Fix typo in pragma #196
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name: unifrac-binaries CI | |
on: | |
push: | |
branches: [ main ] | |
pull_request: | |
branches: [ main ] | |
# A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
jobs: | |
build-and-test: | |
strategy: | |
matrix: | |
os: [ubuntu-latest, macos-latest, linux-gpu-cuda] | |
offload: [acc, ompgpu] | |
runs-on: ${{ matrix.os }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniconda-version: "latest" | |
auto-update-conda: true | |
- name: Install | |
shell: bash -l {0} | |
run: | | |
df -h . | |
if [[ "$(uname -s)" == "Linux" ]]; | |
then | |
conda create -q --yes --strict-channel-priority -n unifrac -c conda-forge -c bioconda gxx_linux-64 gfortran_linux-64 hdf5 mkl-include lz4 zlib hdf5-static libcblas liblapacke make curl | |
else | |
conda create -q --yes --strict-channel-priority -n unifrac -c conda-forge -c bioconda clangxx_osx-64 hdf5 mkl-include lz4 hdf5-static libcblas liblapacke make curl | |
fi | |
conda clean --yes -t | |
df -h . | |
conda activate unifrac | |
echo "$(uname -s)" | |
if [[ "$(uname -s)" == "Linux" ]]; | |
then | |
which x86_64-conda-linux-gnu-gcc | |
x86_64-conda-linux-gnu-gcc -v | |
x86_64-conda-linux-gnu-g++ -v | |
else | |
which clang | |
clang -v | |
fi | |
which h5c++ | |
if [[ "$(uname -s)" == "Linux" ]]; | |
then | |
# install PGI but do not source it | |
# the makefile will do it automatically | |
./scripts/install_hpc_sdk.sh </dev/null | |
fi | |
df -h . | |
export PERFORMING_CONDA_BUILD=True | |
export BUILD_OFFLOAD=${{ matrix.offload }} | |
echo "======= begin env =====" | |
env | |
echo "======= end env =====" | |
# all == build (shlib,bins,tests) and install | |
make all | |
df -h . | |
- name: Tests | |
shell: bash -l {0} | |
run: | | |
conda activate unifrac | |
if [[ "$(uname -s)" == "Linux" ]]; | |
then | |
lscpu | |
fi | |
# keep it low for runs in containers | |
# and a weird number to potentially catch potential bugs | |
export OMP_NUM_THREADS=3 | |
# diagnostic messages for debugging, if needed | |
export UNIFRAC_CPU_INFO=Y | |
export UNIFRAC_GPU_INFO=Y | |
pushd src | |
./test_su | |
./test_api | |
./test_ska | |
popd | |
pushd test | |
./capi_test 1 | |
# explicitly check that we do not have hdf5 dependencies | |
if [[ "$(uname -s)" == "Linux" ]]; | |
then | |
ldd ./capi_test |awk 'BEGIN{a=0}/hdf/{a=a+1;print $0}END{if (a==0) {print "No dynamic hdf5 found"} else {exit 2}}' | |
else | |
otool -L ./capi_test|awk 'BEGIN{a=0}/hdf/{a=a+1;print $0}END{if (a==0) {print "No dynamic hdf5 found"} else {exit 2}}' | |
fi | |
popd | |
pushd src/testdata | |
conda install --yes -c conda-forge h5py | |
# weighted_unnormalized | |
time ssu -m weighted_unnormalized_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5 | |
./compare_unifrac_matrix.py test500.weighted_unnormalized_fp32.h5 t1.h5 1.e-5 | |
./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1 | |
rm -f t1.h5 | |
# retry with default precision handling | |
time ssu -m weighted_unnormalized -i test500.biom -t test500.tre --pcoa 4 -r hdf5 -o t1.h5 | |
./compare_unifrac_matrix.py test500.weighted_unnormalized_fp32.h5 t1.h5 1.e-5 | |
./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1 | |
rm -f t1.h5 | |
time ssu -f -m weighted_unnormalized_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5 | |
# matrrix will be different, but PCOA similar | |
./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1 | |
rm -f t1.h5 | |
time ssu -m weighted_unnormalized_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5 | |
# minimal precision loss between fp32 and fp64 | |
./compare_unifrac_matrix.py test500.weighted_unnormalized_fp32.h5 t1.h5 1.e-5 | |
./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1 | |
rm -f t1.h5 | |
# weighted_normalized | |
time ssu -f -m weighted_normalized -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5 | |
./compare_unifrac_matrix.py test500.weighted_normalized_fp32.f.h5 t1.h5 1.e-5 | |
./compare_unifrac_pcoa.py test500.weighted_normalized_fp32.f.h5 t1.h5 3 0.1 | |
rm -f t1.h5 | |
time ssu -f -m weighted_normalized_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5 | |
./compare_unifrac_matrix.py test500.weighted_normalized_fp32.f.h5 t1.h5 1.e-5 | |
./compare_unifrac_pcoa.py test500.weighted_normalized_fp32.f.h5 t1.h5 3 0.1 | |
rm -f t1.h5 | |
# unweighted | |
time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5 | |
./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
rm -f t1.h5 | |
time ssu -f -m unweighted_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5 | |
