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.travis.yml
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# https://travis-ci.org/ParBLiSS/kmerind
language: cpp
dist: trusty
sudo: false
#compiler:
# - gcc
# - clang
#different compilers
#env:
# - envCXX=g++-4.8 envCC=gcc-4.8
# - envCXX=g++-4.9 envCC=gcc-4.9
# - envCXX=g++-5 envCC=gcc-5
# - envCXX=clang++-3.5 envCC=clang-3.5
# - envCXX=clang++-3.6 envCC=clang-3.6
# - envCXX=clang++-3.7 envCC=clang-3.7
#addons:
# apt:
# sources:
# - ubuntu-toolchain-r-test
# packages:
# - openmpi
# - llvm-toolchain-trusty-3.5
# - llvm-toolchain-trusty-3.6
# - llvm-toolchain-trusty-3.7
# include specific compiler combinations combinations
matrix:
include:
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-4.8
- g++-4.8
env: envCXX=g++-4.8 envCC=gcc-4.8 envMPI=openmpi18 CACHE_NAME=gcc48openmpi18
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-4.9
- g++-4.9
env: envCXX=g++-4.9 envCC=gcc-4.9 envMPI=openmpi18 CACHE_NAME=gcc49openmpi18
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-5
- g++-5
env: envCXX=g++-5 envCC=gcc-5 envMPI=openmpi18 CACHE_NAME=gcc5openmpi18
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-6
- g++-6
env: envCXX=g++-6 envCC=gcc-6 envMPI=openmpi18 CACHE_NAME=gcc6openmpi18
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-3.5
packages:
- clang-3.5
env: envCXX=clang++-3.5 envCC=clang-3.5 envMPI=openmpi18 CACHE_NAME=clang35openmpi18
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-3.6
packages:
- clang-3.6
env: envCXX=clang++-3.6 envCC=clang-3.6 envMPI=openmpi18 CACHE_NAME=clang36openmpi18
# - compiler: clang
# addons:
# apt:
# sources:
# - ubuntu-toolchain-r-test
# - llvm-toolchain-trusty-3.7 # not whitelisted.
# packages:
# - clang-3.7
# env: envCXX=clang++-3.7 envCC=clang-3.7 envMPI=openmpi18 CACHE_NAME=clang37openmpi18
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-3.8
packages:
- clang-3.8
env: envCXX=clang++-3.8 envCC=clang-3.8 envMPI=openmpi18 CACHE_NAME=clang38openmpi18
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-3.9
packages:
- clang-3.9
env: envCXX=clang++-3.9 envCC=clang-3.9 envMPI=openmpi18 CACHE_NAME=clang39openmpi18
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-4.0
packages:
- clang-4.0
env: envCXX=clang++-4.0 envCC=clang-4.0 envMPI=openmpi18 CACHE_NAME=clang40openmpi18
# - compiler: clang
# addons:
# apt:
# sources:
# - ubuntu-toolchain-r-test
# - llvm-toolchain-trusty
# packages:
# - clang-5.0
# env: envCXX=clang++-5.0 envCC=clang-5.0 envMPI=openmpi18 CACHE_NAME=clang50openmpi18
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-4.8
- g++-4.8
env: envCXX=g++-4.8 envCC=gcc-4.8 envMPI=mpich2 CACHE_NAME=gcc48mpich2
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-4.9
- g++-4.9
env: envCXX=g++-4.9 envCC=gcc-4.9 envMPI=mpich2 CACHE_NAME=gcc49mpich2
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-5
- g++-5
env: envCXX=g++-5 envCC=gcc-5 envMPI=mpich2 CACHE_NAME=gcc5mpich2
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-6
- g++-6
env: envCXX=g++-6 envCC=gcc-6 envMPI=mpich2 CACHE_NAME=gcc6mpich2
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-3.5
packages:
- clang-3.5
env: envCXX=clang++-3.5 envCC=clang-3.5 envMPI=mpich2 CACHE_NAME=clang35mpich2
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-3.6
packages:
- clang-3.6
env: envCXX=clang++-3.6 envCC=clang-3.6 envMPI=mpich2 CACHE_NAME=clang36mpich2
# - compiler: clang
# addons:
# apt:
# sources:
# - ubuntu-toolchain-r-test
# - llvm-toolchain-trusty-3.7 # not whitelisted
# packages:
# - clang-3.7
# env: envCXX=clang++-3.7 envCC=clang-3.7 envMPI=mpich2 CACHE_NAME=clang37mpich2
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-3.8
packages:
- clang-3.8
env: envCXX=clang++-3.8 envCC=clang-3.8 envMPI=mpich2 CACHE_NAME=clang38mpich2
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-3.9
packages:
- clang-3.9
env: envCXX=clang++-3.9 envCC=clang-3.9 envMPI=mpich2 CACHE_NAME=clang39mpich2
- compiler: clang
