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.gitlab-ci.yml
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workflow:
rules:
- if: $CI_COMMIT_BRANCH =~ /-WIP$/
when: never
- when: always
variables:
GIT_STRATEGY: fetch
REGISTRY: registry.gitlab.com
APPLICATION: mhm2
TEST_IMAGE: $REGISTRY/$REGISTRY_USER/$APPLICATION:latest
RELEASE_IMAGE: $REGISTRY/$REGISTRY_USER/$APPLICATION:$CI_BUILD_REF_NAME
HULK_UPCXX_VER: 2021.3.0
stages:
- build
- validation
- accuracy
#
# cori
#
Cori:build:
stage: build
tags:
- Cori
script:
- set -e
- set -x
- git submodule init
- git submodule sync
- git submodule update
- uname -a
- pwd
- date
- echo "Establishing variables"
- export MHM2_SOURCE=$(pwd)
- export BASE=${SCRATCH}/tmp/gitlab-runner-scratch-Cori-mhm2-${USER}
- export SCRATCH=${BASE}/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export INSTALL_PREFIX=${SCRATCH}/install
- export BUILD_PREFIX=${SCRATCH}/build
- export RUN_PREFIX=${SCRATCH}/runs
- echo "BASE=${BASE} SCRATCH=${SCRATCH}"
- mkdir -p ${BASE}
- rm -rf ${SCRATCH}
- echo "Cleaning out old installs"
- find ${BASE} -maxdepth 1 -name 'mhm*' -mtime +4 -type d -exec rm -rf '{}' ';' || /bin/true
- mkdir -p ${SCRATCH} ${RUN_PREFIX}
- exec > >(tee -ia ${SCRATCH}/build.log)
- exec 2> >(tee -ia ${SCRATCH}/build.err >&2)
- echo "Logging to ${SCRATCH}/build.log and .err at $(date) on $(uname -n) in $(pwd)"
- lmstat -a -c $INTEL_LICENSE_FILE || /bin/true
- echo "Loading Haswell modules for upcxx GNU"
- source ${MHM2_SOURCE}/contrib/environments/cori-haswell/gnu.sh
- module list
- export MHM2_BUILD=${BUILD_PREFIX}-haswell-dbg
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building Haswell GNU Debug"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-haswell -DCMAKE_BUILD_TYPE=Debug ${MHM2_SOURCE}
- make -j 12 all check install
- export MHM2_BUILD=${BUILD_PREFIX}-haswell
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building Haswell GNU Release"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-haswell -DCMAKE_BUILD_TYPE=Release ${MHM2_SOURCE}
- make -j 12 all check install
- echo "Loading KNL modules for upcxx on cori GNU"
- source ${MHM2_SOURCE}/contrib/environments/cori-knl/gnu.sh
- module list
- export MHM2_BUILD=${BUILD_PREFIX}-knl-dbg
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building KNL GNU Debug"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-knl-dbg -DCMAKE_BUILD_TYPE=Debug ${MHM2_SOURCE}
- make -j 12 all install # cannot check knl build on haswell
- export MHM2_BUILD=${BUILD_PREFIX}-knl-rwdi
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building KNL GNU RelWithDebInfo"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-knl-rwdi -DCMAKE_BUILD_TYPE=RelWithDebInfo ${MHM2_SOURCE}
- make -j 12 all install # cannot check knl build on haswell
- export MHM2_BUILD=${BUILD_PREFIX}-knl
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building KNL GNU Release"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-knl -DCMAKE_BUILD_TYPE=Release ${MHM2_SOURCE}
- make -j 12 all install # cannot check knl build on haswell
- echo "Done building"
Cori:validation:
stage: validation
tags:
- Cori
script:
- set -e
- set -x
- uname -a
- pwd
- date
- export GASNET_BACKTRACE=1
- echo "Establishing variables"
- export MHM2_SOURCE=$(pwd)
- export BASE=${SCRATCH}/tmp/gitlab-runner-scratch-Cori-mhm2-${USER}
