foss 2018b

Deprecated: Use of this version of foss is deprecated. More information on our Applications Support and Retention Policy.

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 2018b

To load the module for foss 2018b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load foss/2018b

BEAR Apps Version

2018b

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 2018b provides

  • GCC 7.3.0
  • OpenMPI 3.1.1
  • OpenBLAS 0.3.1 (patched)
  • 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-2018b GCC/7.3.0-2.30 OpenBLAS/0.3.1-GCC-7.3.0-2.30 OpenMPI/3.1.6-GCC-7.3.0-2.30 ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1

Required By

This version of foss is a direct dependent of: Amber/18-foss-2018b-AmberTools-18-patchlevel-10-8 amplimap/0.4.16-foss-2018b-Python-3.6.6 amplimap/0.4.5-foss-2018b-Python-3.6.6 ariba/2.13.5-foss-2018b-Python-3.6.6 AUGUSTUS/3.3.2-foss-2018b-Python-2.7.15 bamaddrg/3fccbf0-foss-2018b bam-readcount/0.8.0-foss-2018b BamTools/2.5.1-foss-2018b BaseMount/0.15.81.2123-20171219-foss-2018b bc/1.06.95-foss-2018b BCFtools/1.9-foss-2018b BEDTools/2.25.0-foss-2018b Bio-MLST-Check/2.1.1706216-foss-2018b-Perl-5.28.0 BioPerl/1.7.2-foss-2018b-Perl-5.28.0 Biopython/1.72-foss-2018b-Python-3.6.6 Biopython/1.73-foss-2018b-Python-2.7.15 Biopython/1.72-foss-2018b-Python-2.7.15 BLAST+/2.8.1-foss-2018b BOLT-LMM/2.3.2-foss-2018b Boost/1.67.0-foss-2018b Boost.Python/1.67.0-foss-2018b-Python-2.7.15 Boost.Python/1.67.0-foss-2018b-Python-3.6.6 Bowtie/1.2.2-foss-2018b Bowtie2/2.3.4.2-foss-2018b brms/2.8.0-foss-2018b-R-3.5.1 BUSCO/3.0.2-foss-2018b-Python-2.7.15 C50/0.1.2-foss-2018b-R-3.5.1 CALMET/6.5.0_L150223-foss-2018b CALPOST/7.1.0_L141010-foss-2018b CALPUFF/7.2.1_L150618-foss-2018b CASTEP/16.1-foss-2018b CD-HIT/4.8.1-foss-2018b cellphonedb/1.1.0-foss-2018b-Python-3.6.6 CGAL/4.11.1-foss-2018b-Python-3.6.6 CGAL/4.8.1-foss-2018b-Python-2.7.15 CGAL/4.11.1-foss-2018b-Python-2.7.15 cget/0.1.7-foss-2018b-Python-3.6.6 chiron/0.4.2-foss-2018b-Python-3.6.6 CIRI-full/2.0-foss-2018b-Perl-5.28.0-Java-1.8 clusterCrit/1.2.8-foss-2018b-R-3.5.1 Cufflinks/2.2.1-foss-2018b dask/0.19.4-foss-2018b-Python-3.6.6 dbscan/1.1-3-foss-2018b-R-3.5.1 dealii/9.0.1-foss-2018b Deepbinner/0.2.0-foss-2018b-Python-3.6.6 