foss 2019b

There is a newer version of foss

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

Accessing foss 2019b

To load the module for foss 2019b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load foss/2019b

BEAR Apps Version

2019b

Architectures

EL8-cascadelakeEL8-haswellUbuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

foss 2019b provides

  • GCC 8.3.0
  • OpenMPI 3.1.4
  • OpenBLAS 0.3.7
  • FFTW 3.3.8
  • ScaLAPACK 2.0.2

More Information

For more information visit the foss website.

Dependencies

This version of foss has a direct dependency on: FFTW/3.3.8-gompi-2019b GCC/8.3.0 OpenBLAS/0.3.7-GCC-8.3.0 OpenMPI/3.1.6-GCC-8.3.0 ScaLAPACK/2.0.2-gompi-2019b

Required By

This version of foss is a direct dependent of: aenet/2.0.4-foss-2019b-Python-3.7.4 aenet/2.0.4-foss-2019b-mpi ANTs/2.3.4-foss-2019b-Python-3.7.4 Armadillo/9.900.2-foss-2019b arpack-ng/3.7.0-foss-2019b Arrow/0.16.0-foss-2019b-Python-3.7.4 ASE/3.19.1-foss-2019b-Python-3.7.4 astropy/4.0-foss-2019b-Python-3.7.4 AUCell/1.8.0-foss-2019b-R-3.6.2 AUGUSTUS/3.3.3-foss-2019b basemap/1.2.1-foss-2019b-Python-3.7.4 BEAR-Python-DataScience/2019b-foss-2019b-Python-3.7.4 BEAR-Python-DataScience/2019b-foss-2019b-Python-2.7.16 BEAR-Python-Sciences/2019b-foss-2019b-Python-3.7.4 BEAR-R-bio/2019b-foss-2019b-R-3.6.2 BEAR-R-geo/2019b-foss-2019b-R-3.6.2 Bio-DB-BigFile/1.07-foss-2019b-Perl-5.30.0 Bio-DB-BigFile-jksrc/v395-foss-2019b biofluff/2.1.4-foss-2019b-Python-2.7.16 biofluff/3.0.3-foss-2019b-Python-3.7.4 BIOMASS/2.1.3-foss-2019b-R-3.6.2 biom-format/2.1.8-foss-2019b-Python-3.7.4 Biopython/1.75-foss-2019b-Python-2.7.16 Biopython/1.75-foss-2019b-Python-3.7.4 Bismark/0.22.3-foss-2019b bokeh/1.4.0-foss-2019b-Python-3.7.4 Bracken/2.6.0-foss-2019b-Python-3.7.4 BUSCO/4.0.5-foss-2019b-Python-3.7.4 Cartopy/0.18.0-foss-2019b-Python-3.7.4 CATALYST/1.10.3-foss-2019b-R-3.6.2 cba/0.2-21-foss-2019b-R-3.6.2 cdsapi/0.2.7-foss-2019b-Python-3.7.4 cellassign/520de59-foss-2019b-Python-3.7.4-R-3.6.2 cellphonedb/2.1.1-foss-2019b-Python-3.7.4-R-3.6.2 ceres-solver/1.14.0-foss-2019b cf-plot/3.0.6-foss-2019b-Python-3.7.4 cf-python/3.4.0-foss-2019b-Python-3.7.4 CGAL/4.14.1-foss-2019b-Python-3.7.4 cgat/0.6.5-foss-2019b-Python-3.7.4 CLHEP/2.4.1.3-foss-2019b ClustalW2/2.1-foss-2019b ClusterR/1.2.1-foss-2019b-R-3.6.2 clustrd/1.3.7-foss-2019b-R-3.6.2 CNVnator/0.4.1-foss-2019b-Python-3.7.4 colorRamps/2.3-foss-2019b-R-3.6.2 CSTools/3.1.0-foss-2019b-R-3.6.2 ctffind/4.1.14-foss-2019b dask/2.8.0-foss-2019b-Python-3.7.4 