Merge pull request #55 from precice/PreCICE.jl-v3.0.0

Release v3.0.0
precice · Feb 6, 2024 · 0e6a0c4 · 0e6a0c4
2 parents 5de44e3 + b1efd68
commit 0e6a0c4
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diff --git a/.github/workflows/TestJuliaVersions.yml b/.github/workflows/TestJuliaVersions.yml
@@ -1,4 +1,4 @@
-name: Building Package on stable Julia versions >1.4 and on the latest Julia version under development 'nightly'
+name: Building package on the latest Julia version and on the latest Julia version under development 'nightly'
 on: 
   workflow_dispatch:
   schedule:
@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        julia-version: ['1.6', 'nightly']
+        julia-version: ['1.10.0', 'nightly']
 
     steps:
       - name: Update System
@@ -28,19 +28,19 @@ jobs:
         id: cache-libprecice
         uses: actions/cache@v2
         with:
-          path: libprecice2_2.3.0_focal.deb
-          key: libprecice2_2.3.0_focal.deb1
-          restore-keys: libprecice2_2.3.0_focal.deb1
+          path: libprecice3_3.0.0_focal.deb
+          key: libprecice3_3.0.0_focal.deb1
+          restore-keys: libprecice3_3.0.0_focal.deb1
 
       - name: Download preCICE
         if: steps.cache-libprecice.outputs.cache-hit != 'true'
-        run: wget https://github.com/precice/precice/releases/download/v2.3.0/libprecice2_2.3.0_focal.deb
+        run: wget https://github.com/precice/precice/releases/download/v3.0.0/libprecice3_3.0.0_focal.deb
 
       - name: Install preCICE
-        run: sudo apt install ./libprecice2_2.3.0_focal.deb
+        run: sudo apt install ./libprecice3_3.0.0_focal.deb
 
       - name: Build Package
         uses: julia-actions/julia-buildpkg@v1
 
       - name: Run tests
-        uses: julia-actions/julia-runtest@v1
+        uses: julia-actions/julia-runtest@v1
diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
@@ -1,55 +1,64 @@
 name: Run Tests
-on: [push,pull_request]
+on: # run on every push to main and develop, and on every pull request to main and develop
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - main
+      - develop
 
 jobs:
   build:
     runs-on: ubuntu-latest
-    container: precice/precice
     strategy:
+      fail-fast: false
       matrix:
-        julia-version: ['1.6.0','1.6.5','1.7.0','^1.7']
+        julia-version: ["1.8.0", "1.9.0", "1.10.0"]
         julia-arch: [x64, x86]
-    
+
     steps:
       - name: Install Julia
         uses: julia-actions/setup-julia@v1
         with:
-          version: ${{ matrix.julia-version }}     
-        
-      - uses: actions/checkout@v2
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v4
 
       - name: Build Package
         uses: julia-actions/julia-buildpkg@v1
 
   run_tests:
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     needs: [build]
     strategy:
+      fail-fast: false
       matrix:
-        julia-version: ['1.6.0','1.6.5','1.7.0','^1.7']
+        julia-version: ["1.8.0", "1.9.0", "1.10.0"]
         julia-arch: [x64, x86]
-    
+
     steps:
       - name: Install Julia
         uses: julia-actions/setup-julia@v1
         with:
-          version: ${{ matrix.julia-version }}     
-        
-      - uses: actions/checkout@v2
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v4
 
       - name: Build Package
         uses: julia-actions/julia-buildpkg@v1
 
-      - name: install make
-        run: |
-         apt update
-         apt install make
-
-      - name: Build Fake Solverinterface
+      - name: Build fake Solverinterface
         run: |
           cd test
           make
 
+      - name: Add libprecice to LD_LIBRARY_PATH and adjust LD_PRELOAD
+        run: |
+          echo "LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+          echo "LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6:/usr/lib/x86_64-linux-gnu/libcurl.so.4" >> $GITHUB_ENV
+
       - name: Run tests
         uses: julia-actions/julia-runtest@v1
diff --git a/.github/workflows/format.yml b/.github/workflows/format.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: [1.6.0]
+        julia-version: [1.10.0]
         os: [ubuntu-latest]
     steps:
       - uses: julia-actions/setup-julia@latest

diff --git a/.gitignore b/.gitignore
@@ -5,4 +5,6 @@ solverdummy/*.json
 solverdummy/precice-run/
 *.o
 *.so
-deps/build.log
+deps/build.log
+build/
+.vscode/
diff --git a/Project.toml b/Project.toml
@@ -1,10 +1,10 @@
 name = "PreCICE"
 uuid = "57fbd4af-5cc3-4712-aac0-6930e7658184"
 authors = ["preCICE <https://precice.org/> and contributors"]
-version = "2.5.0"
+version = "3.0.0"
 
 [compat]
-julia = "1.6"
+julia = "1.10"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

diff --git a/README.md b/README.md
@@ -8,6 +8,8 @@ This package provides Julia language bindings for the C++ library [preCICE](http
 
 Note that the first two digits of the version number of the bindings indicate the preCICE major and minor version that the bindings support. The last digit represents the version of the bindings. Example: `v2.5.1` and `v2.5.2` of the bindings represent versions `1` and `2` of the bindings that are compatible with preCICE `v2.5.0`.
 
