From a70149c1ef7deb0a693f1ed478af6a4e259b6305 Mon Sep 17 00:00:00 2001
From: Benjamin Lee <130000039+benlee0423@users.noreply.github.com>
Date: Tue, 17 Dec 2024 14:13:09 -0800
Subject: [PATCH 1/7] add empirical model to ngiab

---
 singularity/templates/guide/HelloNGEN.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/singularity/templates/guide/HelloNGEN.sh b/singularity/templates/guide/HelloNGEN.sh
index bb478f9..3673d36 100644
--- a/singularity/templates/guide/HelloNGEN.sh
+++ b/singularity/templates/guide/HelloNGEN.sh
@@ -89,9 +89,9 @@ select option in "${options[@]}"; do
   case $option in
     "Run NextGen model framework in serial mode"|"Run NextGen model framework in parallel mode")
       echo -e "\n"
-      n1=${selected_catchment:-$(read -p "Enter the hydrofabric catchment file path: " n1; echo "$n1")}
-      n2=${selected_nexus:-$(read -p "Enter the hydrofabric nexus file path: " n2; echo "$n2")}
-      n3=${selected_realization:-$(read -p "Enter the Realization file path: " n3; echo "$n3")}
+      n1=${selected_catchment:-$(read -erp "Enter the hydrofabric catchment file path: " n1; echo "$n1")}
+      n2=${selected_nexus:-$(read -erp "Enter the hydrofabric nexus file path: " n2; echo "$n2")}
+      n3=${selected_realization:-$(read -erp "Enter the Realization file path: " n3; echo "$n3")}
 
       echo -e "${GREEN}Selected files:\nCatchment: $n1\nNexus: $n2\nRealization: $n3${RESET}\n"
 

From 678bbf8300c31aa4b5bc66982c45fc1fbe1b0c91 Mon Sep 17 00:00:00 2001
From: Benjamin Lee <130000039+benlee0423@users.noreply.github.com>
Date: Tue, 17 Dec 2024 14:18:41 -0800
Subject: [PATCH 2/7] add empirical model to ngiab

---
 singularity/singularity_ngen.def | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/singularity/singularity_ngen.def b/singularity/singularity_ngen.def
index f14792d..d3f9b6a 100644
--- a/singularity/singularity_ngen.def
+++ b/singularity/singularity_ngen.def
@@ -5,7 +5,7 @@ From: rockylinux:9.1
     export TROUTE_REPO="CIROH-UA/t-route"
     export TROUTE_BRANCH="datastream"
     export NGEN_REPO="CIROH-UA/ngen"
-    export NGEN_BRANCH="main"
+    export NGEN_BRANCH="ngiab"
     export PATH="/usr/lib64/mpich/bin:$PATH"
     export PATH="/root/.cargo/bin:$PATH"
     export PATH="/ngen/.venv/bin:$PATH"
@@ -140,6 +140,9 @@ From: rockylinux:9.1
     uv pip install --no-cache-dir netCDF4==1.6.3
     uv pip install numpy==$(/dmod/bin/ngen --info | grep -e 'NumPy Version: ' | cut -d ':' -f 2 | uniq | xargs)
 
+    # Install lstm
+    uv pip install --no-cache-dir /ngen/ngen/extern/lstm --extra-index-url https://download.pytorch.org/whl/cpu
+
     # Make everything in /ngen accessible
     chmod -R 755 /ngen
     

From 8b90cb361c979d24e6c9dfa4fda1eb65b3c1821c Mon Sep 17 00:00:00 2001
From: Benjamin Lee <130000039+benlee0423@users.noreply.github.com>
Date: Tue, 17 Dec 2024 14:53:05 -0800
Subject: [PATCH 3/7] copy lstm before install

---
 singularity/singularity_ngen.def | 1 +
 1 file changed, 1 insertion(+)

diff --git a/singularity/singularity_ngen.def b/singularity/singularity_ngen.def
index d3f9b6a..ce5d279 100644
--- a/singularity/singularity_ngen.def
+++ b/singularity/singularity_ngen.def
@@ -141,6 +141,7 @@ From: rockylinux:9.1
     uv pip install numpy==$(/dmod/bin/ngen --info | grep -e 'NumPy Version: ' | cut -d ':' -f 2 | uniq | xargs)
 
     # Install lstm
+    cp /ngen/ngen/extern/lstm/lstm /ngen/ngen/extern/lstm
     uv pip install --no-cache-dir /ngen/ngen/extern/lstm --extra-index-url https://download.pytorch.org/whl/cpu
 
