_N timesteps)..."
+    mkdir -p "$DEST_DIR/$FOLDER_NAME/$dir"
+
+    if [[ $SOURCE_BASE == *:* ]]; then
+        # Remote: get base names of last N VTU files, then copy both VTU and BIN
+        REMOTE_HOST="${SOURCE_BASE%%:*}"
+        REMOTE_DIR="~/svFSGe/$FOLDER_NAME/$dir"
+
+        BASENAMES=$(ssh $SSH_OPTS "$REMOTE_HOST" "ls -1v $REMOTE_DIR/*_*.vtu 2>/dev/null | sort -V | tail -$KEEP_LAST_N | xargs -I{} basename {} .vtu" | tr -d '\r')
+
+        echo "$BASENAMES" | while read base; do
+            if [ -n "$base" ]; then
+                for ext in vtu bin; do
+                    rsync -av -e "ssh $SSH_OPTS" "$REMOTE_HOST:$REMOTE_DIR/$base.$ext" "$DEST_DIR/$FOLDER_NAME/$dir/" 2>/dev/null || true
+                done
+            fi
+        done
+    else
+        # Local: copy last N VTU and BIN files
+        BASENAMES=$(ls -1v "$LATEST_DIR/$dir"/*_*.vtu 2>/dev/null | sort -V | tail -$KEEP_LAST_N | xargs -I{} basename {} .vtu)
+
+        echo "$BASENAMES" | while read base; do
+            if [ -n "$base" ]; then
+                for ext in vtu bin; do
+                    [ -f "$LATEST_DIR/$dir/$base.$ext" ] && cp "$LATEST_DIR/$dir/$base.$ext" "$DEST_DIR/$FOLDER_NAME/$dir/"
+                done
+            fi
+        done
+    fi
+done
+
+echo ""
+echo "=== Copy completed successfully! ==="
+echo "Folder location: $DEST_DIR/$FOLDER_NAME"
+
+# Clean up SSH master connection
+if [[ $SOURCE_BASE == *:* ]]; then
+    ssh $SSH_OPTS -O exit "$SSH_HOST" 2>/dev/null || true
+fi

fsg.py

@@ -211,6 +211,10 @@ def plot_convergence(self):
         plt.close(fig)
 
     def archive(self):
+        # save debug QR data if enabled
+        if self.p["coup"].get("iqn_ils_debug", False):
+            np.save(os.path.join(self.p["f_out"], "debug_qr.npy"), self.debug_qr)
+
         # save stored results
         self.p["error"] = self.err
 
@@ -283,6 +287,19 @@ def coup_step_iqn_ils(self, i, t, n, times):
             if ((t == 0) or (t == 1 and n < 5)):# or n == 0:
                 self.coup_relax("solid", "disp", i, t, n)
             else:
+                # reset history vectors at start of each new load step if requested
+                if n == 0 and self.p["coup"].get("iqn_ils_reset", False):
+                    self.mat_V = []
+                    self.mat_W = []
+                    # also clear dk and res so difference vectors don't span load steps
+                    self.dk["disp"] = [self.dk["disp"][-1]]
+                    self.res = [self.res[-1]]
+
+                # fall back to relaxation if no history vectors available yet
+                if not self.mat_V:
+                    self.coup_relax("solid", "disp", i, t, n)
+                    return
+
                 # maximum number of time steps used in IQN-ILS
                 nq = self.p["coup"]["iqn_ils_q"]
 
@@ -294,12 +311,33 @@ def coup_step_iqn_ils(self, i, t, n, times):
                 tmp_V = np.array(self.mat_V).T
                 tmp_W = np.array(self.mat_W).T
                 eps = self.p["coup"]["iqn_ils_eps"]
+
+                # debug: save V and W before filtering
+                if self.p["coup"].get("iqn_ils_debug", False):
+                    self.debug_qr["V_before"] += [tmp_V.copy()]
+                    self.debug_qr["W_before"] += [tmp_W.copy()]
+                    self.debug_qr["ncols_before"] += [tmp_V.shape[1]]
+
                 qq, rr, tmp_V, tmp_W = QRfiltering_mod(tmp_V, tmp_W, eps)
 
