From 49b010dba07558f0a51c970a1a56e92fc33d5c06 Mon Sep 17 00:00:00 2001
From: chun9l <97897047+chun9l@users.noreply.github.com>
Date: Mon, 20 May 2024 10:28:59 +0100
Subject: [PATCH 1/3] Add missing python package

---
 models/achlys/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/models/achlys/Dockerfile b/models/achlys/Dockerfile
index 65baac4..f0e0db8 100644
--- a/models/achlys/Dockerfile
+++ b/models/achlys/Dockerfile
@@ -2,7 +2,7 @@ FROM linusseelinger/achlys-ubuntu
 
 RUN apt update && apt install -y inotify-tools python3-pip python3-venv && \
     python3 -m venv venv && . venv/bin/activate && \
-    pip3 install umbridge && \
+    pip3 install umbridge numpy scipy pandas && \
     rm -rf /var/lib/apt/lists/*
 
 COPY server.py /server.py

From efe1c0c8910bcf611539d1d8c94722462739ec3d Mon Sep 17 00:00:00 2001
From: chun9l <97897047+chun9l@users.noreply.github.com>
Date: Mon, 20 May 2024 11:24:20 +0100
Subject: [PATCH 2/3] Add flag to suppress ompi error

---
 models/gs2/server.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/models/gs2/server.py b/models/gs2/server.py
index d2d392b..308e291 100644
--- a/models/gs2/server.py
+++ b/models/gs2/server.py
@@ -34,7 +34,7 @@ def __call__(self, parameters, config):
         
         # Run the model 
         mpirank = config.get("ranks", 4)
-        os.system(f"mpirun -n {mpirank} /usr/gs2/bin/gs2 {input_file}")
+        os.system(f"mpirun --allow-run-as-root -n {mpirank} /usr/gs2/bin/gs2 {input_file}") # --allow-run-as-root to suppress OMPI error, not reccomended when running outside of docker!
         
         # Read results using Pyrokinetics package and print output
         gs2_input = input_file

From 5d3062efed76d18d166ef8f1d1a991c17cab780d Mon Sep 17 00:00:00 2001
From: chun9l <97897047+chun9l@users.noreply.github.com>
Date: Mon, 20 May 2024 12:21:19 +0100
Subject: [PATCH 3/3] Change achlys base image

---
 models/achlys/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/models/achlys/Dockerfile b/models/achlys/Dockerfile
index f0e0db8..ff87b08 100644
--- a/models/achlys/Dockerfile
+++ b/models/achlys/Dockerfile
@@ -1,4 +1,4 @@
-FROM linusseelinger/achlys-ubuntu
+FROM sdixonukaea/achlys-ubuntu:latest
 
 RUN apt update && apt install -y inotify-tools python3-pip python3-venv && \
     python3 -m venv venv && . venv/bin/activate && \