Merge pull request #78 from UM-Bridge/CI-fix

CI fixes for gs2 and achlys

.github/workflows/benchmark-achlys.yml

@@ -46,4 +46,4 @@ jobs:
        -
         name: Validate
         run: |
-          docker run --network=host -e model_host=http://localhost:4243 linusseelinger/testing-protocol-conformity-current:latest
+          docker run --network=host -e input_value="[0.8,1.0,1.3,9e-4,9e-4]" -e model_host=http://localhost:4243 linusseelinger/testing-protocol-conformity-current:latest

.github/workflows/model-achlys.yml

@@ -56,4 +56,4 @@ jobs:
        -
         name: Validate protocol
         run: |
-          docker run --network=host -e model_host=http://localhost:4242 linusseelinger/testing-protocol-conformity-current:latest
+          docker run --network=host -e input_value="[0.8,1.0,1.3,9e-4,9e-4]" -e model_host=http://localhost:4242 linusseelinger/testing-protocol-conformity-current:latest

.github/workflows/model-gs2.yml

@@ -46,4 +46,4 @@ jobs:
        -
         name: Validate
         run: |
-          docker run --network=host -e model_host=http://localhost:4242 linusseelinger/testing-protocol-conformity-current:latest
+          docker run --network=host -m 4g -e input_value="[4.98536245337014,0.011195269013375201]" -e model_host=http://localhost:4242 linusseelinger/testing-protocol-conformity-current:latest

benchmarks/achlys/Dockerfile

@@ -2,9 +2,5 @@ FROM linusseelinger/model-achlys
 
 COPY . /benchmark-server
 
-RUN apt update && \
-    DEBIAN_FRONTEND="noninteractive" apt install -y python3-pip python3-scipy
-
-RUN pip3 install umbridge
-
-CMD /server/server & python3 /benchmark-server/benchmark-server.py
+CMD . venv/bin/activate && python3 /server.py & \
+    . venv/bin/activate && python3 /benchmark-server/benchmark-server.py

benchmarks/achlys/benchmark-server.py

@@ -1,6 +1,6 @@
 import umbridge
 
-import numpy
+import numpy as np
 import scipy.stats as stats
 
 from scipy.interpolate import interp1d

models/gs2/README.md

@@ -42,7 +42,7 @@ None |
 
 ## Source code
 
-[Model sources here.](https://github.com/UM-Bridge/benchmarks/tree/gs2/models/gs2)
+[Model sources here.](https://github.com/UM-Bridge/benchmarks/tree/main/models/gs2)
 
 ## Description
 GS2 is developed to study low frequency turbulence in magnetised plasma. In this benchmark, it solves the gyrokinetic Vlasov-Maxwell system of equations that are widely adopted to describe the turbulent component of the electromagnetic fields and particle distribution functions of the species present in a plasma. The problem is five-dimensional and takes the form 

models/gs2/server.py

@@ -1,10 +1,6 @@
 import umbridge
-import json
 import os
-import csv
 from pyrokinetics import Pyro
-from datetime import datetime
-from fileinput import FileInput
 
 
 
@@ -20,25 +16,26 @@ def get_output_sizes(self, config):
 
     def __call__(self, parameters, config):
         input_file = "fast.in" # Select input file
+        pyro = Pyro(gk_file=input_file, gk_code="GS2")
         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:
-                if "&species_parameters_3" in line:
-                    checkpoint += 1
-                if "tprim" in line and checkpoint == 1:
-                    line = f"    tprim = {parameters[0][0]}"
-                if "vnewk" in line and checkpoint == 1:
-                    line = f"    vnewk = {parameters[0][1]}"
-                print(line.rstrip()) # FileInput redirects stdout to file
+        if True: # Added to make it fast! Remove for production runs!
+            pyro.gs2_input["knobs"]["nstep"] = 50
+            pyro.gs2_input["theta_grid_parameters"]["ntheta"] = 10
+            pyro.gs2_input["theta_grid_parameters"]["nperiod"] = 2
+            pyro.gs2_input["le_grids_knobs"]["ngauss"] = 5
+            pyro.gs2_input["le_grids_knobs"]["negrid"] = 2
+
+        pyro.gs2_input["species_parameters_3"]["tprim"] = float(parameters[0][0])
+        pyro.gs2_input["species_parameters_3"]["vnewk"] = float(parameters[0][1])
+        pyro.gk_input.data = pyro.gs2_input
+        pyro.gk_input.write(input_file)
 
         # Run the model 
         mpirank = config.get("ranks", 4)
         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
-        pyro = Pyro(gk_file=gs2_input, gk_code="GS2")
+        # Read results and print output
+        pyro = Pyro(gk_file=input_file, gk_code="GS2")
         pyro.load_gk_output()
         data = pyro.gk_output
         print(data)