Kenneth Hoste

JSONDecodeError when determining list of installed Python packages

2

It seems like `pip list ... --format json` sometimes returns nothing at all, which isn't being handled well. ``` == 2023-01-25 17:38:10,411 pythonpackage.py:455 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list...

building with g++ and -march=native fails because of missing header files like fwd2s1_simd.h

2

I'm trying to build spaln v2.4.12 with GCC 10.2 and using "`-O2 -march=native`" as compiler options. This fails with: ``` g++ -O2 -ftree-vectorize -march=native -fno-math-errno -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c fwd2b1.cc...

When running `make` in `test_data` to check the installation of `find_circ` I did, I ran into this: ``` >>> building bowtie2 index bowtie2-build CDR1as_locus.fa bt2_cdr1as_locus > bt2_build.log 2>&1; >>> aligning...

At https://github.com/UoB-HPC/benchmarks/tree/master/openfoam#run-notes, the following is mentioned: "We use the DrivAer test case from the 2nd Isambard Hackathon. This isn't available online, so the script only copies it if it is...

C++ warnings being treated as errors with GCC 12.3.0

7

# Issue Report ## Please describe the issue: Multiple compiler warnings being treated as errors are resulting in a failure to build from source, unless `-Wno-error` is used: ``` /tmp/easybuild_build/dorado/0.6.1/foss-2023a-CUDA-12.1.1/dorado/dorado/utils/tensor_utils.cpp:18:6:...

fix for compilation error with GCC 12.3.0: ``` error: variable std::ofstream summary_out has initializer but incomplete type ``` Note: to make the build of dorado 0.6.1 fully work with GCC...

compilation error with GCC 11.3.0 + CUDA 11.7.0

5

I'm trying to build dorado 0.3.4 from source using GCC 11.3.0 + CUDA 11.7.0, and I'm hitting the following compilation error: ``` /tmp/easybuild_build/dorado/0.3.4/foss-2022a-CUDA-11.7.0/dorado/dorado/nn/CudaCRFModel.cpp: In member function void dorado::CudaCaller::cuda_thread_fn(): /tmp/easybuild_build/dorado/0.3.4/foss-2022a-CUDA-11.7.0/dorado/dorado/nn/CudaCRFModel.cpp:283:45: error:...

requirements.txt is missing from PyPI source tarball

2

`requirements.txt` is required by `setup.py`, but it's missing from the PyPI source tarball, which leads to the following when trying to install `arboreto` 0.1.6 from source: ``` Running command python...

segmentation fault with numpy on POWER9 (only) when using FlexiBLAS

13

I'm seeing a `Segmentation fault` when running the `numpy` 1.20.3 tests when using FlexiBLAS 3.0.4 with OpenBLAS 0.3.15, but not when linking to OpenBLAS 0.3.15 directly, which tells me FlexiBLAS...