./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
# hdf5 without distance matrix, just PCoA | |
echo "hdf5_nodist" | |
time ssu -f -m unweighted_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_nodist -o t1.h5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_nodist -o t1.h5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
# permanova | |
echo "permanova" | |
time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5 --permanova 999 -g test500.tsv -c empo_2 -o t1.h5 | |
# compare to values given by skbio.stats.distance.permanova | |
python compare_unifrac_stats.py t1.h5 5 999 1.001112 0.456 0.001 0.1 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5 --permanova 99 -g test500.tsv -c empo_2 -o t1.h5 | |
python compare_unifrac_stats.py t1.h5 5 99 1.001112 0.456 0.001 0.2 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
time ssu -m weighted_unnormalized_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_nodist -g test500.tsv -c empo_3 -o t1.h5 | |
# compare to values given by skbio.stats.distance.permanova | |
python compare_unifrac_stats.py t1.h5 17 999 0.890697 0.865 0.001 0.1 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
# partials | |
echo "partials" | |
ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --mode partial-report --n-partials 2 | |
time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --mode partial --start 0 --stop 125 -o t1.partial.1 | |
time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --mode partial --start 125 --stop 250 -o t1.partial.2 | |
ls -l t1.partial* | |
ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --mode check-partial --partial-pattern 't1.partial.*' | |
time ssu -f -m unweighted_fp64 -i test500.biom -t test500.tre --pcoa 4 --mode merge-partial --partial-pattern 't1.partial.*' -r hdf5_fp64 -o t1.h5 | |
./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --pcoa 4 --mode merge-partial --partial-pattern 't1.partial.*' -r hdf5_fp32 -o t1.h5 | |
./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --pcoa 4 --mode merge-partial --partial-pattern 't1.partial.*' -r hdf5_nodist -o t1.h5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
rm -f t1.partial.* | |
# subsample | |
echo "subsample" | |
time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 --subsample-depth 100 -o t1.h5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.3 | |
rm -f t1.h5 | |
time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 --subsample-depth 100 --subsample-replacement with -o t1.h5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.3 | |
rm -f t1.h5 | |
time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 --subsample-depth 100 --subsample-replacement without -o t1.h5 | |
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.3 | |
rm -f t1.h5 | |
time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_nodist --permanova 99 -g test500.tsv -c empo_2 --subsample-depth 100 -o t1.h5 | |
python compare_unifrac_stats.py t1.h5 5 99 1.001112 0.456 0.05 0.6 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
# multi | |
echo "multi" | |
time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 --mode multi --subsample-depth 100 --n-subsamples 10 -o t1.h5 | |
./compare_unifrac_pcoa_multi.py test500.unweighted_fp32.f.h5 t1.h5 10 3 0.3 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 --mode multi --n-subsamples 10 --permanova 99 -g test500.tsv -c empo_2 --subsample-depth 100 -o t1.h5 | |
python compare_unifrac_stats_multi.py t1.h5 10 5 99 1.001112 0.456 0.08 0.6 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 --mode multi --n-subsamples 10 --permanova 99 -g test500.tsv -c empo_2 --subsample-depth 100 --subsample-replacement without -o t1.h5 | |
python compare_unifrac_stats_multi.py t1.h5 10 5 99 1.001112 0.456 0.08 0.6 | |
ls -l t1.h5 | |
rm -f t1.h5 | |
popd | |
# finally, test rapi, too | |
pushd src | |
if [[ "$(uname -s)" == "Linux" ]]; | |
then | |
make clean | |
rm -f ~/.R/Makevars | |
conda install -q --yes --strict-channel-priority -c conda-forge r-base | |
unset CXXFLAGS | |
unset CFLAGS | |
unset DEBUG_CXXFLAGS | |
unset DEBUG_CFLAGS | |
# the r-base package has a broken dependency | |
ln -s $CONDA_PREFIX/lib/libreadline.so $CONDA_PREFIX/lib/libreadline.so.6 | |
R -e 'install.packages("Rcpp", repos="http://lib.stat.cmu.edu/R/CRAN/")' | |
make rapi_test | |
fi | |
popd | |
- name: Sanity checks | |
shell: bash -l {0} | |
run: | | |
conda activate unifrac | |
# keep it low for runs in containers | |
export OMP_NUM_THREADS=2 | |
pushd ci | |
./crawford_test.sh | |
popd |