DBD-mysql/4.050-foss-2019b-Perl-5.30.0 Deepbinner/c261ae9-foss-2019b-Python-3.7.4 DiffBind/2.14.0-foss-2019b-R-3.6.2 DirichletMultinomial/1.28.0-foss-2019b-R-3.6.2 DoubletFinder/20200901-foss-2019b-R-3.6.2 dropEst/0.8.6-foss-2019b-R-3.6.2 Dynare/4.6.3-foss-2019b edlib/1.3.8.post1-foss-2019b-Python-3.7.4 eggnog-mapper/1.0.3-foss-2019b-Python-2.7.16 ELPA/2019.11.001-foss-2019b ESMF/8.0.1-foss-2019b ESMPy/8.0.1-foss-2019b-Python-3.7.4 ETE/3.1.2-foss-2019b-Python-3.7.4 ETE/3.1.2-foss-2019b-Python-2.7.16 eXpress/1.5.3-foss-2019b FASTA/36.3.8h_04-May-2020-foss-2019b fasterize/1.0.2-foss-2019b-R-3.6.2 FastQ_Screen/0.14.1-foss-2019b-Perl-5.30.0 FastQTL/2.184_gtex-47180b9-foss-2019b-Python-3.7.4-R-3.6.2 FD/1.0-12-foss-2019b-R-3.6.2 fgeo/1.1.4-foss-2019b-R-3.6.2 fineSTRUCTURE/4.1.1-foss-2019b fineSTRUCTURE/4.0.1-foss-2019b Fiona/1.8.13-foss-2019b-Python-3.7.4 flashpca/20200910-foss-2019b Flye/2.6-foss-2019b-Python-3.7.4 funannotate/1.8.1-foss-2019b-Python-2.7.16 funannotate/1.8.1-foss-2019b-Python-3.7.4 fuzzywuzzy/0.18.0-foss-2019b-Python-3.7.4 GAMESS-US/20190930-R2-foss-2019b GATE/9.0-foss-2019b-Python-3.7.4 GBJ/0.5.0-foss-2019b-R-3.6.2 GCPy/1.0.3-foss-2019b-Python-3.7.4 gcta/1.93.2-foss-2019b GDAL/3.0.2-foss-2019b-Python-3.7.4 GDGraph/1.54-foss-2019b-Perl-5.30.0 Geant4/10.06.p03-foss-2019b GeneSplicer/20130312-foss-2019b geopandas/0.8.1-foss-2019b-Python-3.7.4 GEOS/3.8.0-foss-2019b-Python-3.7.4 GMAP-GSNAP/2020-09-12-foss-2019b GPflow/2.1.1-foss-2019b-Python-3.7.4-TensorFlow-2.2.0 GROMACS/2019.6-foss-2019b gtex-pipeline/gtex_v8-foss-2019b-Python-3.7.4-R-3.6.2 h5py/2.10.0-foss-2019b-Python-3.7.4 h5py/2.10.0-foss-2019b-Python-2.7.16 Hail/0.2.61-foss-2019b-Python-3.7.4-Java-1.8 harmony/0.1-foss-2019b-R-3.6.2 HDDM/0.7.6-foss-2019b-Python-3.7.4 hdf5storage/0.1.15-foss-2019b-Python-3.7.4 HISAT2/2.2.1-foss-2019b HOMER/4.11-foss-2019b HPL/2.3-foss-2019b HTSeq/0.12.4-foss-2019b-Python-3.7.4 HTSeq/0.12.4-foss-2019b-Python-2.7.16 igraph/0.8.0-foss-2019b IJulia/1.21.1-foss-2019b-Julia-1.4.0-Python-3.7.4 imageio/2.6.1-foss-2019b-Python-3.7.4 imageio-ffmpeg/0.3.0-foss-2019b-Python-3.7.4 imgaug/0.4.0-foss-2019b-Python-3.7.4 IPython/7.9.0-foss-2019b-Python-3.7.4 IPython/5.10.0-foss-2019b-Python-2.7.16 iRF/2.0.0-foss-2019b-R-3.6.2 iRF/3.0.0-foss-2019b-R-3.6.2 IRkernel/1.1-foss-2019b-R-3.6.2-Python-3.7.4 ITK/5.0.1-foss-2019b-Python-3.7.4 JupyterLab/1.2.5-foss-2019b-Python-3.7.4 JupyterLab/2.2.8-foss-2019b-Python-3.7.4 kallisto/0.46.1-foss-2019b Kendall/2.2-foss-2019b-R-3.6.2 