DendroPy/4.4.0-foss-2018b-Python-3.6.6 DeNovoGear/387354d-foss-2018b dnaMD/2.1.0-foss-2018b-Python-3.6.6 DNMFilter/0.1.1-foss-2018b-R-3.5.1-Java-1.8 doFuture/0.8.0-foss-2018b-R-3.5.1 do_x3dna/fe91033-foss-2018b EIGENSOFT/6.1.4-foss-2018b EMBOSS/6.6.0-foss-2018b Env-Path/0.19-foss-2018b-Perl-5.28.0 ESMF/7.1.0r-foss-2018b ETE/3.1.1-foss-2018b-Python-3.6.6 fast5_fetcher/1.1.1-foss-2018b-Python-2.7.15 FastTree/2.1.10-foss-2018b FFmpeg/4.0-foss-2018b File-Touch/0.11-foss-2018b-Perl-5.28.0 FLANN/1.8.4-foss-2018b-Python-3.6.6 flappie/1.1.0-foss-2018b flite/2.0.5-foss-2018b FLTK/1.3.4-foss-2018b FreeBayes/1.2.0-foss-2018b freeglut/3.0.0-foss-2018b FSL/6.0.1-foss-2018b fsm-lite/v1.0-stable-foss-2018b FUSE/2.9.9-foss-2018b future/0.16.0-foss-2018b-Python-3.6.6 future/0.16.0-foss-2018b-Python-2.7.15 g2clib/1.6.0-foss-2018b g2lib/3.1.0-foss-2018b GATK/4.1.0.0-foss-2018b-Python-3.6.6 GDAL/2.2.3-foss-2018b-Python-2.7.15 GDAL/2.2.3-foss-2018b-Python-3.6.6 GEMMA/0.98.1-foss-2018b GEOS/3.6.2-foss-2018b-Python-2.7.15 GEOS/3.6.2-foss-2018b-Python-3.6.6 geosphere/1.5-7-foss-2018b-R-3.5.1 gfcanalysis/1.5.0-foss-2018b-R-3.5.1 gffutils/0.9-foss-2018b-Python-2.7.15 ggpubr/0.2-foss-2018b-R-3.5.1 GitPython/2.1.11-foss-2018b-Python-3.6.6 GMAP-GSNAP/2019-02-15-foss-2018b gmsh/4.2.2-foss-2018b-Python-3.6.6 gnuplot/5.2.6-foss-2018b GObject-Introspection/1.54.1-foss-2018b-Python-2.7.15 Graphviz/2.40.1-foss-2018b GROMACS/2018.4-foss-2018b-PLUMED-tMPI GROMACS/2018.4-foss-2018b-PLUMED GROMACS/2018.4-foss-2018b GROMACS/2018.3-foss-2018b GSL/1.16-foss-2018b GTS/0.7.6-foss-2018b gubbins/2.3.4-foss-2018b-Python-3.6.6 GUDHI/2.3.0-foss-2018b-Python-3.6.6 h5py/2.8.0-foss-2018b-Python-2.7.15 h5py/2.8.0-foss-2018b-Python-3.6.6 HAPDeNovo/fe8bcc2-foss-2018b-Python-3.6.6 HarfBuzz/2.2.0-foss-2018b HDF5/1.10.2-foss-2018b HDF5/1.8.21-foss-2018b hdf5storage/0.1.15-foss-2018b-Python-3.6.6 HGT-ID/1.0-foss-2018b-Java-1.8-Perl-5.28.0-R-3.5.1 HMMER/3.2.1-foss-2018b HPL/2.2-foss-2018b HTSeq/0.11.0-foss-2018b-Python-2.7.15 HTSlib/1.9-foss-2018b hypothesis/4.5.0-foss-2018b-Python-3.6.6 Hypre/2.16.0-foss-2018b IEDB_MHC/2.19.1-foss-2018b-Python-2.7.15 IgBlast/1.14.0-foss-2018b IPython/5.7.0-foss-2018b-Python-2.7.15 IPython/6.4.0-foss-2018b-Python-3.6.6 