{2025.06}[foss/2025a] RELION-5.1.0-foss-2025a-CUDA-12.8.0.eb

[jpecar]

Try newer version of Relion. Challenges expected.

[Neves-P]

Hi @jpecar, thanks for the PR! There is a number of CPU only dependencies that we need to get on EESSI first before we build this, and it's better that we work through the big dependencies first (like PyTorch) before we start work here, so I'll mark this as a draft PR for now.

102 out of 318 required modules missing:

* CUDA/12.8.0 (CUDA-12.8.0.eb)
* einops/0.8.1-GCCcore-14.2.0 (einops-0.8.1-GCCcore-14.2.0.eb)
* parameterized/0.9.0-GCCcore-14.2.0 (parameterized-0.9.0-GCCcore-14.2.0.eb)
* utf8proc/2.10.0-GCCcore-14.2.0 (utf8proc-2.10.0-GCCcore-14.2.0.eb)
* flit-core/3.12.0-GCCcore-14.2.0 (flit-core-3.12.0-GCCcore-14.2.0.eb)
* typing-extensions/4.14.0-GCCcore-14.2.0 (typing-extensions-4.14.0-GCCcore-14.2.0.eb)
* pydantic/2.11.7-GCCcore-14.2.0 (pydantic-2.11.7-GCCcore-14.2.0.eb)
* tlparse/0.4.3-GCCcore-14.2.0 (tlparse-0.4.3-GCCcore-14.2.0.eb)
* googlebenchmark/1.9.4-GCCcore-14.2.0 (googlebenchmark-1.9.4-GCCcore-14.2.0.eb)
* pytest-flakefinder/1.1.0-GCCcore-14.2.0 (pytest-flakefinder-1.1.0-GCCcore-14.2.0.eb)
* pytest-rerunfailures/16.1-GCCcore-14.2.0 (pytest-rerunfailures-16.1-GCCcore-14.2.0.eb)
* pytest-shard/0.1.2-GCCcore-14.2.0 (pytest-shard-0.1.2-GCCcore-14.2.0.eb)
* pytest-subtests/0.15.0-GCCcore-14.2.0 (pytest-subtests-0.15.0-GCCcore-14.2.0.eb)
* optree/0.18.0-GCCcore-14.2.0 (optree-0.18.0-GCCcore-14.2.0.eb)
* Abseil/20250512.1-GCCcore-14.2.0 (Abseil-20250512.1-GCCcore-14.2.0.eb)
* RE2/2024-07-02-GCCcore-14.2.0 (RE2-2024-07-02-GCCcore-14.2.0.eb)
* protobuf/31.1-GCCcore-14.2.0 (protobuf-31.1-GCCcore-14.2.0.eb)
* protobuf-python/6.31.1-GCCcore-14.2.0 (protobuf-python-6.31.1-GCCcore-14.2.0.eb)
* grpcio/1.76.0-GCCcore-14.2.0 (grpcio-1.76.0-GCCcore-14.2.0.eb)
* Arrow/22.0.0-gfbf-2025a (Arrow-22.0.0-gfbf-2025a.eb)
* morphosamplers/0.0.16-gfbf-2025a (morphosamplers-0.0.16-gfbf-2025a.eb)
* mrcfile/1.5.4-gfbf-2025a (mrcfile-1.5.4-gfbf-2025a.eb)
* cuDNN/9.10.1.4-CUDA-12.8.0 (cuDNN-9.10.1.4-CUDA-12.8.0.eb)
* absl-py/2.3.1-GCCcore-14.2.0 (absl-py-2.3.1-GCCcore-14.2.0.eb)
* tensorboard/2.20.0-gfbf-2025a (tensorboard-2.20.0-gfbf-2025a.eb)
* unittest-xml-reporting/3.1.0-GCCcore-14.2.0 (unittest-xml-reporting-3.1.0-GCCcore-14.2.0.eb)
* cuSPARSELt/0.8.0.4-CUDA-12.8.0 (cuSPARSELt-0.8.0.4-CUDA-12.8.0.eb)
* PyQt-builder/1.18.1-GCCcore-14.2.0 (PyQt-builder-1.18.1-GCCcore-14.2.0.eb)
* UCX-CUDA/1.18.0-GCCcore-14.2.0-CUDA-12.8.0 (UCX-CUDA-1.18.0-GCCcore-14.2.0-CUDA-12.8.0.eb)
* libclc/20.1.8-GCCcore-14.2.0 (libclc-20.1.8-GCCcore-14.2.0.eb)
