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definitions:
# -------------------------------------------------------------------------
# Core packages
# -------------------------------------------------------------------------
- core_codes:
- bzip2
- cmake +ncurses
- emacs
- fastqc
- fio
- git
- git-lfs
- gmp
- gnuplot
- gzip
- intel-oneapi-advisor
- intel-oneapi-inspector
- intel-oneapi-vtune
- libarchive
- libgd
- libjpeg-turbo
- libpng
- libtiff
- libxml2
- likwid
- lmod
- mpfr
- neovim
#- ninja
- papi
- parallel
- picard
- rclone
- sbt
- squashfs
- squashfs-mount
- sratoolkit
- subversion
- tar
- tcl
- tk
- tmux
- trimmomatic
- xclip
- zlib-ng
# -------------------------------------------------------------------------
# Serial codes
# -------------------------------------------------------------------------
- serial_codes:
- fftw +openmp ~~mpi
- fftw ~~openmp ~~mpi
- gsl
- hdf5@1.14.3 ~~mpi
- htslib
- kokkos
- kokkos-kernels
- metis
- netcdf-c ~~mpi
- netcdf-fortran ^netcdf-c ~~mpi
- nfft ^fftw~~mpi~~openmp
- scotch ~~mpi
- gcc_serial_codes:
- bwa
- eigen
- ffmpeg
- glpk+gmp
- hwloc
- intel-oneapi-mkl
- intel-oneapi-tbb
- jasper
- kallisto ^hdf5 ~~mpi
- libxc
- mafft
- muscle
- ncview ^netcdf-c ~~mpi ~parallel-netcdf
- python
- qperf
- sox
- stacks
- star
- subread
- unblur ^fftw~~mpi ~~openmp
- voropp
- xgboost
- oneapi_serial_codes:
- abaqus@2023
- intel-oneapi-ipp
# -------------------------------------------------------------------------
# Blas dependent codes
# -------------------------------------------------------------------------
- blas_codes:
- arpack-ng ~~mpi
- superlu
- suite-sparse
- gcc_blas_codes:
- armadillo +hdf5 ^arpack-ng ~~mpi ^hdf5 ~~mpi
- octave
# -------------------------------------------------------------------------
# Python packages
# -------------------------------------------------------------------------
- python_codes:
- bedtools2
- bowtie2
- cairo
- mercurial
- prinseq-lite
- py-absl-py
- py-astunparse
- py-backports-entry-points-selectable
- py-certifi
- py-charset-normalizer
- py-cycler
- py-cython
- py-distlib
- py-filelock
- py-gast
- py-google-pasta
- py-idna
- py-kiwisolver
- py-mpmath
- py-packaging
- py-pillow
- py-pip
- py-platformdirs
- py-ply
- py-protobuf
- py-pybind11
- py-pyparsing
- py-python-dateutil
- py-pytz
- py-requests
- py-semver
- py-six
- py-sympy
- py-termcolor
- py-urllib3
- py-virtualenv
- py-wheel
- py-wrapt
- samtools
- scons
- snakemake
- python_blas_codes:
- boost ~~mpi
#- gmsh ~~mpi +hdf5 +cgns +eigen ~opencascade +openmp ~fltk ~med
- iq-tree
- py-biopython
- py-keras-preprocessing
- py-macs3
- py-matplotlib
- py-numpy
- py-opt-einsum
- py-pandas
- py-pybigwig
- py-xarray
- valgrind ~~mpi
- gcc_python_codes:
- blast-plus
- cistem ^fftw ~~mpi
- ctffind ^fftw ~~mpi
- gatk
- hisat2
- imagemagick +ghostscript
- julia+openlibm
- mesa
- mummer
- node-js
- rust
- spades
- gcc_python_blas_codes:
- caffe +python ^hdf5 ~mpi
- gdb +tui +source-highlight +xz
- openbabel ++python ^boost ~~mpi
- polymake ^cddlib@0.94h
- py-cryolobm
- py-deeptools
- py-h5py ~~mpi
- py-pymol ^hdf5~mpi
- py-scikit-learn
- py-scipy
#- py-statsmodels
- py-theano
- r
# -------------------------------------------------------------------------
# Parallel codes
# -------------------------------------------------------------------------
- mpi_codes:
- fftw ++mpi +openmp
- hdf5@1.14.3 ++mpi
- hpcg
- osu-micro-benchmarks +graphing
- parmetis
- openfoam-org +metis
- phylobayesmpi
- wrf ~pnetcdf build_type=dm+sm
- nvhpc_mpi_codes:
- boost ++mpi
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- mpi_python_codes:
- py-mpi4py
- mpi_blas_codes:
- arpack-ng ++mpi
- hypre@2.31.0
- mumps@5.6.2
- superlu-dist@8.2.1
#- quantum-espresso ++mpi +scalapack +gipaw
- quantum-espresso
- gcc_mpi_blas_codes:
- armadillo +hdf5 ^arpack-ng ++mpi ^hdf5 ++mpi
- gmsh ++mpi +eigen +openmp +hdf5 ~fltk ~opencascade ~med ^mmg ~vtk
- cpmd ~openmp
- elmerfem +mumps +openmp +hypre
- hpl
- netlib-scalapack
- relion ~mklfft
- trilinos
- vtk
- yambo ++mpi io=iotk,etsf-io
- mpi_blas_python_codes:
- petsc
- slepc
- sirius
- gcc_mpi_blas_python_codes:
- adios2
- cp2k ++mpi +plumed +openmp smm=blas
- fenics-dolfinx
- gromacs ++mpi +plumed
- paraview@5.12.0 +shared +python +hdf5 +opengl2 ++mpi
- plumed
- py-fenics-dolfinx
- py-h5py ++mpi
- py-keras
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- py-tensorflow
- py-torch
- py-torchvision
- topaz
# -------------------------------------------------------------------------
# External packages
# -------------------------------------------------------------------------
- external_packages: []
- when: env['environment_type'] != 'cloud'
external_packages:
- ansys
- cfdplusplus
- comsol
- fdtd
- gurobi
- gaussian
- matlab
- maple
- mathematica
- molpro
- smr
- when: env['environment_type'] != 'cloud'
blas_mpi_codes:
- vasp +hdf5 +scalapack +shmem +wannier90