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Makefile
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DATADIR=data
DBNAME?=${DATADIR}/timings.db
NUM_REPEATS?=1
CMDS_FILE?=etc/cmds.tab
BASIC_GNUPLOT_CONF=etc/basic.gnuplot.conf
VPATH = $(DATADIR)
TIMING_NAME=blastx-555-vs-nr09
GRAPHS=$(TIMING_NAME).png
TITLE=blastx search of nr.09
GNUPLOT_DATA=data/$(TIMING_NAME).dat
#GNUPLOT_CONF=etc/basic.gnuplot.conf
#GNUPLOT_CONF=etc/timings.gnuplot.conf
GNUPLOT_CONF=etc/multi-series.gnuplot.conf
#GNUPLOT_CONF_SIMPLE=etc/simple.gnuplot.conf
# Plots histograms of repeated tests
### GRAPHS=\
### blastx-185kb-query.png \
### blastx-209kb-query.png \
### blastx-214kb-query.png \
### megablast-185kb-query.png \
### megablast-209kb-query.png \
### megablast-214kb-query.png
## Plots simple runtimes
#GRAPH_SIMPLE=estimatePiMesos.png
#TITLE_SIMPLE=Replace me
#GNUPLOT_DATA_SIMPLE=data/timings-simple.dat
.PHONY: all
all: ${DBNAME}
bin/driver.pl -v -v -v -v -skip_failures -repeats $(NUM_REPEATS) -cmds ${CMDS_FILE}
#bin/driver.pl -v -v -v -v -skip_failures -repeats $(NUM_REPEATS) -rm_core_files
run_parallel: ${DBNAME}
bin/driver.pl -v -v -v -v -skip_failures -parallel -cmds ${CMDS_FILE}
# target to run tests in EB-785, for didactical purposes
eb785: ${DBNAME}
for n in 1 2 4 8 16 32; do \
make -C ${DATADIR} timings-$$n.db; \
bin/driver.pl -v -v -v -skip_failures -parallel -db ${DATADIR}/timings-$$n.db -cmds etc/cmds-$$n.tab; \
bin/reports.pl -db ${DATADIR}/timings-$$n.db -label megablast-$$n ; \
done
$(DBNAME):
make -C ${DATADIR} `basename $@`
%.png: %.dat
if [ -z "$T" ] ; then echo "Must define the T make variable for graph title"; exit 1; fi
gnuplot -e "output='$@';title='$T'; data_file='$^'" $(BASIC_GNUPLOT_CONF)
%.dat: $(DBNAME)
if [ -z "$Q" ] ; then echo "Must define the Q make variable to query $(DBNAME)"; exit 1; fi
sqlite3 $^ "select label, elapsed_time from runtime where label like '$Q-%'" | sed -e 's/$Q-//' | sort -n > $@
# This doesn't work, needs to be invoked by hand for each graph
##1336.png:
## echo $(MAKE) $@ Q=1336q T=\"1336 WGS queries vs nt on spark mesos\"
##15795.png:
## echo $(MAKE) $@ Q=15795q T=\"15795 WGS queries vs nt on spark mesos\"
##139340.png:
## echo $(MAKE) $@ Q=139340q T=\"139340 WGS queries vs nt on spark mesos\"
.PHONY: dump
dump: ${DBNAME}
sqlite3 ${DBNAME} .dump
.PHONY: show
show: ${DBNAME}
sqlite3 -header -column ${DBNAME} < ddl/report-full.sql
#sqlite3 -header -column ${DBNAME} < ddl/report-brief.sql
bin/reports.pl -db ${DBNAME} -label all | sort -n
.PHONY: reset
reset:
make -C ${DATADIR} clean
make -C ddl clean
.PHONY: check_perl_syntax
check_perl_syntax:
for f in bin/*.pl; do perl -c $$f ; done
bin/driver.pl --version
bin/reports.pl --version
.PHONY: test_sql
test_sql:
make -C ddl test
.PHONY: test
test: check_perl_syntax test_sql test_consecutive test_parallel test_config
TEST_CMD_FILE=test-cmd.tab
${TEST_CMD_FILE}:
printf "foo\tdate >{LABEL}.out\n" > $@
printf "bar\tjunk\n" >> $@
.PHONY: test_consecutive
test_consecutive: ${TEST_CMD_FILE}
[ -f ${DATADIR}/testdb.db ] || make -C ${DATADIR} testdb.db
bin/driver.pl -v -v -v -v -v -skip_failures -repeats 3 -cmds ${TEST_CMD_FILE} -db ${DATADIR}/testdb.db
sqlite3 -header -column ${DATADIR}/testdb.db < ddl/select.sql
bin/reports.pl -label all -db ${DATADIR}/testdb.db
${RM} $< ${DATADIR}/testdb.db
TEST_CMD_FILE_PARALLEL=test-cmd-parallel.tab
${TEST_CMD_FILE_PARALLEL}:
printf "job1\tsleep 5\n" > $@
printf "job2\tsleep 2\n" >> $@
.PHONY: test_parallel
