search

BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
Other
119 stars 48 forks source link

Concoct endless warning due to OpenBLAS #329

Open HouyuZhang opened 10 months ago

HouyuZhang commented 10 months ago

Dear devlopers, Thank you for developing this package. I met endless warnings OpenBLAS Warning: Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option. I have checked through each page on the internet related to this issue:

  1. Have gone through GitHub https://github.com/BinPro/CONCOCT/issues/232, and I got a sense that the OpenMP and OpenBLAS modules have problems. But, neither of conda install -y blas=2.5=mkl, conda install -y blas=*=*mkl works for me.
  2. https://github.com/BinPro/CONCOCT/issues/316. I installed the concoct in a new environment using py3, instead of py2, but still did not work.
  3. https://github.com/conda-forge/openblas-feedstock/issues/79. I tried to install OpenBLAS and openMP against in conda by conda install libopenblas==openmp* --channel conda-forge, not work.

Lastly, I used -t 1 to give up parallel running, but also did not work.

Do you have further suggestions on this issue? Also, it will help if you tell me an approximation of the running time of concoct. Thanks in advance!

Houyu

HouyuZhang commented 10 months ago

Below is my conda env: name: metawrap-env channels:

intel bioconda/label/cf201901 conda-forge ursky bioconda defaults dependencies: _libgcc_mutex=0.1=conda_forge _openmp_mutex=4.5=2_kmp_llvm biopython=1.81=py310h1fa729e_0 blas=2.106=mkl bowtie2=2.5.1=py310ha0a81b8_2 brotli=1.0.9=h166bdaf_9 brotli-bin=1.0.9=h166bdaf_9 brotli-python=1.0.9=py310hd8f1fbe_9 bwa=0.7.17=he4a0461_11 bzip2=1.0.8=h7f98852_4 c-ares=1.19.1=hd590300_0 ca-certificates=2023.7.22=hbcca054_0 certifi=2023.7.22=pyhd8ed1ab_0 charset-normalizer=3.2.0=pyhd8ed1ab_0 checkm-genome=1.2.2=pyhdfd78af_1 concoct=1.1.0=py310h74abf4b_3 contourpy=1.1.0=py310hd41b1e2_0 cycler=0.11.0=pyhd8ed1ab_0 cython=3.0.0=py310hc6cd4ac_0 dendropy=4.6.1=pyhdfd78af_0 fonttools=4.42.1=py310h2372a71_0 fraggenescan=1.31=h031d066_6 freetype=2.12.1=hca18f0e_1 gettext=0.21.1=h27087fc_0 gsl=2.7=he838d99_0 hmmer=3.3.2=hdbdd923_4 htslib=1.17=h81da01d_2 icu=72.1=hcb278e6_0 idba=1.1.3=1 idna=3.4=pyhd8ed1ab_0 intel-openmp=2023.1.0=hdb19cb5_46305 jellyfish=1.1.12=h2d50403_0 joblib=1.3.0=pyhd8ed1ab_1 keyutils=1.6.1=h166bdaf_0 kiwisolver=1.4.4=py310hbf28c38_1 kraken=1.1=h470a237_2 krb5=1.21.1=h659d440_0 krona=2.7=0 lcms2=2.15=haa2dc70_1 ld_impl_linux-64=2.40=h41732ed_0 lerc=4.0.0=h27087fc_0 libblas=3.9.0=6_mkl