Kent_tools/401-foss-2019b Keras/2.3.1-foss-2019b-TensorFlow-1.15.0-Python-3.7.4 Keras/2.3.1-foss-2019b-Python-3.7.4 keras-tuner/1.0.2-foss-2019b-Python-3.7.4 kim-api/2.1.3-foss-2019b KneadData/0.7.6-foss-2019b-Python-3.7.4-Java-11 LAMMPS/3Mar2020-foss-2019b-Python-3.7.4-kokkos LEfSe/1.1-foss-2019b-Python-3.7.4 leidenalg/0.8.0-foss-2019b-Python-3.7.4 libRmath/3.6.2-foss-2019b Liftoff/1.4.2-foss-2019b-Python-3.7.4 Lighter/1.1.2-foss-2019b LongQC/1.0-foss-2019b-Python-3.7.4 MACS2/2.2.7.1-foss-2019b-Python-3.7.4 mappy/2.17-foss-2019b-Python-3.7.4 MariaDB/10.4.12-foss-2019b Mash/2.2-foss-2019b matplotlib/2.2.5-foss-2019b-Python-2.7.16 matplotlib/3.1.1-foss-2019b-Python-3.7.4 mayavi/4.7.1-foss-2019b-Python-3.7.4 MedPy/0.4.0-foss-2019b-Python-3.7.4 MEGAN_Calc_Code/3.1-foss-2019b MEGAN_Preprocessor/3.1-foss-2019b Metal/2011-03-25-foss-2019b MetaXcan/0.7.3-foss-2019b-Python-3.7.4 MIRTK/20210104-foss-2019b-Python-3.7.4 mitre/1.0b1-foss-2019b-Python-2.7.16 mlpy/3.5.0-foss-2019b-Python-2.7.16 mlst/2.19.0-foss-2019b MNE-Python/0.20.4-foss-2019b-Python-3.7.4 molmod/1.4.5-foss-2019b-Python-3.7.4 Monocle3/0.2.1-foss-2019b-R-3.6.2 mosfit/1.1.6-foss-2019b-Python-3.7.4 MPI3SNP/f03aecf-foss-2019b MRtrix/3.0-rc-20200326-foss-2019b-Python-3.7.4 MultiQC/1.9-foss-2019b-Python-3.7.4 n2v/0.1.11-foss-2019b-Python-3.7.4 NAMD/2.14-foss-2019b-mpi NanoMod/0.2.2-foss-2019b-Python-2.7.16 ncdf4/1.16.1-foss-2019b-R-3.6.2 netcdf4-python/1.5.3-foss-2019b-Python-3.7.4 networkx/2.4-foss-2019b-Python-3.7.4 neuropythy/0.11.8-foss-2019b-Python-3.7.4-Java-11 ngspice/31-foss-2019b ngsplot/2.63-foss-2019b-Python-2.7.16-R-3.6.2 NiBabel/3.1.0-foss-2019b-Python-3.7.4 numba/0.47.0-foss-2019b-Python-3.7.4 numexpr/2.7.1-foss-2019b-Python-3.7.4 oceanmap/0.1.1-foss-2019b-R-3.6.2 ont-fast5-api/2.0.1-foss-2019b-Python-2.7.16 OpenCV/4.2.0-foss-2019b-Python-3.7.4 OpenFOAM-Extend/4.1-20200408-foss-2019b-Python-2.7.16 OpenFOAM (OpenCFD Ltd)/v1912-foss-2019b OpenFOAM (The OpenFOAM Foundation)/6-foss-2019b OpenMC/0.11.0-foss-2019b-Python-3.7.4 OpenMC/0.12.0-foss-2019b-Python-3.7.4 ParaView/5.6.2-foss-2019b-Python-3.7.4-mpi PASApipeline/2.4.1-foss-2019b pavian/81d784d-foss-2019b-R-3.6.2 pept/0.1.6-foss-2019b-Python-3.7.4 pept/0.2.2-foss-2019b-Python-3.7.4 Peridigm/cb9979d-foss-2019b-Python-3.7.4 phenoptrReports/0.2.6-foss-2019b-R-3.6.2 PIMD/2.4.0-foss-2019b-aenet Pingouin/0.3.8-foss-2019b-Python-3.7.4 plotly.py/4.5.3-foss-2019b PLUMED/2.5.3-foss-2019b-Python-3.7.4 poLCA/1.4.1-foss-2019b-R-3.6.2 poppler/0.90.1-foss-2019b