     # Make everything in /ngen accessible

From 933bfd884c821865ab206dc9db6e31480b51683a Mon Sep 17 00:00:00 2001
From: Benjamin Lee <130000039+benlee0423@users.noreply.github.com>
Date: Tue, 17 Dec 2024 16:33:24 -0800
Subject: [PATCH 4/7] add debug

---
 singularity/singularity_ngen.def | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/singularity/singularity_ngen.def b/singularity/singularity_ngen.def
index ce5d279..1b2d000 100644
--- a/singularity/singularity_ngen.def
+++ b/singularity/singularity_ngen.def
@@ -141,6 +141,8 @@ From: rockylinux:9.1
     uv pip install numpy==$(/dmod/bin/ngen --info | grep -e 'NumPy Version: ' | cut -d ':' -f 2 | uniq | xargs)
 
     # Install lstm
+    ls -l /ngen/ngen/extern
+    ls -l /ngen/ngen/extern/lstm
     cp /ngen/ngen/extern/lstm/lstm /ngen/ngen/extern/lstm
     uv pip install --no-cache-dir /ngen/ngen/extern/lstm --extra-index-url https://download.pytorch.org/whl/cpu
 

From b3136e71fd1302d6911344283aee312ccab02155 Mon Sep 17 00:00:00 2001
From: Benjamin Lee <130000039+benlee0423@users.noreply.github.com>
Date: Tue, 17 Dec 2024 21:28:24 -0800
Subject: [PATCH 5/7] ngen branch to ngiab

---
 singularity/singularity_ngen.def | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/singularity/singularity_ngen.def b/singularity/singularity_ngen.def
index 1b2d000..34850f5 100644
--- a/singularity/singularity_ngen.def
+++ b/singularity/singularity_ngen.def
@@ -15,7 +15,7 @@ From: rockylinux:9.1
     TROUTE_REPO="CIROH-UA/t-route"
     TROUTE_BRANCH="datastream"
     NGEN_REPO="CIROH-UA/ngen"
-    NGEN_BRANCH="main"
+    NGEN_BRANCH="ngiab"
 
     # Install system dependencies
     echo "max_parallel_downloads=10" >> /etc/dnf/dnf.conf

From 94db557328d8cdfa0e8b1216b781acfefc5ab571 Mon Sep 17 00:00:00 2001
From: Benjamin Lee <130000039+benlee0423@users.noreply.github.com>
Date: Tue, 17 Dec 2024 21:46:35 -0800
Subject: [PATCH 6/7] copy with recursive

---
 singularity/singularity_ngen.def | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/singularity/singularity_ngen.def b/singularity/singularity_ngen.def
index 34850f5..313a1a2 100644
--- a/singularity/singularity_ngen.def
+++ b/singularity/singularity_ngen.def
@@ -143,7 +143,7 @@ From: rockylinux:9.1
     # Install lstm
     ls -l /ngen/ngen/extern
     ls -l /ngen/ngen/extern/lstm
-    cp /ngen/ngen/extern/lstm/lstm /ngen/ngen/extern/lstm
+    cp -r /ngen/ngen/extern/lstm/lstm /ngen/ngen/extern/lstm
     uv pip install --no-cache-dir /ngen/ngen/extern/lstm --extra-index-url https://download.pytorch.org/whl/cpu
 
     # Make everything in /ngen accessible

From 2548f0034e27f9e7a77a8a80b69c4241d6152ecb Mon Sep 17 00:00:00 2001
From: Benjamin Lee <130000039+benlee0423@users.noreply.github.com>
Date: Tue, 17 Dec 2024 22:08:23 -0800
Subject: [PATCH 7/7] fix copy

---
 singularity/singularity_ngen.def | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/singularity/singularity_ngen.def b/singularity/singularity_ngen.def
index 313a1a2..b5e6bfa 100644
--- a/singularity/singularity_ngen.def
+++ b/singularity/singularity_ngen.def
@@ -143,7 +143,7 @@ From: rockylinux:9.1
     # Install lstm
     ls -l /ngen/ngen/extern
     ls -l /ngen/ngen/extern/lstm
-    cp -r /ngen/ngen/extern/lstm/lstm /ngen/ngen/extern/lstm
+    cp -r /ngen/ngen/extern/lstm/lstm/* /ngen/ngen/extern/lstm/
     uv pip install --no-cache-dir /ngen/ngen/extern/lstm --extra-index-url https://download.pytorch.org/whl/cpu
 
     # Make everything in /ngen accessible