From 01eead686d5b428502bf275e8950d5e7b0e30270 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 23 Sep 2024 09:46:21 +0200 Subject: [PATCH] progress on #409 CIRCE --- 409_CIRCE/CIRCE-20240722-foss-2023a.eb | 42 ++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/409_CIRCE/CIRCE-20240722-foss-2023a.eb b/409_CIRCE/CIRCE-20240722-foss-2023a.eb index 7ce16fff..4303e00e 100644 --- a/409_CIRCE/CIRCE-20240722-foss-2023a.eb +++ b/409_CIRCE/CIRCE-20240722-foss-2023a.eb @@ -39,6 +39,8 @@ exts_list = [ {'circe_py-0.2.2.tar.gz': '0b828b8819bf1f0a6884016deb73e8551ac1d505c9091fbff2643dd48ebcc20e'}, {'CIRCE-20240722_requirements.patch': '8d957f12732118cc36d2700ba2f18ebb260d288c1db372951d435e5aabe3a606'}, ], + # build the C components and link `flexiblas` instead of `lapack` + 'preinstallopts': "sed -i 's/lapack/flexiblas/g' build.py && echo here1 && poetry build && echo here2 && ", }), ] @@ -68,3 +70,43 @@ moduleclass = 'bio' # ^^^^^^^^^^^ # AttributeError: module 'circe.pyquic' has no attribute 'quic' +# TODO still no `quic.py` in `lib/python3.11/site-packages/circe/pyquic/` +# Creating virtualenv circe-py-yjxQWa7c-py3.11 in /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/xdg-cache-home/pypoetry/virtualenvs +# +# ESC[1GESC[2KPreparing build environment with build-system requirements poetry>=0.12, setuptools, numpy<2.0Building circe-py (0.2.2) +# A setup.py file already exists. Using it. +# /tmp/vsc45304/eb-l3l1f3o9/tmplde8q1zg/.venv/lib/python3.11/site-packages/setuptools/_distutils/extension.py:139: UserWarning: Unknown Extension options: 'packages' +# warnings.warn(msg) +# running build +# running build_py +# creating /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/ccan_module.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/quic_graph_lasso.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/metacells.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/rank_correlation.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/inverse_covariance.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/metrics.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/circe.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/draw.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/__init__.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/ccan_module.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/quic_graph_lasso.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/metacells.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/rank_correlation.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/inverse_covariance.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/metrics.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/circe.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/draw.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# copying circe/__init__.py -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe +# creating /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe/pyquic +# copying circe/pyquic/pyquic.cpp -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe/pyquic +# copying circe/pyquic/QUIC.h -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe/pyquic +# copying circe/pyquic/QUIC.C -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe/pyquic +# copying circe/pyquic/pyquic.pyx -> /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe/pyquic +# running build_ext +# skipping 'circe/pyquic/pyquic.cpp' Cython extension (up-to-date) +# building 'circe.pyquic' extension +# creating /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/temp.linux-x86_64-cpython-311/circe/pyquic +# gcc -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -fPIC -I/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2023.07-gfbf-2023a/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include -I/tmp/vsc45304/eb-l3l1f3o9/tmplde8q1zg/.venv/include -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/include/python3.11 -c circe/pyquic/QUIC.C -o /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/temp.linux-x86_64-cpython-311/circe/pyquic/QUIC.o -msse2 -O2 -fPIC -w +# g++ -O2 -ftree-vectorize -march=native -fno-math-errno -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -fPIC -I/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2023.07-gfbf-2023a/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include -I/tmp/vsc45304/eb-l3l1f3o9/tmplde8q1zg/.venv/include -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/include/python3.11 -c circe/pyquic/pyquic.cpp -o /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/temp.linux-x86_64-cpython-311/circe/pyquic/pyquic.o -msse2 -O2 -fPIC -w +# g++ -O2 -ftree-vectorize -march=native -fno-math-errno -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -shared -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/ScaLAPACK/2.2.0-gompi-2023a-fb/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/ScaLAPACK/2.2.0-gompi-2023a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/12.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/12.3.0/lib -O2 -ftree-vectorize -march=native -fno-math-errno -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/temp.linux-x86_64-cpython-311/circe/pyquic/QUIC.o /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/temp.linux-x86_64-cpython-311/circe/pyquic/pyquic.o -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/lib -o /tmp/vsc45304/easybuild/build/CIRCE/0.2.2/foss-2023a/circe_py/circe_py-0.2.2/build/lib.linux-x86_64-cpython-311/circe/pyquic.cpython-311-x86_64-linux-gnu.so -lflexiblas