BinPro/CONCOCT

endless OpenBLAS Warning again

Xiaoyu2425 opened this issue · 1 comments

Xiaoyu2425 commented

Hi, I got endless "OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option" when I ran concoct with -t argument. I saw it in a previous threads where people suggested solutions such as "conda install blas=1.0=mkl" or "conda install -c conda-forge openblas=0.3.3" and then re-install "python setup.py install". However, I tried all those methods and it still didn't work.

Below are my "conda env export"

name: concoct_env2
channels:

  • conda-forge
  • bioconda
  • defaults
  • biobakery
  • anaconda
    dependencies:
  • _libgcc_mutex=0.1=conda_forge
  • _openmp_mutex=4.5=2_kmp_llvm
  • blas=1.0=mkl
  • bzip2=1.0.8=h7f98852_4
  • c-ares=1.18.1=h7f98852_0
  • ca-certificates=2022.6.15=ha878542_0
  • curl=7.83.1=h2283fc2_0
  • gsl=2.7=he838d99_0
  • joblib=1.1.0=pyhd8ed1ab_0
  • keyutils=1.6.1=h166bdaf_0
  • krb5=1.19.3=h08a2579_0
  • ld_impl_linux-64=2.36.1=hea4e1c9_2
  • libblas=3.9.0=16_linux64_mkl
  • libcblas=3.9.0=16_linux64_mkl
  • libcurl=7.83.1=h2283fc2_0
  • libedit=3.1.20191231=he28a2e2_2
  • libev=4.33=h516909a_1
  • libffi=3.4.2=h7f98852_5
  • libgcc-ng=12.1.0=h8d9b700_16
  • libgfortran=3.0.0=1
  • libgfortran-ng=12.1.0=h69a702a_16
  • libgfortran5=12.1.0=hdcd56e2_16
  • liblapack=3.9.0=16_linux64_mkl
  • libnghttp2=1.47.0=hff17c54_1
  • libnsl=2.0.0=h7f98852_0
  • libsqlite=3.39.3=h753d276_0
  • libssh2=1.10.0=hf14f497_3
  • libstdcxx-ng=12.1.0=ha89aaad_16
  • libuuid=2.32.1=h7f98852_1000
  • libzlib=1.2.12=h166bdaf_2
  • llvm-openmp=14.0.4=he0ac6c6_0
  • mkl=2022.1.0=h84fe81f_915
  • mpi=1.0=openmpi
  • ncurses=6.3=h27087fc_1
  • nose=1.3.7=py_1006
  • openblas=0.3.3=ha44fe06_1
  • openmpi=4.1.4=ha1ae619_100
  • openssl=3.0.5=h166bdaf_1
  • pip=22.2.2=pyhd8ed1ab_0
  • python=3.10.6=ha86cf86_0_cpython
  • python-dateutil=2.8.2=pyhd8ed1ab_0
  • python_abi=3.10=2_cp310
  • pytz=2022.2.1=pyhd8ed1ab_0
  • readline=8.1.2=h0f457ee_0
  • samtools=1.6=h3f2fef4_8
  • setuptools=65.3.0=pyhd8ed1ab_1
  • six=1.16.0=pyh6c4a22f_0
  • tbb=2021.5.0=h924138e_1
  • threadpoolctl=3.1.0=pyh8a188c0_0
  • tk=8.6.12=h27826a3_0
  • tzdata=2022c=h191b570_0
  • wheel=0.37.1=pyhd8ed1ab_0
  • xz=5.2.6=h166bdaf_0
  • zlib=1.2.12=h166bdaf_2
  • pip:
    • biopython==1.79
    • concoct==1.1.0
    • cython==0.29.32
    • numpy==1.23.2
    • pandas==1.4.4
    • scikit-learn==1.1.2
    • scipy==1.9.1

Any suggestions would be appreciated!

kalen-rasmussen commented

Hey @Xiaoyu2425 I was able to work around this issue by doing the following on a linux server. Hopefully it will work for you too.

conda create -n concoct python=3.8
conda activate concoct
conda config --env --add channels defaults
conda config --env --add channels conda-forge
conda config --env --add channels bioconda
conda install concoct

At this point you can try entering concoct -h to see if the basic help menu will show up. In my experience I received the following error: "ImportError: libmkl_rt.so: cannot open shared object file: No such file or directory". Which I was able to fix by running:

conda install mkl

  • 👍1