Run works locally. Problem in ports UI: integer types don't show corr… (

#1) * Run works locally. Problem in ports UI: integer types don't show correct default * Works in local oSPARC deploy * Adding more vars to ci
ITISFoundation · Jun 26, 2023 · 10cb3b7 · 10cb3b7
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diff --git a/.github/workflows/build-test-publish.yml b/.github/workflows/build-test-publish.yml
@@ -9,7 +9,8 @@ env:
   DOCKER_REGISTRY: ${{ secrets.DOCKER_REGISTRY }}
   DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
   DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
-
+  KWAVE_LOGIN: ${{ secrets.KWAVE_LOGIN }}
+  KWAVE_PASSWORD: ${{ secrets.KWAVE_PASSWORD }}
 jobs:
   build:
     name: building k-wave
@@ -39,14 +40,12 @@ jobs:
           make VERSION
           make build
           make info-build
-      - name: test
-        run: make tests
-      - if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+      - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
         name: push
         run: |
           ./.github/dockerhub_login.bash
           make push
-      - if: github.event_name == 'push' && github.ref != 'refs/heads/master'
+      - if: github.event_name == 'push' && github.ref != 'refs/heads/main'
         name: push
         run: |
           ./.github/dockerhub_login.bash

diff --git a/.osparc/docker-compose.overwrite.yml b/.osparc/docker-compose.overwrite.yml
@@ -4,3 +4,6 @@ services:
     build:
       dockerfile: docker/custom/Dockerfile
       target: production
+      args: 
+        - KWAVE_LOGIN
+        - KWAVE_PASSWORD
diff --git a/.osparc/metadata.yml b/.osparc/metadata.yml
@@ -3,7 +3,7 @@ key: simcore/services/comp/k-wave
 type: computational
 integration-version: 1.0.0
 version: 1.0.0
-description: A MATLAB toolbox for the time-domain simulation of acoustic wave fields. It uses the kspaceFirst3DG function to run 3D time-domain simulation of wave propagation on a GPU using C++ CUDA code.
+description: k-Wave is a MATLAB toolbox for the time-domain simulation of acoustic wave fields. This service uses the kspaceFirstOrder-CUDA function to run 3D time-domain simulation of wave propagation on a GPU using C++ CUDA code (k-Wave version 1.3). <br><br> Have an issue? Create one at https://github.com/ITISFoundation/k-wave/issues 
 contact: [email protected]
 thumbnail: https://pbs.twimg.com/media/ER4wiXEWkAAY-GD.jpg
 authors:
@@ -13,19 +13,128 @@ authors:
 inputs:
   input_1:
     displayOrder: 1
-    label: input_1_label
-    description: The input 1 description
-    type: string
-    defaultValue: some_value(optional)
+    label: Input HDF5
+    description: Compatible HDF5 file (check [k-Wave User Manual](http://www.k-wave.org/manual/k-wave_user_manual_1.1.pdf) to know how to create it.)
+    type: data:*/*
     fileToKeyMap:
-      somefilename.ext: input_1
-
+      input.h5: input_1
+  input_2:
+    displayOrder: 2
+    label: Compression level
+    description: Compression level (-c)
+    defaultValue: 0
+    type: ref_contentSchema
+    contentSchema: 
+      title: Compression level
+      type: integer
+      minimum: 0
+      maximum: 9
+  input_3:
+    displayOrder: 3
+    label: Store p_rms
+    description: Store rms of p (acoustic pressure)
+    type: boolean
+    defaultValue: false
+  input_4:
+    displayOrder: 4
+    label: Store p_max
+    description: Store max of p (acoustic pressure)
+    type: boolean
+    defaultValue: false
+  input_5:
+    displayOrder: 5
+    label: Store p_min
+    description: Store min of p (acoustic pressure)
+    type: boolean
+    defaultValue: false
+  input_6:
+    displayOrder: 6
+    label: Store p_max_all
+    description: Store max of p (whole domain)
+    type: boolean
+    defaultValue: false
+  input_7:
+    displayOrder: 7
+    label: Store p_min_all
+    description: Store min of p (acoustic pressure)
+    type: boolean
+    defaultValue: false
+  input_8:
+    displayOrder: 8
+    label: Store p_final
+    description: Store final pressure field
+    type: boolean
+    defaultValue: false
+  input_9:
+    displayOrder: 9
+    label: Store u
+    description: Store ux, uy, uz
+    type: boolean
+    defaultValue: false
+  input_10:
+    displayOrder: 10
+    label: Store u_non_staggered_raw
+    description: Store non-staggered raw time series of ux, uy, uz
+    type: boolean
+    defaultValue: false
+  input_11:
+    displayOrder: 11
+    label: Store u_rms
+    description: Store rms of ux, uy, uz
+    type: boolean
+    defaultValue: false
+  input_12:
+    displayOrder: 12
+    label: Store u_max
+    description: Store max of ux, uy, uz
+    type: boolean
+    defaultValue: false
+  input_13:
+    displayOrder: 13
+    label: Store u_min
+    description: Store min of ux, uy, uz
+    type: boolean
+    defaultValue: false
+  input_14:
+    displayOrder: 14
+    label: Store u_max_all
+    description: Store max of ux, uy, uz (whole domain)
+    type: boolean
+    defaultValue: false
+  input_15:
+    displayOrder: 15
+    label: Store u_min_all
+    description: Store min of ux, uy, uz (whole domain)
+    type: boolean
+    defaultValue: false
+  input_16:
+    displayOrder: 16
+    label: Store u_final
+    description: Store final acoustic velocity
+    type: boolean
+    defaultValue: false
+  input_17:
+    displayOrder: 17
+    label: Start of data collection
+    description: Time step when data collection begins (-s)
+    defaultValue: 1
+    type: ref_contentSchema
+    contentSchema: 
+      title: Start of data collection
+      type: integer
+  input_18:
+    displayOrder: 18
+    label: Copy sensory mask
+    description: Copy sensor mask to the output file
+    type: boolean
+    defaultValue: fals
+
 outputs:
   output_1:
     displayOrder: 1
-    label: output_1_label
-    description: The input 1 description
-    type: string
+    label: Output HDF5 file
+    description: HDF5 that can be read by k-wave (check [k-Wave documentation](http://www.k-wave.org/documentation/example_cpp_running_simulations.php#heading6))
+    type: data:*/*
     fileToKeyMap:
-      somefilename.ext: output_1
+      output.h5: output_1
 