- export SCRATCH=${BASE}/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export INSTALL_PREFIX=${SCRATCH}/install
- export BUILD_PREFIX=${SCRATCH}/build
- export RUN_PREFIX=${SCRATCH}/runs
- echo "BASE=${BASE} SCRATCH=${SCRATCH}"
- echo "Loading KNL modules for upcxx on cori"
- source ${MHM2_SOURCE}/contrib/environments/cori-knl/gnu.sh
- module list
- cd $SCRATCH
- exec > >(tee -ia ${SCRATCH}/validation.log)
- exec 2> >(tee -ia ${SCRATCH}/validation.err >&2)
- echo "Logging to ${SCRATCH}/validation.log and .err at $(date) on $(uname -n) in $(pwd)"
- FAILED=""
- inst=${INSTALL_PREFIX}-knl
- echo "Testing builds on KNL - $inst"
- export RWDI=${INSTALL_PREFIX}-knl-rwdi/bin/
- export DBG=${INSTALL_PREFIX}-knl-dbg/bin/
- export REL=${INSTALL_PREFIX}-knl/bin/
- export ARCTIC=/global/cscratch1/sd/regan/GitlabCIData/
- export OPTS="-r ${ARCTIC}/arctic_sample_0.fq -v --checkpoint=yes"
- export GASNET_BACKTRACE=1
- echo "Submitting job on 3 nodes - on 2 nodes roughly RWDI=400s, DBG --kmer-lens 63 =456s ...REL=170s"
- knl_job=$(sbatch --parsable --job-name="CImhv-${CI_COMMIT_SHORT_SHA}" --account=mp215 -C knl --nodes=3 --qos=debug --time=30:00 --wrap="${RWDI}/mhm2.py $OPTS -o ${RUN_PREFIX}/rwdi && ${DBG}/mhm2.py ${OPTS} --kmer-lens 63 -o ${RUN_PREFIX}/dbg && echo Good")
- echo "KNL JOB ${knl_job}"
- echo "Submitting build on cori gpu"
- mkdir -p ${SCRATCH}/src
- rsync -a --exclude '.git*' ${MHM2_SOURCE}/ ${SCRATCH}/src/
- gpu_job=$(module load cgpu; sbatch --parsable -C gpu -t 30 -c 5 -G 1 -A m342 --wrap="source ${SCRATCH}/src/contrib/environments/cori-gpu/gnu.sh ; mkdir -p build-cori-gpu && cd build-cori-gpu && cmake \$MHM2_CMAKE_EXTRAS -DCMAKE_INSTALL_PREFIX=install ${SCRATCH}/src && make VERBOSE=1 -j 10 all install && srun install/bin/mhm2_test")
- echo "GPU Build job $gpu_job"
- echo "Waiting for knl job $knl_job"
- date
- while /bin/true ; do sleep 120 ; date ; sacct=$(sacct -j $knl_job -o state -X -n 2>/dev/null || true) ; if [ -n "${sacct}" -a -z "$(echo "${sacct}" | grep ING)" ] ; then break ; fi ; done
- echo "sacct $sacct"
- sacct=$(sacct -j $knl_job -X -n)
- echo "sacct $sacct"
- cat slurm-${knl_job}.out
- wasgood=$(echo "${sacct}" | grep -v '0:0' || true)
- if [ -z "$wasgood" ] ; then true ; else echo "knl job ${knl_job} failed somehow - ${wasgood}"; false ; fi
- if [ ! -f ${RUN_PREFIX}/rwdi/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rwdi" ; fi
- ${RWDI}/check_asm_quality.py --asm-dir ${RUN_PREFIX}/rwdi --expected-quals ${RWDI}/../share/good-arctic-sample0.txt --refs ${ARCTIC}/arcticsynth-refs.fa || FAILED="${FAILED} Did not pass check_asm_quality.py on rwdi"
- if [ ! -f ${RUN_PREFIX}/dbg/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on dbg" ; fi
- ${RWDI}/check_asm_quality.py --asm-dir ${RUN_PREFIX}/dbg --expected-quals ${RWDI}/../share/good-arctic-sample0-k63.txt --refs ${ARCTIC}/arcticsynth-refs.fa || echo "WARN Did not pass check_asm_quality.py on dbg with reduced workflow k63"
- echo "Waiting for gpu job ${gpu_job}"
- module load cgpu
- date
- while /bin/true ; do sleep 120 ; date ; sacct=$(sacct -j $gpu_job -o state -X -n 2>/dev/null || true) ; if [ -n "${sacct}" -a -z "$(echo "${sacct}" | grep ING)" ] ; then break ; fi ; done
- echo "sacct $sacct"
- sacct=$(sacct -j $gpu_job -X -n)
- cat slurm-${gpu_job}.out