poweRlaw/0.70.6-foss-2019b-R-3.6.2 PPN2V/4e822aa-foss-2019b-Python-3.7.4 presto/7f63f96-foss-2019b-R-3.6.2 PRINSEQ/0.20.4-foss-2019b-Perl-5.30.0 Proteinortho/6.0.23-foss-2019b-Python-3.7.4-Perl-5.30.0 Proteinortho/6.0.23-foss-2019b-Python-2.7.16-Perl-5.30.0 pybedtools/0.8.1-foss-2019b pycoQC/2.5.0.21-foss-2019b-Python-3.7.4 pyDNase/0.3.0-foss-2019b-Python-3.7.4 pyfasta/0.5.2-foss-2019b-Python-2.7.16 PyGEOS/0.7.1-foss-2019b-Python-3.7.4 PyMC3/3.8-foss-2019b-Python-3.7.4 PyMieScatt/1.7.5.4-foss-2019b-Python-3.7.4 Pyro/1.5.0-foss-2019b-Python-3.7.4 pytabix/0.1-foss-2019b-Python-2.7.16 PyTables/3.6.1-foss-2019b-Python-3.7.4 python-bioformats/4.0.0-foss-2019b-Python-3.7.4 python-igraph/0.8.0-foss-2019b PyTorch/1.6.0-foss-2019b-Python-3.7.4 PyTorch/1.3.1-foss-2019b-Python-3.7.4 PyTorch/1.4.0-foss-2019b-Python-3.7.4 PyTorch-Geometric/1.4.3-foss-2019b-Python-3.7.4-PyTorch-1.4.0 PyZMQ/18.1.1-foss-2019b-Python-3.7.4 QCTOOL/2.0.8-foss-2019b Qualimap/2.2.1-foss-2019b-R-3.6.2 QuantumESPRESSO/6.6-foss-2019b R/3.6.2-foss-2019b Racon/1.4.10-foss-2019b R-bundle-Bioconductor/3.10-foss-2019b-R-3.6.2 refnx/0.1.17-foss-2019b-Python-3.7.4 RELION/3.1.1-foss-2019b-ppc64le RELION/3.1.1-foss-2019b RFMIX/9505bfa-foss-2019b rgdal/1.4-8-foss-2019b-R-3.6.2 rgeos/0.5-2-foss-2019b-R-3.6.2 R-keras/2.2.5.0-foss-2019b-Python-3.7.4-R-3.6.2 RNA-SeQC/1.1.8-foss-2019b-Java-11 RNAstructure/6.2-foss-2019b-Python-3.7.4 RNetCDF/2.3-1-foss-2019b-R-3.6.2 ROOT/6.20.00-foss-2019b-Python-3.7.4 Rosetta/3.11-foss-2019b-Python-2.7.16 rpy2/3.2.6-foss-2019b-Python-3.7.4 rpy2/2.8.6-foss-2019b-Python-2.7.16 RSEM/1.3.2-foss-2019b rstanarm/2.21.1-foss-2019b-R-3.6.2 rstudio/1.2.5033-foss-2019b-R-3.6.2 rstudio/1.3.959-foss-2019b-R-3.6.2 rts/1.0-49-foss-2019b-R-3.6.2 rworldmap/1.3-6-foss-2019b-R-3.6.2 s2dv/0.0.1-foss-2019b-R-3.6.2 scikit-image/0.16.2-foss-2019b-Python-3.7.4 scikit-learn/0.21.3-foss-2019b-Python-3.7.4 scikit-learn/0.20.4-foss-2019b-Python-2.7.16 SciPy-bundle/2019.10-foss-2019b-Python-3.7.4 SciPy-bundle/2019.10-foss-2019b-Python-2.7.16 Scrappie/1.4.1-foss-2019b-Python-2.7.16 Scrublet/0.2.1-foss-2019b-Python-3.7.4 scVelo/0.1.25-foss-2019b-Python-3.7.4 scVelo/0.1.24-foss-2019b-Python-3.7.4 Seaborn/0.10.0-foss-2019b-Python-3.7.4 Seaborn/0.9.1-foss-2019b-Python-2.7.16 SEPP/4.3.10-foss-2019b-Python-3.7.4 Seurat/3.2.0-foss-2019b-R-3.6.2 Seurat/3.1.5-foss-2019b-R-3.6.2 sf/0.9-0-foss-2019b-R-3.6.2 sf/0.8-1-foss-2019b-R-3.6.2 SHAP/0.35.0-foss-2019b-Python-3.7.4 Shapely/1.7.0-foss-2019b-Python-3.7.4 