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-trusty-4.0
packages:
- clang-4.0
env: envCXX=clang++-4.0 envCC=clang-4.0 envMPI=mpich2 CACHE_NAME=clang40mpich2
# - compiler: clang
# addons:
# apt:
# sources:
# - ubuntu-toolchain-r-test
# - llvm-toolchain-trusty
# packages:
# - clang-5.0
# env: envCXX=clang++-5.0 envCC=clang-5.0 envMPI=mpich2 CACHE_NAME=clang50mpich2
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-4.8
- g++-4.8
env: envCXX=g++-4.8 envCC=gcc-4.8 envMPI=mpich3 CACHE_NAME=gcc48mpich3
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-4.9
- g++-4.9
env: envCXX=g++-4.9 envCC=gcc-4.9 envMPI=mpich3 CACHE_NAME=gcc49mpich3
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-5
- g++-5
env: envCXX=g++-5 envCC=gcc-5 envMPI=mpich3 CACHE_NAME=gcc5mpich3
- compiler: gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
packages:
- gcc-6
- g++-6
env: envCXX=g++-6 envCC=gcc-6 envMPI=mpich3 CACHE_NAME=gcc6mpich3
before_install:
- pip install --user codecov
#addons:
# apt:
# sources:
# - ubuntu-toolchain-r-test
# - llvm-toolchain-trusty-3.5
# - llvm-toolchain-trusty-3.6
# - llvm-toolchain-trusty-3.7
# packages:
# - gcc-4.8
# - g++-4.8
# - gcc-4.9
# - g++-4.9
# - gcc-5
# - g++-5
# - clang-3.5
# - clang-3.6
# - clang-3.7
# caching of the whole `local` directory. Can't cache only the one for this
# `env`, because otherwise the different instances will overwrite the cache.
# For the first test-run, the build has to be run sequentially (limit parallel
# workers to 1) so that the cache can be correctly initialized. Once the cache
# is build, parallel workers can be re-enabled.
cache:
directories:
- $HOME/local
timeout: 600
before_script:
# check if gcc or clang
- if [ "$CXX" = "clang++" ]; then export COMPILER="clang"; else export COMPILER="gnu"; fi
# install MPI - only 1 configuration for each compiler does this
- export CXX="$envCXX" CC="$envCC" OMPI_CC="$envCC" OMPI_CXX="$envCXX" MPI="$envMPI"
# install MPI
- mkdir -p $HOME/local
- sh ./conf/travis-install-mpi.sh $MPI
- ls -r $HOME/local
# set up MPI location
- export PATH=$PATH:$HOME/local/$MPI/bin
- export LIBRARY_PATH=$LIBRARY_PATH:$HOME/local/$MPI/lib
- export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/$MPI/lib
# print out version information
- $CXX --version
- mpiexec --version
- export SRC_DIR=`pwd`
# compile sparsehash
#- cd ext/sparsehash
#- ./configure CXXFLAGS=-std=c++11
#- make
#- cd $SRC_DIR
# prepare build kmerind
- mkdir -p $HOME/build
- cd $HOME/build
script:
# first pass cmake
- if [ "$COMPILER" = "clang" ]; then cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_TESTING=ON -DLOG_ENGINE=PRINTF -DUSE_MPI=ON -DUSE_OPENMP=OFF -DUSE_SIMD_IF_AVAILABLE=ON -DENABLE_BENCHMARKING=OFF $SRC_DIR;
else cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_TESTING=ON -DLOG_ENGINE=PRINTF -DUSE_MPI=ON -DUSE_OPENMP=ON -DUSE_SIMD_IF_AVAILABLE=ON -DENABLE_BENCHMARKING=OFF $SRC_DIR; fi
# do it again else the gtests will not be built
- if [ "$COMPILER" = "clang" ]; then cmake -DBUILD_TEST_APPLICATIONS=ON -DENABLE_COVERAGE=OFF $SRC_DIR;
else cmake -DBUILD_TEST_APPLICATIONS=ON -DENABLE_COVERAGE=ON $SRC_DIR; fi
# build kmerind. here so that if build fails, the tests are not run.
- make -j 2
# run tests.
- ./test/test-mpi-bliss-io-distribute
- ctest -E benchmark
- ./bin/testFASTA_load
- mpiexec -np 4 ./bin/testFASTA_load
- ./bin/testFASTQ_load
- mpiexec -np 4 ./bin/testFASTQ_load
- ./bin/testKmerIndex-fasta
- mpiexec -np 4 ./bin/testKmerIndex-fasta
- ./bin/testKmerIndex-fastq
- mpiexec -np 4 ./bin/testKmerIndex-fastq
- ./bin/test_de_bruijn_graph_construction
- mpiexec -np 4 ./bin/test_de_bruijn_graph_construction
after_success:
# only collect coverage if compiled with gcc
#- if [ "$CXX" = "g++-4.8" ]; then codecov --comp ${SRC_DIR}/config/comp.txt --gcov-exec gcov-4.8; fi
#- if [ "$CXX" = "g++-4.9" ]; then codecov --comp ${SRC_DIR}/config/comp.txt --gcov-exec gcov-4.9; fi
- if [ "$CXX" = "g++-5" ]; then codecov --gcov-exec gcov-5; fi