# This is a Spack Environment file.
#
# It describes a set of packages to be installed, along with
# configuration settings.
#
#
# {{ info_message }}
#

spack:
  include:
  - /dcsrsoft/spack/meleze/v2.1/etc/spack/compilers.yaml
  - /dcsrsoft/spack/meleze/v2.1/etc/spack/packages.yaml

  config:
    module_roots:
      lmod: /dcsrsoft/spack/meleze/v2.1/share/spack/lmod/{{ envname }}
      tcl: /dcsrsoft/spack/meleze/v2.1/share/spack/modules/{{ envname }}
  definitions:

  - mygcc: [ gcc@8.3.0 +nvptx]
  - mybasegcc: [ gcc@4.8.5 ]
  - mygccmpi: [ {{ gccmpi }} ]
  - mygccblas: [openblas@0.3.9]
  - myintel: [ intel@19.1.0.166 ]
  - mymkl: [ intel-mkl@2020.0.166 ]
  - myintelmpi: [ intel-mpi@2019.6.166 ]
  - mypython3: [ python@3.7.7 ]
  - mypython2: [ python@2.7.16 ]
  - mygccr:   [ r@3.6.3+external-lapack ^cmake@3.16.2 ^openjdk@11.0.2 ^openblas threads=openmp ]
  - myintelr: [ r@3.6.3+external-lapack ^intel-mkl ^freetype@2.7.1 ^harfbuzz@2.1.3 ^cairo~X ^cmake@3.16.2 ^fontconfig@2.12.1 ]  

  - rootpackages:
    - cellranger@3.1.0
    - cmake@3.16.2
    - cuda@10.2.89
    - git@2.27.0
    - guppy@3.6.0
    - guppy-gpu@3.6.0
    - gurobi@9.0.2
    - intel-parallel-studio~mkl~mpi~tbb~daal+vtune+advisor+inspector+itac@cluster.2020.1
    - matlab-runtime@2019a
    - sas@9.4
    - singularity@3.5.2
    - stata-se@16
  - basepackages:
    - angsd@20191105
    - bcftools@1.10.2 ^cmake@3.16.2
    - bcl2fastq2@2.20.0.422 ^cmake@3.16.2
    - bedtools2@2.27.1
    - blast-plus@2.9.0 ^cmake@3.16.2
    - bowtie2@2.3.5.1 ^cmake@3.16.2
    - bwa@0.7.17
    - cmake@3.16.2
    - eigen@3.3.7 ^cmake@3.16.2
    - freebayes@1.3.2 ^cmake@3.16.2
    - gatk@4.1.5.0 ^cmake@3.16.2
    - gdal@3.0.4 ^cmake@3.16.2
    - gdb@9.1
    - gmsh@4.4.1~mpi+openmp+hdf5^hdf5~mpi^cmake@3.16.2
    - gsl@2.5
    - fastqc@0.11.7
    - fftw@3.3.8~mpi
    - hal@2.1
    - htslib@1.10.2
    - iq-tree@2.0.4+lsd2 ^cmake@3.16.2
    - kallisto@0.46.2 ^hdf5~mpi ^cmake@3.16.2
    - mafft@7.453
    - maven@3.6.3
    - miniconda3@4.7.12.1
    - mummer@3.23 ^cmake@3.16.2
    - muscle@3.8.1551
    - parallel@20190222
    - picard@2.20.8
    - prinseq-lite@0.20.4^cairo+png+pdf
    - python@2.7.16
    - python@3.7.7
    - samtools@1.10
    - shapeit4@4.1.3
    - slim@3.3.2 ^cmake@3.16.2
    - spades@3.13.0 ^cmake@3.16.2
    - snakemake@3.11.2
    - sratoolkit@2.10.7
    - stacks@2.3b
    - stream@5.10
    - stream@5.10+openmp
    - julia@1.3.1
  - blaspackages:
    - octave@5.2.0
  - gccblasmpi:
    - openblas@0.3.9
    - $mygccmpi
  - pypackages:
    - py-cutadapt@2.5
    - py-biopython@1.73
    - py-cycler@0.10.0
    - py-kiwisolver@1.1.0
    - py-matplotlib@3.2.1 ^cmake@3.16.2
    - py-networkx@2.4
    - py-numpy@1.18.4
    - py-pandas@1.0.4
    - py-pip@19.3
    - py-pyparsing@2.4.2
    - py-sonlib@20200401
    - py-statsmodels@0.10.1 ^cmake@3.16.2
    - py-virtualenv@16.7.6
    - ragout@2.3
    - whatshap@1.0
  - pyblaspackages:
    - py-scipy@1.5.2 ^cmake@3.16.2
  - rpackages:
    - r-devtools@2.1.0
  - mpipackages:
    - amg@1.2
    - openfoam@1912  ^cmake@3.16.2
    - openfoam-org@7+metis  ^cmake@3.16.2
    - fftw@3.3.8
    - gromacs@2020.2 ^cmake@3.16.2
    - iq-tree@2.0.4+lsd2+mpi ^cmake@3.16.2
    - kripke@1.2.4 ^cmake@3.16.2
    - laghos@3.0 ^cmake@3.16.2
    - lulesh@2.0.3
    - macsio@1.1 ^cmake@3.16.2
    - osu-micro-benchmarks@5.6.2
    - phylobayesmpi@1.8b
    - py-mpi4py@3.0.3
  - mpiblaspackages:
    - gmsh@4.4.1+openmp+hdf5^cmake@3.16.2
    - mumps@5.2.0
    - elmerfem@ice20200517+mumps+scatt2d+openmp+mpi ^cmake@3.16.2
    - hpl@2.3

