Homec4science
Diffusion dcsr-spack-site (master) Browse

dcsr-spack-site/spack.yaml.j2
65202a41e414master

Last Change
Raw File

spack.yaml.j2
View Options

# 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
c4science · Help