From 94796938851836a5fb826a00e821bb9221032c05 Mon Sep 17 00:00:00 2001
From: Edward Yang <yang.e@wehi.edu.au>
Date: Thu, 22 Aug 2024 10:57:05 +1000
Subject: [PATCH 1/4] bump apptainer v

---
 ollama-submit.sh | 2 +-
 run-chatbot.sh   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/ollama-submit.sh b/ollama-submit.sh
index dc972a7..45c5511 100755
--- a/ollama-submit.sh
+++ b/ollama-submit.sh
@@ -7,7 +7,7 @@
 set -eu
 
 module purge
-module load apptainer/1.2.3
+module load apptainer/1.2.5
 
 ollama_models=/vast/scratch/users/$USER/ollama-models
 ollama_tmp=/vast/scratch/users/$USER/tmp
diff --git a/run-chatbot.sh b/run-chatbot.sh
index 2d76410..ed4f9f7 100755
--- a/run-chatbot.sh
+++ b/run-chatbot.sh
@@ -6,7 +6,7 @@ set -eu
 ollama_host=$1
 
 module purge
-module load apptainer/1.2.3
+module load apptainer/1.2.5
 
 ollama_models=/vast/scratch/users/$USER/ollama-models
 ollama_tmp=/vast/scratch/users/$USER/tmp

From d914043b200ed0719f38ac0fea62ab6cdc58f0a9 Mon Sep 17 00:00:00 2001
From: Edward Yang <yang.e@wehi.edu.au>
Date: Thu, 22 Aug 2024 11:04:19 +1000
Subject: [PATCH 2/4] supply port on run-chatbot.sh

---
 README.md      |  7 +++++++
 run-chatbot.sh | 10 +++++++++-
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 19d936c..465fa3f 100644
--- a/README.md
+++ b/README.md
@@ -58,6 +58,13 @@ Password: 123
 NOTE: the models' dropdowns are pre-populated, but you need to pull them first 
 to use them. Future work will automatically pull the models.
 
+To run the chatbot on a different port, supply the port as the second arg:
+
+```bash
+# port could be 12345
+./run-chatbot.sh <host> <port>
+```
+
 4. Add data to database
 
 Fill out:
diff --git a/run-chatbot.sh b/run-chatbot.sh
index ed4f9f7..d971e52 100755
--- a/run-chatbot.sh
+++ b/run-chatbot.sh
@@ -5,6 +5,14 @@ set -eu
 
 ollama_host=$1
 
+# set port that chatbot is listening to
+if [ -z "${2}" ]
+then
+	chatbot_port_flag=""
+else
+	chatbot_port_flag="--port $2"
+fi
+
 module purge
 module load apptainer/1.2.5
 
@@ -14,4 +22,4 @@ ollama_tmp=/vast/scratch/users/$USER/tmp
 apptainer run \
      -B $TMPDIR:/tmp \
      -B /vast,/stornext \
-     oras://ghcr.io/wehi-researchcomputing/rag:0.1.0 --ollama-host $ollama_host
+     oras://ghcr.io/wehi-researchcomputing/rag:0.1.0 --ollama-host $ollama_host $chatbot_port_flag

From 43bb17ca0f028e80c745497bccc8fc4df6726833 Mon Sep 17 00:00:00 2001
From: Edward Yang <yang.e@wehi.edu.au>
Date: Thu, 22 Aug 2024 11:04:55 +1000
Subject: [PATCH 3/4] remove TMPDIR binding

---
 run-chatbot.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/run-chatbot.sh b/run-chatbot.sh
index d971e52..680f06c 100755
--- a/run-chatbot.sh
+++ b/run-chatbot.sh
@@ -20,6 +20,5 @@ ollama_models=/vast/scratch/users/$USER/ollama-models
 ollama_tmp=/vast/scratch/users/$USER/tmp
 
 apptainer run \
-     -B $TMPDIR:/tmp \
      -B /vast,/stornext \
      oras://ghcr.io/wehi-researchcomputing/rag:0.1.0 --ollama-host $ollama_host $chatbot_port_flag

From 0261201e116b02399a0def9ae757c16068951d60 Mon Sep 17 00:00:00 2001
From: Edward Yang <yang.e@wehi.edu.au>
Date: Thu, 22 Aug 2024 11:46:19 +1000
Subject: [PATCH 4/4] mount tmp on vast as /tmp

---
 run-chatbot.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/run-chatbot.sh b/run-chatbot.sh
index 680f06c..15746c5 100755
--- a/run-chatbot.sh
+++ b/run-chatbot.sh
@@ -19,6 +19,10 @@ module load apptainer/1.2.5
 ollama_models=/vast/scratch/users/$USER/ollama-models
 ollama_tmp=/vast/scratch/users/$USER/tmp
 
+export TMPDIR=/vast/scratch/users/$USER/tmp
+mkdir -p $TMPDIR
+
 apptainer run \
+     -B $TMPDIR:/tmp \
      -B /vast,/stornext \
      oras://ghcr.io/wehi-researchcomputing/rag:0.1.0 --ollama-host $ollama_host $chatbot_port_flag