+Technical information about the initial design of these bindings can be found in the [Bachelor thesis of Pavel Kharitenko](http://dx.doi.org/10.18419/opus-11836).
+
 ## Adding and using the package
 
 The Julia bindings for preCICE can be used by either by adding them as a package in a Julia environment or also directly including the package in a Julia script. For both type of usages preCICE needs to be installed on the system. For preCICE installation, have a look at the [installation documentation](https://precice.org/installation-overview.html).
@@ -49,6 +51,8 @@ pkg> add https://github.com/precice/PreCICE.jl#<branch-name>
 
 ## Troubleshooting
 
+### Custom preCICE installation path
+
 If preCICE is installed at a custom path, errors of the form ```ERROR: could not load library "/..."``` can occur after adding the Julia bindings package. Make sure the preCICE library is in the system library path through `echo $LD_LIBRARY_PATH` and otherwise update the variable with the correct path.
 
 ```bash
@@ -66,6 +70,64 @@ julia> using PreCICE
 ...
 ```
 
+### Incompatible version of libstdc++
+
+If you get an error message like:
+
+```julia-repl
+ERROR: LoadError: could not load library "libprecice"
+/usr/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/local/lib/libprecice.so)
+```
+
+It is caused by an incompatible version of `libstdc++` as described [in the issue](https://github.com/precice/PreCICE.jl/issues/44#issuecomment-1259655654). Julia ships its own libraries, which are older than the ones shipped by the system or the ones used to compile preCICE.
+
+As a first solution, consider updating your julia version. The versions used in Julia are fairly up to date and should work with older systems. The problem is also known to the developers of Julia and they are [working on a solution](https://github.com/JuliaGL/GLFW.jl/issues/198). From Julia `v1.8.3` on, the problem [should be fixed](https://github.com/JuliaLang/julia/pull/46976).
+
+If you cannot update your julia version, or the problem persists, you can try preloading the system `libstdc++`:
+
+<details>
+<summary>Click to expand</summary>
+
+Preload the system `libstdc++` with
+
+```bash
+LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 julia
+```
+
+You may have to [compile preCICE from source](https://precice.org/installation-source-preparation.html) for this to work.
+
+On newer systems, preloading only the system `libstdc++` may not be sufficient. Errors of the form
+
+```julia-repl
+ERROR: ERROR: LoadError: LoadError: could not load library "libprecice"
+/path/to/julia-1.8.1/bin/../lib/julia/libcurl.so: version `CURL_OPENSSL_4' not found (required by /lib/x86_64-linux-gnu/libhdf5_openmpi.so.103)could not load library "libprecice"
+/path/to/julia-1.8.1/bin/../lib/julia/libcurl.so: version `CURL_OPENSSL_4' not found (required by /lib/x86_64-linux-gnu/libhdf5_openmpi.so.103)
+```
+
+can be resolved by preloading the system `libcurl`:
+
+```bash
+LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6:/usr/lib/x86_64-linux-gnu/libcurl.so.4" julia
+```
+
+Again, you may have to [compile preCICE from source](https://precice.org/installation-source-preparation.html).
+
+Adding the following lines to your `~/.bashrc` will help to avoid this error in the future:
+
+```bash
+alias julia='LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6:/usr/lib/x86_64-linux-gnu/libcurl.so.4" julia'
+```
+
+You could instead move the julia libraries out of the way and create a symlink to the system libraries:
+
+```bash
+mv /path/to/julia/lib/julia/libstdc++.so.6 /path/to/julia/lib/julia/libstdc++.so.6.bak
+ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /path/to/julia/lib/julia/libstdc++.so.6
+```
+
+If the above approaches do not work, you may have to [compile preCICE from source](https://precice.org/installation-source-preparation.html) using the version of `libstdc++` that is shipped with Julia.
+</details>
+
 ## Usage
 
 The [solverdummy](https://github.com/precice/julia-bindings/tree/main/solverdummy) shows an example of how to use the Julia bindings for preCICE.
@@ -82,7 +144,7 @@ pkg> test PreCICE
 This checks if the preCICE bindings can be found and accessed correctly.
 You can also test the full functionality of PreCICE.jl. If not set up, the output of the previous test shows an info on what command you need to execute. It will be along the lines of:
 