- wasgood=$(echo "${sacct}" | grep -v '0:0' || true)
- if [ -z "$wasgood" ] ; then true ; else FAILED="${FAILED} -- gpu job ${gpu_job} failed somehow - ${wasgood}"; fi
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}"; false ; fi
- echo "Completed"
Cori:accuracy:
stage: accuracy
tags:
- Cori
script:
- set -e
- set -x
- uname -a
- pwd
- date
- export GASNET_BACKTRACE=1
- echo "Establishing variables"
- export MHM2_SOURCE=$(pwd)
- export BASE=${SCRATCH}/tmp/gitlab-runner-scratch-Cori-mhm2-${USER}
- export SCRATCH=${BASE}/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export INSTALL_PREFIX=${SCRATCH}/install
- export BUILD_PREFIX=${SCRATCH}/build
- export RUN_PREFIX=${SCRATCH}/runs
- echo "BASE=${BASE} SCRATCH=${SCRATCH}"
- echo "Loading KNL modules for upcxx on cori"
- source ${MHM2_SOURCE}/contrib/environments/cori-knl/gnu.sh
- exec > >(tee -ia ${SCRATCH}/accuracy.log)
- exec 2> >(tee -ia ${SCRATCH}/accuracy.err >&2)
- echo "Logging to ${SCRATCH}/accuracy.log and .err at $(date) on $(uname -n) in $(pwd)"
- module list
- cd $SCRATCH
- FAILED=""
- echo "Testing accuracy"
- export REL=${INSTALL_PREFIX}-knl/bin/
- export ARCTIC=/global/cscratch1/sd/regan/GitlabCIData/
- export OPTS="-r ${ARCTIC}/arctic_sample_0.fq --checkpoint=no"
- echo "Submitting job on 5 nodes... on 2 nodes is is roughly REL=170s"
- knl_job=$(sbatch --parsable --job-name="CImha-${CI_COMMIT_SHORT_SHA}" --account=mp215 -C knl --nodes=5 --qos=debug --time=10:00 --wrap="${REL}/mhm2.py $OPTS -o ${RUN_PREFIX}/rel && echo Good")
- echo "Submitting full arctic job on 15 nodes"
- export OPTS2="-r ${ARCTIC}/arctic_samples.fq --checkpoint=no"
- knl_job2=$(sbatch --parsable --job-name="CI-mhm2-${CI_COMMIT_SHORT_SHA}" --account=mp215 -C knl --nodes=15 --qos=debug --time=30:00 --wrap="${REL}/mhm2.py $OPTS2 -o ${RUN_PREFIX}/rel-full && echo Good")
- echo "Submitting GPU full arctic job on 2 cori GPU nodes"
- gpu_job=$(module load cgpu; sbatch --parsable -C gpu -t 30 --exclusive --nodes=2 -G 16 -A m342 --wrap="source ${SCRATCH}/src/contrib/environments/cori-gpu/gnu.sh ; build-cori-gpu/install/bin/mhm2.py $OPTS2 -o ${RUN_PREFIX}/rel-gpu && echo Good")
- echo "Waiting for knl job $knl_job"
- date
- while /bin/true ; do sleep 120 ; date ; sacct=$(sacct -j $knl_job -o state -X -n 2>/dev/null || true) ; if [ -n "${sacct}" -a -z "$(echo "${sacct}" | grep ING)" ] ; then break ; fi ; done
- echo "sacct $sacct"
- sacct=$(sacct -j $knl_job -X -n)
- echo "sacct $sacct"
- cat slurm-${knl_job}.out
- wasgood=$(echo "${sacct}" | grep -v '0:0' || true)
- if [ -z "$wasgood" ] ; then true ; else echo "knl job ${knl_job} failed somehow - ${wasgood}"; false ; fi
- if [ ! -f ${RUN_PREFIX}/rel/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rel" ; fi
- ${REL}/check_asm_quality.py --asm-dir ${RUN_PREFIX}/rel --expected-quals ${REL}/../share/good-arctic-sample0.txt --refs ${ARCTIC}/arcticsynth-refs.fa || FAILED="${FAILED} Did not pass check_asm_quality.py"
- echo "Waiting for second (full) job to finish ${knl_job2}"
- while /bin/true ; do sleep 120 ; date ; sacct=$(sacct -j $knl_job2 -o state -X -n 2>/dev/null || true) ; if [ -n "${sacct}" -a -z "$(echo "${sacct}" | grep ING)" ] ; then break ; fi ; done
- echo "sacct $sacct"
- sacct=$(sacct -j $knl_job2 -X -n)
- echo "sacct $sacct"
- cat slurm-${knl_job2}.out