+                # debug: save Q, R and V, W after filtering
+                if self.p["coup"].get("iqn_ils_debug", False):
+                    self.debug_qr["Q"] += [qq.copy()]
+                    self.debug_qr["R"] += [rr.copy()]
+                    self.debug_qr["V_after"] += [tmp_V.copy()]
+                    self.debug_qr["W_after"] += [tmp_W.copy()]
+                    self.debug_qr["ncols_after"] += [tmp_V.shape[1]]
+
                 # solve for coefficients
                 ss = np.dot(np.transpose(qq), -self.res[-1])
                 cc = np.linalg.solve(rr, ss)
 
+                # debug: save coefficients and load step/sub-iter indices
+                if self.p["coup"].get("iqn_ils_debug", False):
+                    self.debug_qr["cc"] += [cc.copy()]
+                    self.debug_qr["t"] += [t]
+                    self.debug_qr["n"] += [n]
+
                 # update
                 vec_new = dtk + np.dot(tmp_W, cc)
                 self.curr.add(("solid", "disp", "int"), vec_new.reshape((-1, 3)))

in_sim/partitioned_full.json

@@ -27,7 +27,8 @@
         "method": "iqn_ils",
         "omega0": 0.1,
         "iqn_ils_q": 20,
-        "iqn_ils_eps": 1.0e-1
+        "iqn_ils_eps": 1.0e-1,
+        "iqn_ils_reset": false
     },
     "nmax": 10,
     "fmax": 1.0,

in_sim/partitioned_full_debug.json

@@ -0,0 +1,85 @@
+{
+    "fsi": true,
+    "debug": false,
+    "tortuosity": false,
+    "mesh": "fsg_full_coarse.json",
+    "n_procs": {
+        "fluid": 4,
+        "mesh": 1,
+        "solid": 1
+    },
+    "fluid": {
+        "mu": 4e-06,
+        "rho": 1.06e-6,
+        "p0": 13.9868,
+        "q0": 1000.0,
+        "q0_rate": 200.0
+    },
+    "n_max": {
+        "fluid": 10,
+        "mesh": 1,
+        "solid": 1
+    },
+    "coup": {
+        "nmax": 200,
+        "nmin": 1,
+        "tol": 1.0e-3,
+        "method": "iqn_ils",
+        "omega0": 0.1,
+        "iqn_ils_q": 20,
+        "iqn_ils_eps": 1.0e-1,
+        "iqn_ils_debug": true,
+        "iqn_ils_reset": false
+    },
+    "nmax": 10,
+    "fmax": 1.0,
+    "predict_file": false,
+    "exe": {
+        "fluid": "/svfsi/svFSI-build/bin/svFSI",
+        "mesh": "/svfsi/svFSI-build/bin/svFSI",
+        "solid": "/svfsi/svFSI-build/bin/svFSI"
+    },
+    "inp": {
+        "fluid": "steady_full.xml",
+        "mesh": "mesh_full.xml",
+        "solid": "gr_full_restart.xml"
+    },
+    "interfaces": {
+        "bc_flow": "steady_flow.dat",
+        "bc_pressure": "steady_pressure.dat",
+        "disp": "interface_displacement.dat",
+        "inflow_vector": "inflow_vector.dat",
+        "geo_fluid": "fluid.vtu",
+        "geo_solid": "solid.vtu",
+        "geo_mesh": "mesh.vtu",
+        "load_pressure": "interface_pressure.vtp",
+        "load_wss": "interface_wss.vtp"
+    },
+    "out": {
+        "fluid": "steady",
+        "mesh": "mesh",
+        "solid": "gr_restart"
+    },
+    "name": "partitioned",
+    "paths_linux_ubuntu": {
+        "in_geo": "/svFSGe/in_geo",
+        "in_petsc": "/svFSGe/in_petsc",
+        "in_svfsi": "/svFSGe/in_svfsi_plus",
+        "exe": "/",
+        "root": "."
+    },
+    "paths_linux_centos": {
+        "in_geo": "/home/users/pfaller/work/repos/FSG/in_geo",
+        "in_petsc": "/home/users/pfaller/work/repos/FSG/in_petsc",
+        "in_svfsi": "/home/users/pfaller/work/repos/FSG/in_svfsi_plus",
+        "exe": "/home/users/pfaller/work/repos",
+        "root": "."
+    },
+    "paths_darwin": {
+        "in_geo": "/Users/pfaller/work/repos/FSG/in_geo",
+        "in_petsc": "/Users/pfaller/work/repos/FSG/in_petsc",
+        "in_svfsi": "/Users/pfaller/work/repos/FSG/in_svfsi_plus",
+        "exe": "/Users/pfaller/work/repos",
+        "root": "."
+    }
+}