-```
+```bash
 cd /home/<user>/.julia/packages/PreCICE/<code>/test && make
 ```
 
@@ -94,6 +156,6 @@ This package works with official Julia binaries listed below. See the [Platform
 
 ## Supported versions
 
-The package is tested for Julia versions `1.6.0`, `1.6.5`, `1.7.0` and the two newest [Julia releases](https://github.com/JuliaLang/julia/releases). Julia versions prior to `v1.6.0` are not supported.
+The package is actively tested for Julia versions `1.8.0`, `1.9.0`, and `1.10.0`. Julia versions prior to `1.6.0` are not supported.
 
 [Unofficial Julia binaries](https://julialang.org/downloads/platform/#platform_specific_instructions_for_unofficial_binaries) may not be compatible.
diff --git a/solverdummy/precice-config.xml b/solverdummy/precice-config.xml
@@ -9,53 +9,51 @@
       enabled="true" />
   </log>
 
-  <solver-interface dimensions="3">
-    <data:vector name="dataOne" />
-    <data:vector name="dataTwo" />
+  <data:vector name="Data-One" />
+  <data:vector name="Data-Two" />
 
-    <mesh name="MeshOne">
-      <use-data name="dataOne" />
-      <use-data name="dataTwo" />
-    </mesh>
+  <mesh name="SolverOne-Mesh"  dimensions="3">
+    <use-data name="Data-One" />
+    <use-data name="Data-Two" />
+  </mesh>
 
-    <mesh name="MeshTwo">
-      <use-data name="dataOne" />
-      <use-data name="dataTwo" />
-    </mesh>
+  <mesh name="SolverTwo-Mesh"  dimensions="3">
+    <use-data name="Data-One" />
+    <use-data name="Data-Two" />
+  </mesh>
 
-    <participant name="SolverOne">
-      <use-mesh name="MeshOne" provide="yes" />
-      <write-data name="dataOne" mesh="MeshOne" />
-      <read-data name="dataTwo" mesh="MeshOne" />
-    </participant>
+  <participant name="SolverOne">
+    <provide-mesh name="SolverOne-Mesh" />
+    <write-data name="Data-One" mesh="SolverOne-Mesh" />
+    <read-data name="Data-Two" mesh="SolverOne-Mesh" />
+  </participant>
 
-    <participant name="SolverTwo">
-      <use-mesh name="MeshOne" from="SolverOne" />
-      <use-mesh name="MeshTwo" provide="yes" />
-      <mapping:nearest-neighbor
-        direction="write"
-        from="MeshTwo"
-        to="MeshOne"
-        constraint="conservative" />
-      <mapping:nearest-neighbor
-        direction="read"
-        from="MeshOne"
-        to="MeshTwo"
-        constraint="consistent" />
-      <write-data name="dataTwo" mesh="MeshTwo" />
-      <read-data name="dataOne" mesh="MeshTwo" />
-    </participant>
+  <participant name="SolverTwo">
+    <receive-mesh name="SolverOne-Mesh" from="SolverOne" />
+    <provide-mesh name="SolverTwo-Mesh" />
+    <mapping:nearest-neighbor
+      direction="write"
+      from="SolverTwo-Mesh"
+      to="SolverOne-Mesh"
+      constraint="conservative" />
+    <mapping:nearest-neighbor
+      direction="read"
+      from="SolverOne-Mesh"
+      to="SolverTwo-Mesh"
+      constraint="consistent" />
+    <write-data name="Data-Two" mesh="SolverTwo-Mesh" />
+    <read-data name="Data-One" mesh="SolverTwo-Mesh" />
+  </participant>
 
-    <m2n:sockets from="SolverOne" to="SolverTwo" />
+  <m2n:sockets acceptor="SolverOne" connector="SolverTwo" />
 
-    <coupling-scheme:serial-implicit>
-      <participants first="SolverOne" second="SolverTwo" />
-      <max-time-windows value="2" />
-      <time-window-size value="1.0" />
-      <max-iterations value="2" />
-      <min-iteration-convergence-measure min-iterations="5" data="dataOne" mesh="MeshOne" />
-      <exchange data="dataOne" mesh="MeshOne" from="SolverOne" to="SolverTwo" />
-      <exchange data="dataTwo" mesh="MeshOne" from="SolverTwo" to="SolverOne" />
-    </coupling-scheme:serial-implicit>
-  </solver-interface>
-</precice-configuration>
+  <coupling-scheme:serial-implicit>
+    <participants first="SolverOne" second="SolverTwo" />
+    <max-time-windows value="2" />
+    <time-window-size value="1.0" />
+    <max-iterations value="2" />
+    <min-iterations value="2"/>
+    <exchange data="Data-One" mesh="SolverOne-Mesh" from="SolverOne" to="SolverTwo" />
+    <exchange data="Data-Two" mesh="SolverOne-Mesh" from="SolverTwo" to="SolverOne" />
+  </coupling-scheme:serial-implicit>
+</precice-configuration>