Merge pull request #75 from UM-Bridge/CI-fix

Revert achlys image and update gs2 model

models/achlys/Dockerfile

@@ -1,9 +1,9 @@
-FROM achlys-ubuntu
+FROM linusseelinger/achlys-ubuntu
 
 RUN apt update && apt install -y inotify-tools && \
     rm -rf /var/lib/apt/lists/*
 
-RUN apt install -y python3-pip python3-venv && \
+RUN apt install -y python3-pip python3-virtualenv && \
     python3 -m venv venv && \
     . venv/bin/activate && \
     pip install umbridge

models/gs2/Dockerfile

@@ -36,7 +36,8 @@ RUN echo 'alias pip=pip3' >> $HOME/.bashrc
 
 RUN echo 'export GK_SYSTEM=gnu_ubuntu' >> $HOME/.bashrc
 
-RUN pip install ford netCDF4==1.6.2
+RUN python -m venv venv && . venv/bin/activate && \
+    pip install ford netCDF4==1.6.2 umbridge pyrokinetics 
 
 RUN git clone https://[email protected]/gyrokinetics/gs2.git /usr/gs2
 
@@ -51,5 +52,8 @@ RUN echo ${GK_SYSTEM}
 RUN make -IMakefiles depend
 
 RUN make -IMakefiles gs2
-
 #RUN make -IMakefiles tests
+
+COPY server.py fast.in .
+
+CMD . venv/bin/activate && python server.py

models/gs2/server.py

@@ -3,7 +3,6 @@
 import os
 import csv
 from pyrokinetics import Pyro
-import numpy as np
 from datetime import datetime
 from fileinput import FileInput
 
@@ -21,7 +20,7 @@ def get_output_sizes(self, config):
 
     def __call__(self, parameters, config):
         input_file = "fast.in" # Select input file
-        os.system("mkdir restart") # GS2 needs this folder otherwise will fail
+        os.system("mkdir -p restart") # GS2 needs this folder otherwise will fail
         with FileInput(files=input_file, inplace=True) as file:
             checkpoint = 0
             for line in file: