OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option

Question

[v.berriosfarias]

Hello ther, I was running metawrap binning module using concoct and got the following error message:

OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option

this seems to be a bug where one solution may be rebuilding openblas via make USE_OPENMP=1 as suggested here: https://stackoverflow.com/questions/34578526/how-to-make-openblas-work-with-openmp

but as I installed libopenblas via conda I'm trying to figure out if there is a way that I can set USE_OPENMP=1 on a "conda way"

Additionaly there is a list of versions and want to know if there is a version that have USE_OPENMP=1 as default :

conda search libopenblas --channel conda-forge

Name Version Build Channel
libopenblas 0.2.20 h9ac9557_4 pkgs/main
libopenblas 0.2.20 h9ac9557_7 pkgs/main
libopenblas 0.2.20 hae245c1_3 pkgs/main
libopenblas 0.3.2 h5a2b251_1 pkgs/main
libopenblas 0.3.2 h7aa55d7_0 pkgs/main
libopenblas 0.3.2 h9ac9557_0 pkgs/main
libopenblas 0.3.2 h9ac9557_1 pkgs/main
libopenblas 0.3.3 h5a2b251_1 pkgs/main
libopenblas 0.3.3 h5a2b251_2 pkgs/main
libopenblas 0.3.3 h5a2b251_3 pkgs/main
libopenblas 0.3.6 h5a2b251_0 pkgs/main
libopenblas 0.3.6 h5a2b251_1 pkgs/main
libopenblas 0.3.6 h5a2b251_2 pkgs/main
libopenblas 0.3.6 h6e990d7_3 conda-forge
libopenblas 0.3.6 h6e990d7_4 conda-forge
libopenblas 0.3.6 h6e990d7_5 conda-forge
libopenblas 0.3.6 h6e990d7_6 conda-forge
libopenblas 0.3.7 h5ec1e0e_4 conda-forge
libopenblas 0.3.7 h5ec1e0e_5 conda-forge
libopenblas 0.3.7 h5ec1e0e_6 conda-forge
libopenblas 0.3.7 h5ec1e0e_7 conda-forge
libopenblas 0.3.7 h6e990d7_0 conda-forge
libopenblas 0.3.7 h6e990d7_1 conda-forge
libopenblas 0.3.7 h6e990d7_2 conda-forge
libopenblas 0.3.7 h6e990d7_3 conda-forge
libopenblas 0.3.8 h5ec1e0e_0 conda-forge
libopenblas 0.3.9 h5ec1e0e_0 conda-forge
libopenblas 0.3.10 h5a2b251_0 pkgs/main
libopenblas 0.3.10 h5ec1e0e_0 conda-forge
libopenblas 0.3.10 openmp_h59f9010_5 conda-forge
libopenblas 0.3.10 openmp_h709eae2_1 conda-forge
libopenblas 0.3.10 openmp_h709eae2_2 conda-forge
libopenblas 0.3.10 openmp_h709eae2_3 conda-forge
libopenblas 0.3.10 openmp_h709eae2_4 conda-forge
libopenblas 0.3.10 openmp_h709eae2_5 conda-forge
libopenblas 0.3.10 pthreads_h4812303_5 conda-forge libopenblas 0.3.10 pthreads_hb3c22a3_1 conda-forge libopenblas 0.3.10 pthreads_hb3c22a3_2 conda-forge libopenblas 0.3.10 pthreads_hb3c22a3_3 conda-forge libopenblas 0.3.10 pthreads_hb3c22a3_4 conda-forge libopenblas 0.3.10 pthreads_hb3c22a3_5 conda-forge libopenblas 0.3.12 openmp_h59f9010_0 conda-forge
libopenblas 0.3.12 openmp_h59f9010_1 conda-forge
libopenblas 0.3.12 openmp_h709eae2_0 conda-forge
libopenblas 0.3.12 openmp_h709eae2_1 conda-forge
libopenblas 0.3.12 pthreads_h4812303_0 conda-forge libopenblas 0.3.12 pthreads_h4812303_1 conda-forge libopenblas 0.3.12 pthreads_hb3c22a3_0 conda-forge libopenblas 0.3.12 pthreads_hb3c22a3_1 conda-forge libopenblas 0.3.13 h4367d64_0 pkgs/main
libopenblas 0.3.13 openmp_h3d5035f_0 conda-forge
libopenblas 0.3.13 pthreads_h8fe5266_0 conda-forge

i'll be so thankful if you can help me with this :)

Answer 1

[Mensur Dlakic]

The error message couldn't be any clearer than it already is: you need to rebuild using the suggested switch. If the binary was already build using a different version of the OpenMP library, you could hopefully figure it out by installing a library that it needs, or sometimes a newer version will work as well. Yet it seems like your binary was build without OpenMP at all, so either you find a conda version that was built with OpenMP, or rebuild the binary by following the suggestion.

PS I just realized that this is only a warning, and not an error. You may still be able to run the program as is, but will not have the OpenMP functionality.

Answer 2

[shengweima]

conda install libopenblas==openmp* --channel conda-forge