- wasgood=$(echo "${sacct}" | grep -v '0:0' || true)
- if [ -z "$wasgood" ] ; then true ; else echo "knl job ${knl_job2} failed somehow - ${wasgood}"; false ; fi
- if [ ! -f ${RUN_PREFIX}/rel-full/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rel-full" ; fi
- ${REL}/check_asm_quality.py --thres 0.015 --rna --asm-dir ${RUN_PREFIX}/rel-full --expected-quals ${REL}/../share/good-arcticsynth.txt --refs ${ARCTIC}/arcticsynth-refs.fa || FAILED="${FAILED} Did not pass check_asm_quality.py (full)"
- echo "Waiting for GPU job to finish ${gpu_job}"
- while /bin/true ; do sleep 120 ; date ; sacct=$(module load cgpu; sacct -j $gpu_job -o state -X -n 2>/dev/null || true) ; if [ -n "${sacct}" -a -z "$(echo "${sacct}" | grep ING)" ] ; then break ; fi ; done
- echo "sacct $sacct"
- sacct=$(module load cgpu; sacct -j $gpu_job -X -n)
- echo "sacct $sacct"
- cat slurm-${gpu_job}.out
- wasgood=$(echo "${sacct}" | grep -v '0:0' || true)
- if [ -z "$wasgood" ] ; then true ; else echo "gpu job ${gpu_job} failed somehow - ${wasgood}"; false ; fi
- if [ ! -f ${RUN_PREFIX}/rel-gpu/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rel-gpu" ; fi
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}" ; false ; fi
- echo "Completed"
#
# hulk
#
HULK:build:
stage: build
tags:
- HULK
script:
- set -e
- set -x
- git submodule init
- git submodule sync
- git submodule update
- BASE=/work/gitlab-ci
- CI_INSTALL=$BASE/ci-install-mhm2-upcxx-${HULK_UPCXX_VER}
- export PATH=$CI_INSTALL/bin:/bin:/usr/bin:/usr/local/bin
- export HIPMER_DATA=${BASE}/scratch/
- mkdir -p ${HIPMER_DATA}
- export SCRATCH=${BASE}/scratch/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export RUN_PREFIX=${SCRATCH}/runs
- export GASNET_BACKTRACE=1
- echo "Verifing and/or downloading test arctic data set"
- export ARCTIC_URL=https://portal.nersc.gov/project/hipmer/MetaHipMer_datasets_12_2019/ArcticSynth/samples/
- bash -c "[ -f ${HIPMER_DATA}/arcticsynth-refs.fa ] || ( curl -LO ${ARCTIC_URL}/arcticsynth-refs.fa.gz && gunzip arcticsynth-refs.fa.gz && mv arcticsynth-refs.fa ${HIPMER_DATA}/arcticsynth-refs.fa )"
- bash -c "for i in 0 1 2 3 4 5 6 7 8 9 10 11 ; do [ -f ${HIPMER_DATA}/arctic_sample_\$i.fq ] || ( curl -LO ${ARCTIC_URL}/arctic_sample_\$i.fq.gz && gunzip arctic_sample_\$i.fq.gz && mv arctic_sample_\$i.fq ${HIPMER_DATA}/arctic_sample_\$i.fq ) ; done"
- echo "Establishing all tests under BASE=$BASE and SCRATCH=$SCRATCH"
- rm -rf ${SCRATCH}
- mkdir -p ${SCRATCH}
- chmod a+rx ${SCRATCH}
- chmod g+s ${SCRATCH}
- mkdir -p ${RUN_PREFIX}
- exec > >(tee -ia ${SCRATCH}/build.log)
- exec 2> >(tee -ia ${SCRATCH}/build.err >&2)
- echo "Logging to ${SCRATCH}/build.log and .err at $(date) on $(uname -n) in $(pwd)"
- export MHM2_SOURCE=$(pwd)
- env
- uname -a
- pwd
- find * -type d -ls
- date
- echo "Purging any old tests"
- find ${BASE}/scratch -maxdepth 1 -name 'mhm*' -mtime +4 -type d -exec rm -rf '{}' ';' || /bin/true
- df -h
- FAILED=""
- echo "Checking for cmake, Berkeley UPC and UPC++"
- which cmake && cmake --version || FAILED="${FAILED} cmake not found"
- echo "Checking or building upcxx"
- which upcxx || UPCXXVER=${HULK_UPCXX_VER} ./upcxx-utils/contrib/install_upcxx.sh $CI_INSTALL || FAILED="${FAILED} could not install upcxx"
- upcxx --version || FAILED="${FAILED} no upcxx was found"
- echo "Building all flavors"
