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Add workaround for GLIBCXX Error #48

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Jan 10, 2023
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Add workaround for GLIBCXX Error #48

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47e27f1
Add preloading to the README.md
erikscheurer Jan 6, 2023
967e661
Minor updates to README
IshaanDesai Jan 10, 2023
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62 changes: 61 additions & 1 deletion README.md
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Expand Up @@ -49,6 +49,8 @@ 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
Expand All @@ -66,6 +68,64 @@ julia> using PreCICE
...
```

### Incompatible version of libstdc++

If you get an error message like:

```julia-repl
ERROR: ERROR: LoadError: 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.
Expand All @@ -82,7 +142,7 @@ 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
```

Expand Down