shovill/1.1.0-foss-2019b-Python-3.7.4 Signac/0.2.5-foss-2019b-R-3.6.2 Signac/1.0.0-foss-2019b-R-3.6.2 SigProfilerMatrixGenerator/1.1.7-foss-2019b-Python-3.7.4 SigProfilerMatrixGeneratorR/1.1-foss-2019b-R-3.6.2-Python-3.7.4 SimpleITK/1.2.4-foss-2019b-Python-3.7.4 singlecellmethods/6f3a00d-foss-2019b-R-3.6.2 SingleR/1.0.6-foss-2019b-R-3.6.2 SKESA/2.4.0-foss-2019b sklearn-crfsuite/0.3.6-foss-2019b-Python-3.7.4 snippy/4.6.0-foss-2019b-Perl-5.30.0 SoupX/1.4.8-foss-2019b-R-3.6.2 spant/1.4.0-foss-2019b-R-3.6.2 Spark/2.4.1-foss-2019b-Python-3.7.4-Java-1.8 spatialreg/1.1-5-foss-2019b-R-3.6.2 SquiggleKit/4a8abb5-foss-2019b-Python-2.7.16 statsmodels/0.11.0-foss-2019b-Python-3.7.4 statsmodels/0.10.2-foss-2019b-Python-2.7.16 SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0 SunPy/1.1.3-foss-2019b-Python-3.7.4 Taxonstand/2.2-foss-2019b-R-3.6.2 TC-Python/2020a-foss-2019b-Python-3.7.4 TensorFlow/2.2.0-foss-2019b-Python-3.7.4 TensorFlow/2.0.0-foss-2019b-Python-3.7.4 TensorFlow/1.15.0-foss-2019b-Python-3.7.4 tensorflow-probability/0.10.1-foss-2019b-Python-3.7.4-TensorFlow-2.2.0 tensorflow_probability/0.8.0-foss-2019b-Python-3.7.4 texlive/20200406-foss-2019b Theano/1.0.4-foss-2019b-Python-3.7.4 Thermo-Calc/2020a-foss-2019b tifffile/2019.7.26.2-foss-2019b-Python-3.7.4 TIGRAMITE/4.2.0.3-foss-2019b-Python-3.7.4 tombo/1.5.1-foss-2019b-Python-3.7.4 tombo/7473afe-foss-2019b-Python-3.7.4-cowplot torchvision/0.4.2-foss-2019b-Python-3.7.4 TransDecoder/5.5.0-foss-2019b-Perl-5.30.0 trend/1.1.4-foss-2019b-R-3.6.2 Trilinos/12.12.1-foss-2019b-Python-3.7.4 trimesh/3.9.1-foss-2019b-Python-3.7.4 Trinity/2.9.1-foss-2019b-Python-2.7.16 Trinity/2.9.1-foss-2019b-Python-3.7.4 TwoSampleMR/0.5.5-foss-2019b-R-3.6.2 ukbtools/0.11.3-foss-2019b-R-3.6.2 uncertainties/3.1.2-foss-2019b UTMOST/88e9d1d-foss-2019b-Python-2.7.16-R-3.6.2 V8/3.2.0-foss-2019b-R-3.6.2 Valgrind/3.16.0-foss-2019b variant_tools/3.1.3-foss-2019b-Python-3.7.4 vcf2maf/1.6.18-foss-2019b-Perl-5.30.0 veclib/77ad285-foss-2019b Velvet/1.2.10-foss-2019b-mt-kmer_191 VEP/99.2-foss-2019b-Perl-5.30.0 VGAM/1.1-3-foss-2019b-R-3.6.2 Voro++/0.4.6-foss-2019b VOTCA/1.5.1-foss-2019b vt/2187ff6-foss-2019b VTK/8.2.0-foss-2019b-Python-3.7.4 WPS/4.1-foss-2019b-dmpar WRF/4.1.3-foss-2019b-dmpar xarray/0.15.1-foss-2019b-Python-3.7.4 xESMF/0.3.0-foss-2019b-Python-3.7.4 xgboost/1.0.0.2-foss-2019b-R-3.6.2 yaff/1.6.0-foss-2019b-Python-3.7.4

Other Versions

These versions of foss are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 18th November 2019