diff --git a/.osparc/runtime.yml b/.osparc/runtime.yml
@@ -4,6 +4,13 @@ settings:
     type: Resources
     value:
       Limits:
-        NanoCPUs: 1000000000 # 100% of CPU cycles on 1 CPU 
-        MemoryBytes: 2147483648 # 2 Gigabytes
+        NanoCPUs: 8000000000
+        MemoryBytes: 17179869184
+      Reservations:
+        NanoCPUs: 8000000000
+        MemoryBytes: 17179869184
+        GenericResources:
+          - DiscreteResourceSpec:
+              Kind: VRAM
+              Value: 1
 
diff --git a/README.md b/README.md
@@ -1,33 +1,32 @@
 # k-Wave
 
-Source code of the o²S²PARC Service for k-Wave, A MATLAB toolbox for the time-domain simulation of acoustic wave fields. It uses the kspaceFirst3DG function to run 3D time-domain simulation of wave propagation on a GPU using C++ CUDA code. Find more information about k-Wave [here](http://www.k-wave.org/index.php).
+Source code of the k-Wave Service on o²S²PARC. k-Wave is MATLAB/C++ toolbox for the time-domain simulation of acoustic wave fields. This Service uses the C++ function to run 3D time-domain simulation of wave propagation on a GPU using C++ CUDA code. You can find more information about k-Wave [here](http://www.k-wave.org/index.php).
 
-## Usage
+The Service runs the kspaceFirstOrder-CUDA function (v1.3)
+
+## Citing the k-Wave Toolbox
+If you find the toolbox useful for your academic work, please consider citing one or more of the associated papers, more information [here](http://www.k-wave.org/license.php).
+
+## Information for developers of the o²S²PARC Service
+### Usage
 
 ```console
 $ make help
-
 $ make build
-$ make info-build
-$ make tests
+$ make publish-local 
 ```
+**Note**: to build the image, you need an account [to download k-Wave](http://www.k-wave.org/download.php). In version 1.0.0 the pre-compiled executables are used.
 
-## Workflow
-
-1. The source code shall be copied to the [src](k-wave/src/k_wave) folder.
-2. The [Dockerfile](k-wave/src/Dockerfile) shall be modified to compile the source code.
-3. The [.osparc](.osparc) is the configuration folder and source of truth for metadata: describes service info and expected inputs/outputs of the service.
-4. The [execute](k-wave/service.cli/execute) shell script shall be modified to run the service using the expected inputs and retrieve the expected outputs.
-5. The test input/output shall be copied to [validation](k-wave/validation).
-6. The service docker image may be built and tested as ``make build tests`` (see usage above)
-7. Optional: if your code requires specific CPU/RAM resources, edit [runtime.yml](.osparc/runtime.yml). In doubt, leave it as default.
+### How to test
+Use as input the file `validation/input/input.h5`. Running the service should generate an `output.h5` file. 
+Is you provide optional boolean flags (either in the UI of in `inputs.json`), you should see additional data fields in the `output.h5` file. To inspect the output file you can use `h5ls -d output.h5`.
 