- mkdir -p ${RUN_PREFIX}
- export GASNET_BACKTRACE=1
- export INSTALL_PREFIX=${SCRATCH}
- rm -rf $SCRATCH/build
- mkdir -p $SCRATCH/build
- cd $SCRATCH/build
- echo "Building Debug"
- cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}/mhm2-dbg -DCMAKE_BUILD_TYPE=Debug ${MHM2_SOURCE} || FAILED="${FAILED} Could not configure Debug"
- make -j 16 all check install || FAILED="${FAILED} Could not build Debug"
- make clean
- export UPCXX_CODEMODE=debug
- echo "Building RelWithDebInfo with UPCXX_CODEMODE=$UPCXX_CODEMODE"
- cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}/mhm2-rwdi -DCMAKE_BUILD_TYPE=RelWithDebInfo ${MHM2_SOURCE} || FAILED="${FAILED} could not configure RelWithDebInfo"
- make -j 16 all check install || FAILED="${FAILED} Cuold not build RelWithDebInfo"
- make clean
- unset UPCXX_CODEMODE
- echo "Building Release"
- cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}/mhm2-rel -DCMAKE_BUILD_TYPE=Release ${MHM2_SOURCE} || FAILED="${FAILED} could not configure Release"
- make -j 16 all check install || FAILED="${FAILED} Could not build Release"
- echo "${FAILED}"
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}"; false ; fi
- cd -
- rm -rf $SCRATCH/build
- echo "Completed"
HULK:validation:
stage: validation
tags:
- HULK
script:
- set -e
- set -x
- BASE=/work/gitlab-ci
- CI_INSTALL=$BASE/ci-install-mhm2-upcxx-${HULK_UPCXX_VER}
- export PATH=$CI_INSTALL/bin:/bin:/usr/bin:/usr/local/bin
- export HIPMER_DATA=${BASE}/scratch/
- export SCRATCH=${BASE}/scratch/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export RUN_PREFIX=${SCRATCH}/runs
- export INSTALL_PREFIX=${SCRATCH}
- export GASNET_BACKTRACE=1
- exec > >(tee -ia ${SCRATCH}/validation.log)
- exec 2> >(tee -ia ${SCRATCH}/validation.err >&2)
- echo "Logging to ${SCRATCH}/validation.log and .err at $(date) on $(uname -n) in $(pwd)"
- echo "Validating all tests under BASE=$BASE and SCRATCH=$SCRATCH"
- env
- df -h
- uname -a
- pwd
- date
- upcxx --version
- cd ${SCRATCH}
- FAILED=""
- reads=${HIPMER_DATA}/arctic_sample_0.fq
- export DBG=${INSTALL_PREFIX}/mhm2-dbg/bin/
- export RWDI=${INSTALL_PREFIX}/mhm2-rwdi/bin/
- export REL=${INSTALL_PREFIX}/mhm2-rel/bin/
- echo "Starting RelWithDebInfo mhm2 on Arctic $reads"
- if [ ! -f arctic_sample_0.fq -a -f $reads ] ; then ln -s $reads ; fi
- if [ ! -f arcticsynth-refs.fa -a -f ${HIPMER_DATA}/arcticsynth-refs.fa ] ; then ln -s ${HIPMER_DATA}/arcticsynth-refs.fa ; fi
- ${RWDI}/ci_asm_qual_test.sh || FAILED="${FAILED} Could not run ci_asm_qual_test"
- if [ ! -f ./test-arctic-sample0/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta for rwdi in test-arctic-sample0" ; fi
- mv test-arctic-sample0 ${RUN_PREFIX}/rwdi-test-arctic-sample0
- echo "Starting debug run on with reduced workflow"
- ${DBG}/mhm2.py -r $reads -o ${RUN_PREFIX}/dbg --kmer-lens 31,63 --checkpoint=no -v || FAILED="${FAILED} Could not run dbg"
- echo "verify dbg results $(ls -la ${RUN_PREFIX}/dbg)"
- if [ ! -f ${RUN_PREFIX}/dbg/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on dbg" ; fi
- ${DBG}/check_asm_quality.py --asm-dir ${RUN_PREFIX}/dbg --expected-quals ${DBG}/../share/good-arctic-sample0-k31k63.txt --refs ${HIPMER_DATA}/arcticsynth-refs.fa || echo "WARN did not pass check_asm_quality.py for dbg with reduced workflow k31k63"