IsoformSwitchAnalyzeR/1.2.0-foss-2018b-R-3.5.1 itsadug/2.3-foss-2018b-R-3.5.1 Jansson/2.12-foss-2018b JARVIS/2018.11.7-foss-2018b-Python-3.6.6 Jellyfish/2.2.10-foss-2018b kallisto/0.45.0-foss-2018b Keras/2.2.4-foss-2018b-Python-3.6.6 LAMMPS/stable_17Nov2016-foss-2018b LAMMPS/stable_12Dec2018-foss-2018b libgeotiff/1.4.2-foss-2018b libGLU/9.0.0-foss-2018b libharu/2.3.0-foss-2018b LiBiNorm/56aa414-foss-2018b libmagic/5.37-foss-2018b libStatGen/457bf9e-foss-2018b lmerTest/3.1-0-foss-2018b-R-3.5.1 lpsolve/5.5.2.5-foss-2018b lwgeom/0.1-6-foss-2018b-R-3.5.1 LWP-Protocol-https/6.07-foss-2018b-Perl-5.28.0 lxml/4.2.5-foss-2018b-Python-3.6.6 lxml/4.2.5-foss-2018b-Python-2.7.15 LZO/2.10-foss-2018b Mako/1.0.7-foss-2018b-Python-2.7.15 MAPIT/d0b348a-foss-2018b-R-3.5.1 mappy/2.15-foss-2018b-Python-3.6.6 MariaDB-connector-c/2.3.7-foss-2018b MaSuRCA/3.3.2b-foss-2018b-Perl-5.28.0 matplotlib/3.0.0-foss-2018b-Python-3.6.6 matplotlib/2.2.3-foss-2018b-Python-2.7.15 matplotlib/3.1.0-foss-2018b-Python-3.6.6 mayavi/4.7.0-foss-2018b-Python-3.6.6 mayavi/4.6.2-foss-2018b-Python-3.6.6 Mesa/18.1.1-foss-2018b MetaboliteDetector/3.2.20180913-foss-2018b-Linux METIS/5.1.0-foss-2018b Minimac4/1.0.0-foss-2018b minimap2/2.13-foss-2018b mkl-dnn/0.16-foss-2018b mlpy/3.5.0-foss-2018b-Python-2.7.15 mne/0.17.2-foss-2018b-Python-3.6.6 MoviePy/1.0.0-foss-2018b-Python-3.6.6 MUMmer/4.0.0beta2-foss-2018b NAG/26-foss-2018b NCL/6.6.2-foss-2018b Neper/3.4.0-foss-2018b netCDF/4.6.1-foss-2018b netCDF-C++4/4.3.0-foss-2018b netCDF-Fortran/4.4.4-foss-2018b nettle/3.4-foss-2018b networkx/2.2-foss-2018b-Python-3.6.6 NiBabel/2.3.0-foss-2018b-Python-3.6.6 Ninja/1.8.2-foss-2018b NSM3/1.12-foss-2018b-R-3.5.1 numexpr/2.6.5-foss-2018b-Python-3.6.6 numexpr/2.6.5-foss-2018b-Python-2.7.15 ont-fast5-api/1.3.0-foss-2018b-Python-3.6.6 Open3D/0.5.0.0-foss-2018b-Python-3.6.6 Open3D/0.5.0.0-foss-2018b-Python-2.7.15 OpenFOAM (OpenCFD Ltd)/v1812-foss-2018b openNLP/0.2-6-foss-2018b-R-3.5.1 OptiType/1.3.2-foss-2018b-Python-2.7.15 OptiType/1.3.2-foss-2018b-Python-3.6.6 Pango/1.42.4-foss-2018b Parallel-ForkManager/2.02-foss-2018b-Perl-5.28.0 parasail/2.4.1-foss-2018b ParaView/5.2.0-foss-2018b-mpi ParaView/5.4.1-foss-2018b-mpi ParMETIS/4.0.3-foss-2018b PCL/1.9.1-foss-2018b-Python-3.6.6 PETSc/3.11.1-foss-2018b