test_parallel: ${TEST_CMD_FILE_PARALLEL}
[ -f ${DATADIR}/testdb.db ] || make -C ${DATADIR} testdb.db
bin/driver.pl -v -v -v -v -v -skip_failures -parallel -cmds $< -db ${DATADIR}/testdb.db
sqlite3 -header -column ${DATADIR}/testdb.db < ddl/select.sql
bin/reports.pl -label all -db ${DATADIR}/testdb.db
${RM} $< ${DATADIR}/testdb.db
TEST_CFG_FILE=test-config.ini
${TEST_CFG_FILE}:
printf "[all]\nsetup=true\nteardown=true\nenv=BLASTDB=/blast/blastdb;ELB_CLUSTER_NAME=bar\n" > $@
printf "[foo]\nsetup=date\nteardown=date\nenv=BLASTDB=/dev/null;BATCH_SIZE=100000\n" >> $@
printf "[bar]\nenv=TEST_NAME=bar\n" >> $@
make ${TEST_CMD_FILE}
.PHONY: test_config
test_config: ${TEST_CFG_FILE}
[ -f ${DATADIR}/testdb.db ] || make -C ${DATADIR} testdb.db
bin/driver.pl -v -v -v -v -v -skip_failures -repeats 2 -cmds ${TEST_CMD_FILE} -cfg $< -db ${DATADIR}/testdb.db
sqlite3 -header -column ${DATADIR}/testdb.db < ddl/select.sql
bin/reports.pl -label all -db ${DATADIR}/testdb.db
${RM} $< ${TEST_CMD_FILE}
.PHONY: simple
simple: ${GRAPH_SIMPLE}
.PHONY: graphs
graphs: ${GRAPHS}
#
#${GRAPHS}: ${GNUPLOT_DATA} ${GNUPLOT_CONF}
# gnuplot -e "idx=0; title='megablast runtime: 215kb query vs. nt'; output='megablast-215kb-query.png'; data_file='${GNUPLOT_DATA}'" ${GNUPLOT_CONF}
# gnuplot -e "idx=1; title='megablast runtime: 209kb query vs. nt'; output='megablast-209kb-query.png'; data_file='${GNUPLOT_DATA}'" ${GNUPLOT_CONF}
# gnuplot -e "idx=2; title='megablast runtime: 185kb query vs. nt'; output='megablast-185kb-query.png'; data_file='${GNUPLOT_DATA}'" ${GNUPLOT_CONF}
# gnuplot -e "idx=3; title='blastx runtime: 215kb query vs. nr'; output='blastx-215kb-query.png'; data_file='${GNUPLOT_DATA}'" ${GNUPLOT_CONF}
# gnuplot -e "idx=4; title='blastx runtime: 209kb query vs. nr'; output='blastx-209kb-query.png'; data_file='${GNUPLOT_DATA}'" ${GNUPLOT_CONF}
# gnuplot -e "idx=5; title='blastx runtime: 185kb query vs. nr'; output='blastx-185kb-query.png'; data_file='${GNUPLOT_DATA}'" ${GNUPLOT_CONF}
$(GRAPHS): $(GNUPLOT_DATA) $(GNUPLOT_CONF)
gnuplot -e "title='$(TITLE)'; output='$@'; data_file='$<'" $(GNUPLOT_CONF)
${GNUPLOT_DATA}: ${DBNAME}
#sqlite3 $< < ddl/select.sql | bin/data2gnuplot.pl > $@
sqlite3 $< < ddl/select.sql | bin/multi-series-extractor.pl > $@
${GNUPLOT_DATA_SIMPLE}: ${DBNAME}
bin/reports.pl -label all | sort -n | awk '{print $$1, $$3, $$5, $$7, $$9}' > $@
${GRAPH_SIMPLE}: ${GNUPLOT_DATA_SIMPLE} ${GNUPLOT_CONF_SIMPLE}
gnuplot -e "output='$@'; title='$(TITLE_SIMPLE)'; data_file='$<'" ${GNUPLOT_CONF_SIMPLE}
.PHONY: clean
clean:
$(RM) ${GNUPLOT_DATA} ${GRAPHS} ${GRAPH_SIMPLE} ${GNUPLOT_DATA_SIMPLE} ${TEST_CMD_FILE}
.PHONY: distclean
distclean: clean
make -C ${DATADIR} $@
make -C ddl $@
${RM} *.ini *.tab *.out
BASEDIR=`basename ${PWD}`
archive:
cd .. && tar acvf ${BASEDIR}.tgz ${BASEDIR}
.PHONY: help
help:
@echo "The following targets are available:"
@echo "all (default): initialize database/data/log directories and run driver script. Configure with NUM_REPEATS"
@echo "show: Shows data from database and output from report script"
@echo "test: Run the test suite"
@echo "simple: Creates simple graphs (needs manual customization)"
@echo "graphs: Creates multiple graphs (needs manual customization)"
@echo "dump: Dumps contents of database to stdout"
@echo "reset: Deletes database contents"
@echo "clean: Removes gnuplot data, graphs"
@echo "distclean: Removes database and invokes make clean"
@echo "archive: Creates a tarball of this directory"