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}"; false ; fi
- echo "Completed"
HULK:accuracy:
stage: accuracy
tags:
- HULK
script:
- set -e
- set -x
- git submodule init
- git submodule sync
- git submodule update
- BASE=/work/gitlab-ci
- CI_INSTALL=$BASE/ci-install-mhm2-upcxx-${HULK_UPCXX_VER}
- export PATH=$CI_INSTALL/bin:/bin:/usr/bin:/usr/local/bin
- export HIPMER_DATA=${BASE}/scratch/
- export SCRATCH=${BASE}/scratch/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export RUN_PREFIX=${SCRATCH}/runs
- export INSTALL_PREFIX=${SCRATCH}
- export GASNET_BACKTRACE=1
- exec > >(tee -ia ${SCRATCH}/accuracy.log)
- exec 2> >(tee -ia ${SCRATCH}/accuracy.err >&2)
- echo "Logging to ${SCRATCH}/accuracy.log and .err at $(date) on $(uname -n) in $(pwd)"
- echo "Running accuracy tests under BASE=$BASE and SCRATCH=$SCRATCH"
- env
- df -h
- uname -a
- pwd
- date
- upcxx --version
- cd ${SCRATCH}
- FAILED=""
- export REL=${INSTALL_PREFIX}/mhm2-rel/bin/
- echo "Starting Release mhm2 on Arctic"
- if [ ! -f arctic_sample_0.fq -a -f ${HIPMER_DATA}/arctic_sample_0.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_0.fq ; fi
- if [ ! -f arctic_sample_1.fq -a -f ${HIPMER_DATA}/arctic_sample_1.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_1.fq ; fi
- if [ ! -f arctic_sample_2.fq -a -f ${HIPMER_DATA}/arctic_sample_2.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_2.fq ; fi
- if [ ! -f arctic_sample_3.fq -a -f ${HIPMER_DATA}/arctic_sample_3.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_3.fq ; fi
- if [ ! -f arctic_sample_4.fq -a -f ${HIPMER_DATA}/arctic_sample_4.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_4.fq ; fi
- if [ ! -f arctic_sample_5.fq -a -f ${HIPMER_DATA}/arctic_sample_5.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_5.fq ; fi
- if [ ! -f arctic_sample_6.fq -a -f ${HIPMER_DATA}/arctic_sample_6.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_6.fq ; fi
- if [ ! -f arctic_sample_7.fq -a -f ${HIPMER_DATA}/arctic_sample_7.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_7.fq ; fi
- if [ ! -f arctic_sample_8.fq -a -f ${HIPMER_DATA}/arctic_sample_8.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_8.fq ; fi
- if [ ! -f arctic_sample_9.fq -a -f ${HIPMER_DATA}/arctic_sample_9.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_9.fq ; fi
- if [ ! -f arctic_sample_10.fq -a -f ${HIPMER_DATA}/arctic_sample_10.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_10.fq ; fi
- if [ ! -f arctic_sample_11.fq -a -f ${HIPMER_DATA}/arctic_sample_11.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_11.fq ; fi
- if [ ! -f arcticsynth-refs.fa -a -f ${HIPMER_DATA}/arcticsynth-refs.fa ] ; then ln -s ${HIPMER_DATA}/arcticsynth-refs.fa ; fi
- ${REL}/ci_asm_qual_test.sh || FAILED="${FAILED} Could not run ci_asm_qual_test"
- if [ ! -f ./test-arctic-sample0/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rel" ; fi
- mv test-arctic-sample0 ${RUN_PREFIX}/rel-test-arctic-sample0
- ${REL}/ci_asm_qual_test-full.sh || FAILED="${FAILED} Could not run ci_asm_qual_test-full"
- if [ ! -f ./test-arctic-samples/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rel" ; fi
- mv test-arctic-samples ${RUN_PREFIX}/rel-test-arctic-samples
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}"; false ; fi
- echo "Completed"
after_script:
- date
- echo "Done"