 ## Have an issue or question?
-Please open an issue [in this repository](https://github.com/ITISFoundation/cookiecutter-osparc-service/issues/).
+
+Please open an issue [in this repository](https://github.com/ITISFoundation/k-wave/issues/).
+
 ---
 <p align="center">
 <image src="https://github.com/ITISFoundation/osparc-simcore-python-client/blob/4e8b18494f3191d55f6692a6a605818aeeb83f95/docs/_media/mwl.png" alt="Made with love at www.z43.swiss" width="20%" />
 </p>
 
-## Citing the k-Wave Toolbox
-If you find the toolbox useful for your academic work, please consider citing one or more of the associated papers, more information [here](http://www.k-wave.org/license.php).
diff --git a/docker/custom/Dockerfile b/docker/custom/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:latest as base 
+FROM nvidia/cudagl:11.2.2-runtime-ubuntu20.04 as base
 #
 #  USAGE:
 #     cd services/k-wave
@@ -28,28 +28,39 @@ FROM base as build
 
 ENV SC_BUILD_TARGET build
 
+ARG KWAVE_PASSWORD
+ARG KWAVE_LOGIN
 # ------------------------------------------------------------------------------------
-#TODO:
-# uncomment and adapt if build dependencies shall be installed
-#RUN apt-get update \
-# && apt-get -y install --no-install-recommends \
-# gcc \
-# git \
-# && rm -rf /var/lib/apt/lists/*
-
-# uncomment and adapt if python necessary
-#RUN $SC_PIP install --upgrade pip wheel setuptools
+# build dependencies shall be installed
+RUN apt-get update \
+ && apt-get -y install --no-install-recommends \
+ unzip \
+ gcc \
+ curl \
+&& rm -rf /var/lib/apt/lists/*
+
 # ------------------------------------------------------------------------------------
+# Download binaries (get authentication cookie to login to http://www.k-wave.org/download.php and download the file with the cookie)
+# Note, you need to have a valid login and export credentials as env. variables
 
 WORKDIR /build
+
+
+RUN curl --cookie-jar cookie.txt --form password=$KWAVE_PASSWORD --form user_login=$KWAVE_LOGIN http://www.k-wave.org/forum/bb-login.php && \
+ curl -L -b cookie.txt http://www.k-wave.org/getfile.php?id=117 -o kwave.zip && \
+  unzip kwave.zip && \
+  rm kwave.zip cookie.txt
+# ------------------------------------------------------------------------------------
+
+
 # defines the output of the build
 RUN mkdir --parents /build/bin
-# copy src code
-COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} src/k_wave src/k_wave
+# copy src code: There's none for the moment
+#COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} src/k_wave src/k_wave
 # ------------------------------------------------------------------------------------
 #TODO:
-# uncomment and adapt if build steps are necessary
-# RUN cp -R src/k_wave/* /build/bin
+# uncomment and adapt if build steps are necessary. For now, we use the compiled executable
+RUN cp -R /build/kspaceFirstOrder-CUDA /build/bin
 # ------------------------------------------------------------------------------------
 
 # --------------------------Production stage -------------------
@@ -74,11 +85,11 @@ ENV INPUT_FOLDER="/input" \
 WORKDIR /home/${SC_USER_NAME}
 
 # ------------------------------------------------------------------------------------
-#TODO:
 # uncomment and adapt to install runtime dependencies
-#RUN apt-get update \
-# && apt-get -y install --no-install-recommends \
-# && rm -rf /var/lib/apt/lists/*
+RUN apt-get update \
+ && apt-get -y install --no-install-recommends \
+    libgomp1 \
+ && rm -rf /var/lib/apt/lists/*
 # ------------------------------------------------------------------------------------
 
 # copy docker bootup scripts
@@ -90,16 +101,7 @@ ENV PATH="/home/${SC_USER_NAME}/service.cli:${PATH}"
 
 # copy binaries from build
 COPY --from=build --chown=${SC_USER_NAME}:${SC_USER_NAME} /build/bin k_wave
-
-# ------------------------------------------------------------------------------------
-#TODO:
-# uncomment and provide a healtchecker if possible
-# HEALTHCHECK --interval=30s \
-#             --timeout=120s \
-#             --start-period=30s \
-#             --retries=3 \
-#             CMD ["healthchecker app"]
-# ------------------------------------------------------------------------------------
+RUN chmod +x k_wave/*
 
 ENTRYPOINT [ "/bin/sh", "docker/entrypoint.sh", "/bin/sh", "-c" ]
 CMD ["run"]