* NCCL/2.27.7-GCCcore-14.2.0-CUDA-12.8.0 (NCCL-2.27.7-GCCcore-14.2.0-CUDA-12.8.0.eb)
* Triton/3.5.0-gfbf-2025a-CUDA-12.8.0 (Triton-3.5.0-gfbf-2025a-CUDA-12.8.0.eb)
* tcsh/6.24.16-GCCcore-14.2.0 (tcsh-6.24.16-GCCcore-14.2.0.eb)
* wrapt/1.17.2-GCCcore-14.2.0 (wrapt-1.17.2-GCCcore-14.2.0.eb)
* pyzstd/0.19.0-GCCcore-14.2.0 (pyzstd-0.19.0-GCCcore-14.2.0.eb)
* NVSHMEM/3.3.20-gompi-2025a-CUDA-12.8.0 (NVSHMEM-3.3.20-gompi-2025a-CUDA-12.8.0.eb)
* HMMER/3.4-gompi-2025a (HMMER-3.4-gompi-2025a.eb)
* PyHMMER/0.11.3-gompi-2025a (PyHMMER-0.11.3-gompi-2025a.eb)
* numba/0.62.0-foss-2025a (numba-0.62.0-foss-2025a.eb)
* magma/2.9.0-foss-2025a-CUDA-12.8.0 (magma-2.9.0-foss-2025a-CUDA-12.8.0.eb)
* umap-learn/0.5.9.post2-foss-2025a (umap-learn-0.5.9.post2-foss-2025a.eb)
* bcrypt/4.3.0-GCCcore-14.2.0 (bcrypt-4.3.0-GCCcore-14.2.0.eb)
* OpenSSL/1.1 (OpenSSL-1.1.eb)
* OpenGL/2025.09-GCCcore-14.2.0 (OpenGL-2025.09-GCCcore-14.2.0.eb)
* CMake/3.18.4 (CMake-3.18.4.eb)
* PyOpenGL/3.1.10-GCCcore-14.2.0 (PyOpenGL-3.1.10-GCCcore-14.2.0.eb)
* cxxopts/3.0.0 (cxxopts-3.0.0.eb)
* PBZIP2/1.1.13-GCCcore-14.2.0 (PBZIP2-1.1.13-GCCcore-14.2.0.eb)
* configurable-http-proxy/5.0.1-GCCcore-14.2.0 (configurable-http-proxy-5.0.1-GCCcore-14.2.0.eb)
* Qt5/5.15.16-GCCcore-14.2.0 (Qt5-5.15.16-GCCcore-14.2.0.eb)
* PyQt5/5.15.11-GCCcore-14.2.0 (PyQt5-5.15.11-GCCcore-14.2.0.eb)
* PycURL/7.45.6-GCCcore-14.2.0 (PycURL-7.45.6-GCCcore-14.2.0.eb)
* gmpy2/2.2.0-GCCcore-14.2.0 (gmpy2-2.2.0-GCCcore-14.2.0.eb)
* sympy/1.14.0-gfbf-2025a (sympy-1.14.0-gfbf-2025a.eb)
* CoinUtils/2.11.12-GCC-14.2.0 (CoinUtils-2.11.12-GCC-14.2.0.eb)
* xpdf/4.06-GCCcore-14.2.0 (xpdf-4.06-GCCcore-14.2.0.eb)
* QtPy/2.4.3-GCCcore-14.2.0 (QtPy-2.4.3-GCCcore-14.2.0.eb)
* Osi/0.108.11-GCC-14.2.0 (Osi-0.108.11-GCC-14.2.0.eb)
* aiohttp/3.12.13-GCCcore-14.2.0 (aiohttp-3.12.13-GCCcore-14.2.0.eb)
* Greenlet/3.2.3-GCCcore-14.2.0 (Greenlet-3.2.3-GCCcore-14.2.0.eb)
* jupyter-server-proxy/4.4.0-GCCcore-14.2.0 (jupyter-server-proxy-4.4.0-GCCcore-14.2.0.eb)
* nbclassic/1.3.1-GCCcore-14.2.0 (nbclassic-1.3.1-GCCcore-14.2.0.eb)
* jupyter-resource-usage/1.1.1-GCCcore-14.2.0 (jupyter-resource-usage-1.1.1-GCCcore-14.2.0.eb)
* Clp/1.17.10-foss-2025a (Clp-1.17.10-foss-2025a.eb)
* Cgl/0.60.9-foss-2025a (Cgl-0.60.9-foss-2025a.eb)
* Cbc/2.10.12-foss-2025a (Cbc-2.10.12-foss-2025a.eb)
* psycopg/3.2.9-GCCcore-14.2.0 (psycopg-3.2.9-GCCcore-14.2.0.eb)
* PuLP/3.3.0-foss-2025a (PuLP-3.3.0-foss-2025a.eb)
* SQLAlchemy/2.0.41-GCCcore-14.2.0 (SQLAlchemy-2.0.41-GCCcore-14.2.0.eb)
* PyTorch/2.9.1-foss-2025a-CUDA-12.8.0 (PyTorch-2.9.1-foss-2025a-CUDA-12.8.0.eb)