PfamScan/20170301-foss-2018b-Perl-5.28.0 PheWAS/0.12.2-2-foss-2018b-R-3.5.1 picopore/1.2.0-foss-2018b-Python-3.6.6 Pillow/5.3.0-foss-2018b-Python-3.6.6 Pillow-SIMD/5.0.0-foss-2018b-Python-3.6.6 pkgconfig/1.3.1-foss-2018b-Python-2.7.15 pkgconfig/1.3.1-foss-2018b-Python-3.6.6 PLUMED/2.4.4-foss-2018b poppler/0.70.1-foss-2018b POV-Ray/3.7.0.7-foss-2018b PROJ/5.0.0-foss-2018b protobuf-python/3.6.0-foss-2018b-Python-3.6.6 psutil/5.4.7-foss-2018b-Python-3.6.6 pybind11/2.2.4-foss-2018b-Python-3.6.6 pyblosc/1.8.1-foss-2018b-Python-3.6.6 pyEMMA/2.5.5-foss-2018b-Python-3.6.6 Pylint/1.9.3-foss-2018b-Python-2.7.15 PyNGL/1.6.1-foss-2018b-Python-3.6.6 PyNIO/1.5.5-foss-2018b-Python-3.6.6 Pyomo/5.5.0-foss-2018b-Python-2.7.15 Pyomo/5.5.0-foss-2018b-Python-3.6.6 PyQt5/5.11.3-foss-2018b-Python-3.6.6 Pysam/0.13-foss-2018b-Python-3.6.6 Pysam/0.15.1-foss-2018b-Python-3.6.6 Pysam/0.15.1-foss-2018b-Python-2.7.15 PyTables/3.4.4-foss-2018b-Python-2.7.15 PyTables/3.4.4-foss-2018b-Python-3.6.6 pytest/4.4.0-foss-2018b-Python-2.7.15 pytest/4.4.0-foss-2018b-Python-3.6.6 Python/2.7.15-foss-2018b Python/3.6.6-foss-2018b PyTorch/0.4.1-foss-2018b-Python-3.6.6 PyTorch/1.1.0-foss-2018b-Python-3.6.6 PyTorch/1.0.1-foss-2018b-Python-3.6.6 PyYAML/3.13-foss-2018b-Python-3.6.6 PyYAML/3.13-foss-2018b-Python-2.7.15 Qt/4.8.7-foss-2018b Qt5/5.12.3-foss-2018b R/3.5.1-foss-2018b R/3.5.1-foss-2018b-Python-2.7.15 randomcoloR/1.1.0-foss-2018b-R-3.5.1 rasterVis/0.45-foss-2018b-R-3.5.1 RAxML/8.2.12-foss-2018b-hybrid-avx2 R-bundle-Bioconductor/3.7-foss-2018b-R-3.5.1 RCIT/0.1.0-foss-2018b-R-3.5.1 regex/2019.06.08-foss-2018b-Python-3.6.6 RELION/3.0_beta.2019.01.28-foss-2018b rgeos/0.4-2-foss-2018b-R-3.5.1 rmweather/0.1.3-foss-2018b-R-3.5.1 rnaQUAST/1.5.1-foss-2018b-Python-2.7.15 rpy2/3.0.5-foss-2018b-Python-3.6.6 RSEM/1.3.1-foss-2018b Salmon/0.12.0-foss-2018b SAMtools/0.1.18-foss-2018b SAMtools/0.1.20-foss-2018b SAMtools/1.9-foss-2018b SciencesPo/1.4.1-foss-2018b-R-3.5.1 scikit-image/0.15.0-foss-2018b-Python-3.6.6 scikit-learn/0.20.0-foss-2018b-Python-3.6.6 scikit-learn/0.20.0-foss-2018b-Python-2.7.15 scikit-multiflow/0.2.0-foss-2018b-Python-3.6.6 scipy/1.2.0-foss-2018b-Python-3.6.6 Scoary/1.6.16-foss-2018b-Python-3.6.6 SCOTCH/6.0.6-foss-2018b Scrappie/1.4.2-foss-2018b