  - intelonlypypackages:
    - py-matplotlib@3.2.1 ^freetype@2.7.1 ^cmake@3.16.2

#---------------------------------------------------------------------------------------

  specs:
  
  # BASE

  - matrix:
    - [$rootpackages]
    - [$%mybasegcc]
  # GCC Stack

  # GCC for the environment
  - matrix:
    - [$mygcc]
    - [$%mybasegcc]
  # BLAS and MPI for GCC
  - matrix:
    - [$gccblasmpi]
    - [$%mygcc]
  # Packages that don't use MPI
  - matrix:
    - [$basepackages]
    - [$%mygcc]
  # MPI Packages
  - matrix:
    - [$mpipackages]
    - [$^mygccmpi]
    - [$%mygcc]
  # Packages that depend on OpenBLAS
  - matrix:
    - [$blaspackages]
    - [$^mygccblas]
    - [$%mygcc]
  # MPI + BLAS packages
  - matrix:
    - [$mpiblaspackages]
    - [$^mygccmpi]
    - [$^mygccblas]
    - [$%mygcc]
  # Python packages
  - matrix:
    - [$pypackages]
    - [$^mypython3]
    - [$%mygcc]
  - matrix:
    - [$pyblaspackages]
    - [$^mygccblas]
    - [$^mypython3]
    - [$%mygcc]
  # R packages
  - matrix:
    - [$mygccr]
    - [$%mygcc]
  - matrix:
    - [$rpackages]
    - [$^mygccr]
    - [$%mygcc]
  #
  # Intel Stack
  #

  - matrix:
    - [$myintel]
    - [$%mybasegcc]
  - matrix:
    - [$myintelmpi, $mymkl]
    - [$%myintel]
  - matrix:
    - [$basepackages]
    - [$%myintel]
    exclude:
    - bcftools%intel
    - blast-plus%intel
    - freebayes%intel
    - gatk%intel
    - gdb%intel
    - r%intel
    - julia%intel
    - mummer%intel
    - slim%intel # https://github.unil.ch/ci-dcsr/spack/issues/44
    - spades%intel