libbrotlicommon=1.0.9=h166bdaf_9 libbrotlidec=1.0.9=h166bdaf_9 libbrotlienc=1.0.9=h166bdaf_9 libcblas=3.9.0=6_mkl libcurl=8.2.0=hca28451_0 libdeflate=1.18=h0b41bf4_0 libedit=3.1.20191231=he28a2e2_2 libev=4.33=h516909a_1 libffi=3.4.2=h7f98852_5 libgcc=7.2.0=h69d50b8_2 libgcc-ng=13.1.0=he5830b7_0 libgfortran-ng=13.1.0=h69a702a_0 libgfortran5=13.1.0=h15d22d2_0 libgomp=13.1.0=he5830b7_0 libhwloc=2.9.1=nocuda_h7313eea_6 libiconv=1.17=h166bdaf_0 libidn2=2.3.4=h166bdaf_0 libjpeg-turbo=2.1.5.1=h0b41bf4_0 liblapack=3.9.0=6_mkl liblapacke=3.9.0=6_mkl libnghttp2=1.52.0=h61bc06f_0 libnsl=2.0.0=h7f98852_0 libopenblas=0.3.23=openmp_h2a4e791_0 libpng=1.6.39=h753d276_0 libsqlite=3.42.0=h2797004_0 libssh2=1.11.0=h0841786_0 libstdcxx-ng=13.1.0=hfd8a6a1_0 libtiff=4.5.1=h8b53f26_0 libunistring=0.9.10=h7f98852_0 libuuid=2.38.1=h0b41bf4_0 libwebp-base=1.3.1=hd590300_0 libxcb=1.15=h0b41bf4_0 libxml2=2.11.4=h0d562d8_0 libzlib=1.2.13=hd590300_5 llvm-openmp=16.0.6=h4dfa4b3_0 matplotlib-base=3.7.1=py310he60537e_0 maxbin2=2.2.1=0 metabat2=2.12.1=0 mkl=2020.4=h726a3e6_304 mpi=1.0=openmpi munkres=1.0.7=py_1 ncurses=6.4=hcb278e6_0 nose=1.3.7=py_1006 numpy=1.25.1=py310ha4c1d20_0 openblas=0.3.23=openmp_hef934df_0 openjpeg=2.5.0=hfec8fc6_2 openmpi=4.1.5=h414af15_101 openssl=3.1.2=hd590300_0 packaging=23.1=pyhd8ed1ab_0 pandas=2.0.3=py310h7cbd5c2_1 perl=5.32.1=4_hd590300_perl5 perl-threaded=5.22.0=13 pillow=10.0.0=py310h582fbeb_0 pip=23.2.1=pyhd8ed1ab_0 platformdirs=3.9.1=pyhd8ed1ab_0 pooch=1.7.0=pyha770c72_3 pplacer=1.1.alpha19=h9ee0642_2 prodigal=2.6.3=h031d066_6 pthread-stubs=0.4=h36c2ea0_1001 pyparsing=3.1.1=pyhd8ed1ab_0 pysam=0.21.0=py310h41dec4a_1 pysocks=1.7.1=pyha2e5f31_6 python=3.10.12=hd12c33a_0_cpython python-dateutil=2.8.2=pyhd8ed1ab_0 python-tzdata=2023.3=pyhd8ed1ab_0 python_abi=3.10=3_cp310 pytz=2023.3=pyhd8ed1ab_0 readline=8.2=h8228510_1 rename=1.601=hdfd78af_1 requests=2.31.0=pyhd8ed1ab_0 samtools=1.17=hd87286a_1 scikit-learn=1.2.2=py310hf7d194e_2 scipy=1.11.1=py310ha4c1d20_0 setuptools=68.0.0=pyhd8ed1ab_0 six=1.16.0=pyh6c4a22f_0 spades=3.13.0=0 sqlite=3.42.0=h2c6b66d_0 tbb=2021.9.0=hf52228f_0 threadpoolctl=3.2.0=pyha21a80b_0 tk=8.6.12=h27826a3_0 typing-extensions=4.7.1=hd8ed1ab_0 typing_extensions=4.7.1=pyha770c72_0 tzdata=2023c=h71feb2d_0 unicodedata2=15.0.0=py310h5764c6d_0 urllib3=2.0.4=pyhd8ed1ab_0 wget=1.20.3=ha35d2d1_1 wheel=0.41.0=pyhd8ed1ab_0 xorg-libxau=1.0.11=hd590300_0 xorg-libxdmcp=1.1.3=h7f98852_0 xz=5.2.6=h166bdaf_0 zlib=1.2.13=hd590300_5 zstd=1.5.2=hfc55251_7 prefix: /lustre/home/tangmoran_2021phd/anaconda3/envs/metawrap-env