Peter Heywood

Current plan decided at the Sheffield in person event is to hold off on this until the end of July, hoping that this will be backported upstream to the Ubuntu...

> TestPostProcessingWriter > When building the `chaste/develop` docker image on `noble`, the following tests fail: > > ``` > The following tests FAILED: > 3 - TestCitations (Failed) > 78...

+ Notes on the required functionality from chaste for the standalone test repository have been converted to issues on the repo + Refactoring existing code to provide improved/cleaner structure and...

Switching to a cell based model after detialed investigation into vertex model due to current FLAMEGPU limitations. Detailed justification to follow. Notes on new model at: https://github.com/Chaste/chaste-flamegpu2-prototyping/issues/19

Running `readelf -d /path/to/_pyflamegpu.so` for local builds on ubuntu do not appear to depend on versioned `libnvrtc-builtins.so` explcitly, just `libnvrtc.so.12`. The version installed from the distributed wheel however depends on...

adding the following to CI to readelf in ubuntu and manylinux builds on CI in the `readelf-test` branch confirms that ubuntu ci builds do not depend on `libnvrtc-builtins.so`, but centos...

Checking linker defaults via `gcc -Q -v` ## local Ubuntu ``` Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu1~22.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only...

Linker command for `_pyflamegpu.so` from CI ## Ubuntu 22.04 CI ``` 2024-04-02T15:44:21.7533132Z /usr/bin/g++-12 -fPIC -O3 -DNDEBUG -shared -Wl,-soname,_pyflamegpu.so -o _pyflamegpu.so CMakeFiles/pyflamegpu_swig.dir/pyflamegpu/flamegpuPYTHON_wrap.cxx.o CMakeFiles/pyflamegpu_swig.dir/cmake_device_link.o -L/usr/local/cuda-12.3/targets/x86_64-linux/lib/stubs -L/usr/local/cuda-12.3/targets/x86_64-linux/lib -Wl,-rpath,/usr/local/cuda-12.3/targets/x86_64-linux/lib ../../lib/Release/libflamegpu.a ../../lib/Release/libtinyxml2.a /usr/local/cuda-12.3/targets/x86_64-linux/lib/libnvrtc.so /usr/local/cuda-12.3/targets/x86_64-linux/lib/libnvrtc-builtins.so /usr/local/cuda-12.3/targets/x86_64-linux/lib/stubs/libcuda.so...

Readelf output from CI: notably centos includes `libnvrtc-builtins.so.12.0` which is the problem. ## Ubuntu ``` Dynamic section at offset 0x443a580 contains 32 entries: Tag Type Name/Value 0x0000000000000001 (NEEDED) Shared library:...

A possible fix is to use patchelf to remove the libnvrtc-builtins.so.MM.mm dependency at pyflamegpu build time. Patchelf is availble in manylinux, so doable, but getting the command in the right...