  - matrix:
    - [$mpipackages]
    - [$^myintelmpi]
    - [$%myintel]
    exclude:
    - gromacs%intel
    - openfoam%intel
    - openfoam-org%intel

  - matrix:
    - [$mpiblaspackages]
    - [$^myintelmpi]
    - [$^mymkl]
    - [$%myintel]
  - matrix:
    - [$pypackages]
    - [$^mypython3]
    - [$%myintel]
    exclude:
    - py-matplotlib%intel
    - whatshap%intel

  # R packages
  - matrix:
    - [$myintelr]
    - [$%myintel]
  - matrix:
    - [$rpackages]
    - [$^myintelr]
    - [$%myintel]
  - matrix:
    - [$intelonlypypackages]
    - [$^mypython3]
    - [$%myintel]
  modules:
    lmod:
      hash_length: 0
      core_compilers:
      - gcc@4.8.5
      hierarchy:
      - mpi
#      - lapack
      all:
        suffixes:
          +mpi: mpi
          +openmp: openmp
          threads=openmp: openmp
          ^fftw+openmp: openmp
          +cuda: cuda
        environment:
          set:
            ${PACKAGE}_ROOT: ${PREFIX}
          unset: []
        filter:
          environment_blacklist: []
        conflict: []
        load: []
      mpich:
        environment:
          set:
            FI_PSM_TAGGED_RMA: '0'
          unset: []
        filter:
          environment_blacklist: []
        conflict: []
        load: []
      intel-mpi:
        environment:
          set:
            FI_PROVIDER: verbs
            I_MPI_PMI_LIBRARY: /usr/lib64/libpmi.so
          unset: []
        filter:
          environment_blacklist: []
        conflict: []
        load: []
      whitelist:
      - amg
      - angsd
      - bcftools
      - bcl2fastq2
      - bedtools2
      - blast-plus
      - boost@1.72.0
      - bowtie2
      - bwa
      - cellranger
      - cmake
      - cuda
      - gcc@8.3.0
      - eigen
      - elmerfem+scatt2d
      - fastqc
      - fftw
      - freebayes
      - gatk
      - gdal
      - git
      - go
      - gmsh
      - gromacs
      - guppy
      - guppy-gpu
      - gurobi
      - gsl
      - hal
      - hpl
      - htslib
      - intel
      - intel-daal
      - intel-mkl
      - intel-mpi
      - intel-parallel-studio
      - intel-tbb
      - iq-tree
      - julia
      - kallisto
      - kripke
      - laghos
      - lulesh
      - macsio
      - mafft
      - matlab
      - matlab-runtime
      - maven
      - miniconda3
      - mpich
      - mumps
      - muscle
      - netlib-scalapack
      - octave
      - openblas
      - openfoam
      - openfoam-org
      - openjdk
      - osu-micro-benchmarks
      - perl%gcc@8.3.0
      - perl%intel
      - phylobayesmpi
      - picard
      - prinseq-lite
      - python%gcc@8.3.0
      - python%intel
      - py-biopython
      - py-cutadapt
      - py-cycler
      - py-pyfaidx
      - py-kiwisolver
      - py-matplotlib
      - py-mpi4py
      - py-networkx
      - py-pip
      - py-pyparsing
      - py-pysam
      - py-scipy
      - py-sonlib
      - py-statsmodels
      - py-virtualenv
      - py-xopen
      - r^openjdk@11.0.2
      - r-devtools
      - ragout
      - samtools
      - sas
      - shapeit4
      - singularity
      - slim
      - snakemake
      - spades
      - sratoolkit
      - stacks
      - stata-se
      - stream
      - whatshap
      - xz
      - zlib%gcc@8.3.0
      - zlib%intel

      blacklist: ['%gcc@4.8.5', '%gcc@8.3.0', '%intel']
      verbose: false
      blacklist_implicits: true
      projections: {}
      core_specs: []
    enable: []
  view: false