* torchvision/0.24.0-foss-2025a-CUDA-12.8.0 (torchvision-0.24.0-foss-2025a-CUDA-12.8.0.eb)
* Faiss/1.13.2-foss-2025a-CUDA-12.8.0 (Faiss-1.13.2-foss-2025a-CUDA-12.8.0.eb)
* PyTorch/2.9.1-foss-2025a (PyTorch-2.9.1-foss-2025a.eb)
* Faiss/1.14.3-foss-2025a-CUDA-12.8.0 (Faiss-1.14.3-foss-2025a-CUDA-12.8.0.eb)
* JupyterHub/5.3.0-GCCcore-14.2.0 (JupyterHub-5.3.0-GCCcore-14.2.0.eb)
* ESM-2/2.0.0-foss-2025a (ESM-2-2.0.0-foss-2025a.eb)
* t-SNE-CUDA/3.0.1-foss-2025a-CUDA-12.8.0 (t-SNE-CUDA-3.0.1-foss-2025a-CUDA-12.8.0.eb)
* prompt-toolkit/3.0.52-GCCcore-14.2.0 (prompt-toolkit-3.0.52-GCCcore-14.2.0.eb)
* jupyter-bash-kernel/0.9.3-GCCcore-14.2.0 (jupyter-bash-kernel-0.9.3-GCCcore-14.2.0.eb)
* Jupyter-bundle/20250702-GCCcore-14.2.0 (Jupyter-bundle-20250702-GCCcore-14.2.0.eb)
* Qtconsole/5.7.0-GCCcore-14.2.0 (Qtconsole-5.7.0-GCCcore-14.2.0.eb)
* napari/0.6.6-foss-2025a (napari-0.6.6-foss-2025a.eb)
* ATK/2.38.0-GCCcore-14.2.0 (ATK-2.38.0-GCCcore-14.2.0.eb)
* libepoxy/1.5.10-GCCcore-14.2.0 (libepoxy-1.5.10-GCCcore-14.2.0.eb)
* GStreamer/1.26.6-GCCcore-14.2.0 (GStreamer-1.26.6-GCCcore-14.2.0.eb)
* at-spi2-core/2.56.2-GCCcore-14.2.0 (at-spi2-core-2.56.2-GCCcore-14.2.0.eb)
* at-spi2-atk/2.38.0-GCCcore-14.2.0 (at-spi2-atk-2.38.0-GCCcore-14.2.0.eb)
* GTK3/3.24.43-GCCcore-14.2.0 (GTK3-3.24.43-GCCcore-14.2.0.eb)
* Graphene/1.10.8-GCCcore-14.2.0 (Graphene-1.10.8-GCCcore-14.2.0.eb)
* shared-mime-info/2.4-GCCcore-14.2.0 (shared-mime-info-2.4-GCCcore-14.2.0.eb)
* GST-plugins-base/1.26.6-GCCcore-14.2.0 (GST-plugins-base-1.26.6-GCCcore-14.2.0.eb)
* GST-plugins-bad/1.26.6-GCCcore-14.2.0 (GST-plugins-bad-1.26.6-GCCcore-14.2.0.eb)
* PyCairo/1.28.0-GCCcore-14.2.0 (PyCairo-1.28.0-GCCcore-14.2.0.eb)
* PyGObject/3.54.2-GCCcore-14.2.0 (PyGObject-3.54.2-GCCcore-14.2.0.eb)
* libcroco/0.6.13-GCCcore-14.2.0 (libcroco-0.6.13-GCCcore-14.2.0.eb)
* cargo-c/0.10.13-GCCcore-14.2.0 (cargo-c-0.10.13-GCCcore-14.2.0.eb)
* librsvg/2.61.0-GCCcore-14.2.0 (librsvg-2.61.0-GCCcore-14.2.0.eb)
* GTK4/4.20.2-GCCcore-14.2.0 (GTK4-4.20.2-GCCcore-14.2.0.eb)
* libnotify/0.8.7-GCCcore-14.2.0 (libnotify-0.8.7-GCCcore-14.2.0.eb)
* wxWidgets/3.2.9-GCCcore-14.2.0 (wxWidgets-3.2.9-GCCcore-14.2.0.eb)
* ctffind/4.1.14-foss-2025a (ctffind-4.1.14-foss-2025a.eb)
* RELION/5.1.0-foss-2025a-CUDA-12.8.0 (RELION-5.1.0-foss-2025a-CUDA-12.8.0.eb)

[jpecar]

Yes, I chewed through most of them already and left some notes in the original relion PR. PyTorch is the obvious blocker, others are mostly manageable.

How should these cpu-only deps be processed? As a separate PR?