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Makefile
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.PHONY: clean run small docker run-udocker run-singularity toil-udocker toil-singularity
all: run
SHELL=bash
RUN := $(PWD)/runs/run_$(shell date +%F-%H-%M-%S)
ARCHIVE=ftp://ftp.astron.nl/outgoing/EOSC/datasets/
TINY=L591513_SB000_uv_delta_t_4.MS
PULSAR=GBT_Lband_PSR.fil
SMALL=L570745_SB000_uv_first10.MS
# archive name is different from file name
SMALL_ARCHIVE=L570745_uv_first10.MS.tar.xz
.virtualenv/:
virtualenv -p python2 .virtualenv
.virtualenv/bin/cwltool: .virtualenv/
.virtualenv/bin/pip install -r requirements.txt
.virtualenv/bin/cwltoil: .virtualenv/
.virtualenv/bin/pip install -r requirements.txt
.virtualenv/bin/udocker: .virtualenv/
curl https://raw.githubusercontent.com/indigo-dc/udocker/master/udocker.py > .virtualenv/bin/udocker
chmod u+rx .virtualenv/bin/udocker
.virtualenv/bin/udocker install
data/$(PULSAR):
cd data && wget $(ARCHIVE)$(PULSAR)
data/$(TINY)/:
cd data && wget $(ARCHIVE)$(TINY).tar.xz && tar Jxvmf $(TINY).tar.xz
tiny: data/$(TINY)/
echo "data/$(TINY)/ is downloaded"
data/$(SMALL_ARCHIVE):
cd data && wget $(ARCHIVE)$(SMALL_ARCHIVE)
data/$(SMALL)/: data/$(SMALL_ARCHIVE)
cd data && tar Jxmvf $(SMALL_ARCHIVE)
small: data/$(SMALL)/
echo "data/$(SMALL)/ is downloaded"
run-udocker: .virtualenv/bin/udocker .virtualenv/bin/cwltool
mkdir -p $(RUN)
.virtualenv/bin/cwltool \
--parallel \
--user-space-docker-cmd `pwd`/.virtualenv/bin/udocker \
--cachedir cache \
--outdir $(RUN)/results \
prefactor.cwl \
jobs/job_20sb.yaml > >(tee $(RUN)/output) 2> >(tee $(RUN)/log >&2)
run: .virtualenv/bin/cwltool
mkdir -p $(RUN)
.virtualenv/bin/cwltool \
--parallel \
--leave-tmpdir \
--cachedir cache \
--outdir $(RUN)/results \
prefactor.cwl \
jobs/job_20sb.yaml > >(tee $(RUN)/output) 2> >(tee $(RUN)/log >&2)
run-singularity: .virtualenv/bin/cwltool
mkdir -p $(RUN)
.virtualenv/bin/cwltool \
--parallel \
--singularity \
--leave-tmpdir \
--cachedir cache \
--outdir $(RUN)/results \
prefactor.cwl \
jobs/job_20sb.yaml > >(tee $(RUN)/output) 2> >(tee $(RUN)/log >&2)
toil: data/$(SMALL)/ .virtualenv/bin/cwltoil
mkdir -p $(RUN)/results
.virtualenv/bin/toil-cwl-runner \
--logFile $(RUN)/log \
--outdir $(RUN)/results \
--tmp-outdir-prefix $(PWD)/tmp \
--workDir $(PWD)/work \
--jobStore file://$(RUN)/job_store \
prefactor.cwl \
jobs/job_20sb.yaml | tee $(RUN)/output
toil-singularity: data/$(SMALL)/ .virtualenv/bin/cwltoil
mkdir -p $(RUN)/results
.virtualenv/bin/toil-cwl-runner \
--singularity \
--logFile $(RUN)/log \
--outdir $(RUN)/results \
--tmp-outdir-prefix $(PWD)/tmp \
--workDir $(PWD)/work \
--jobStore file://$(RUN)/job_store \
prefactor.cwl \
jobs/job_20sb.yaml | tee $(RUN)/output
toil-udocker: data/$(SMALL)/ .virtualenv/bin/cwltoil
mkdir -p $(RUN)/results
.virtualenv/bin/toil-cwl-runner \
--user-space-docker-cmd `pwd`/.virtualenv/bin/udocker \
--logFile $(RUN)/log \
--outdir $(RUN)/results \
--tmp-outdir-prefix $(PWD)/tmp \
--workDir $(PWD)/work \
--jobStore file://$(RUN)/job_store \
prefactor.cwl \
jobs/job_20sb.yaml | tee $(RUN)/output
slurm: data/$(SMALL) .virtualenv/bin/cwltoil
mkdir -p $(RUN)/results
.virtualenv/bin/toil-cwl-runner \
--batchSystem=slurm \
--preserve-environment PATH \
--logFile $(RUN)/log \
--outdir $(RUN)/results \
--jobStore file://$(RUN)/job_store \
prefactor.cwl \
jobs/job_20sb.yaml | tee $(RUN)/output
slurm-singularity: data/$(SMALL) .virtualenv/bin/cwltoil
mkdir -p $(RUN)/results
.virtualenv/bin/toil-cwl-runner \
--singularity \
--batchSystem=slurm \
--preserve-environment PATH \
--logFile $(RUN)/log \
--outdir $(RUN)/results \
--jobStore file://$(RUN)/job_store \
prefactor.cwl \
jobs/job_20sb.yaml | tee $(RUN)/output
slurm-udocker: data/$(SMALL) .virtualenv/bin/cwltoil
mkdir -p $(RUN)/results
.virtualenv/bin/toil-cwl-runner \
--user-space-docker-cmd `pwd`/.virtualenv/bin/udocker \
--batchSystem=slurm \
--preserve-environment PATH \
--logFile $(RUN)/log \
--outdir $(RUN)/results \
--jobStore file://$(RUN)/job_store \
prefactor.cwl \
jobs/job_20sb.yaml | tee $(RUN)/output
mesos: data/$(SMALL)
export PYTHONPATH=/usr/lib/python2.7/site-packages
mkdir -p $(RUN)/results
toil-cwl-runner \
--batchSystem=mesos \
--mesosMaster=145.100.59.50:5050 \
--preserve-environment PATH \
--logFile $(RUN)/log \
--outdir $(RUN)/results \
--jobStore file://$(RUN)/job_store \
prefactor.cwl \
jobs/job_20sb.yaml | tee $(RUN)/output
docker:
docker build -t kernsuite/prefactor .