SDL2/2.0.9-foss-2018b sdsl-lite/2.0.3-foss-2018b Seaborn/0.9.0-foss-2018b-Python-3.6.6 SeqAn/2.4.0-foss-2018b SimNIBS/2.1.2-foss-2018b sjstats/0.17.4-foss-2018b-R-3.5.1 SLEPc/3.11.0-foss-2018b sleuth/0.30.0-foss-2018b-R-3.5.1 SMALT/0.7.6-foss-2018b-Python-2.7.15 snakemake/5.2.4-foss-2018b-Python-3.6.6 SnowballC/0.6.0-foss-2018b-R-3.5.1 snp-sites/2.4.1-foss-2018b Sphinx/1.8.1-foss-2018b-Python-3.6.6 splancs/2.01-40-foss-2018b-R-3.5.1 SquiggleKit/1.0.0-foss-2018b-Python-2.7.15 srst2/0.2.0-foss-2018b-Python-2.7.15 ssc/2.0.0-foss-2018b-R-3.5.1 statsmodels/0.9.0-foss-2018b-Python-3.6.6 String-Util/1.26-foss-2018b-Perl-5.28.0 SuiteSparse/5.1.2-foss-2018b-METIS-5.1.0 SUPER/1.20141117-foss-2018b-Perl-5.28.0 svMisc/1.1.0-foss-2018b-R-3.5.1 SWIG/3.0.12-foss-2018b-Python-2.7.15 SWIG/3.0.12-foss-2018b-Python-3.6.6 talos/0.4.9-foss-2018b-Python-3.6.6 tb_nightly/1.14.0a20190509-foss-2018b-Python-3.6.6 TDA/1.6.5-foss-2018b-R-3.5.1 TensorFlow/1.10.1-foss-2018b-Python-3.6.6 TensorFlow/1.13.1-foss-2018b-Python-3.6.6 tensorflow-probability/0.6.0-foss-2018b-Python-3.6.6 Test-MockModule/v0.170.0-foss-2018b-Perl-5.28.0 Test-Toolbox/0.4-foss-2018b-Perl-5.28.0 Theano/1.0.4-foss-2018b-Python-3.6.6 Theano/1.0.3-foss-2018b-Python-3.6.6 TIE-GCM/2.0-foss-2018b tigramite/4.0.0-beta-foss-2018b-Python-3.6.6 Tkinter/3.6.6-foss-2018b-Python-3.6.6 Tkinter/2.7.15-foss-2018b-Python-2.7.15 TopHat/2.1.2-foss-2018b torchvision/0.2.2-foss-2018b-Python-3.6.6 TraCeR/0.6.0-foss-2018b-Python-3.6.6 transIndel/7098bd6-foss-2018b-Python-2.7.15 transIndel/7098bd6-foss-2018b-Python-2.7.15-ScanNeo TRAPeS/e65bb7b-foss-2018b-Python-2.7.15 Trinity/2.8.4-foss-2018b Triodenovo/0.06-foss-2018b truncnorm/1.0-8-foss-2018b-R-3.5.1 UDUNITS/2.2.26-foss-2018b uMatIC/081204-foss-2018b v8/3.14.5.8-foss-2018b VCFtools/0.1.16-foss-2018b-Perl-5.28.0 Velvet/1.2.10-foss-2018b-mt-kmer_191 ViennaRNA/2.4.11-foss-2018b-Python-3.6.6 VMD/1.9.4a12-foss-2018b-Python-2.7.15 VTK/8.1.1-foss-2018b-Python-2.7.15 VTK/8.1.1-foss-2018b-Python-3.6.6 WhatsHap/0.18-foss-2018b-Python-3.6.6 wheel/0.31.1-foss-2018b-Python-3.6.6 x3dna/2.4-foss-2018b xarray/0.12.1-foss-2018b-Python-3.6.6 YARA/3.10.0-foss-2018b ZeroMQ/4.2.5-foss-2018b

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 3rd June 2019