Changeset: 73cafaf6b49d for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=73cafaf6b49d
Modified Files:
monetdb5/extras/pyapi/Benchmarks/monetdb_testing.py
monetdb5/extras/pyapi/Benchmarks/pyapi_test.sh
Branch: pyapi
Log Message:
Added psycopg2 [postgres python client], pytables and castra benchmarks.
diffs (283 lines):
diff --git a/monetdb5/extras/pyapi/Benchmarks/monetdb_testing.py
b/monetdb5/extras/pyapi/Benchmarks/monetdb_testing.py
--- a/monetdb5/extras/pyapi/Benchmarks/monetdb_testing.py
+++ b/monetdb5/extras/pyapi/Benchmarks/monetdb_testing.py
@@ -529,6 +529,7 @@ if str(args_input_database).lower() == "
else:
input_file = os.environ["POSTGRES_INPUT_FILE"]
input_dir = os.environ["POSTGRES_CWD"]
+ drop_cache = os.environ["DROP_CACHE_COMMAND"]
def execute_test(input_type, database_init, database_load,
database_execute, database_clear, database_final):
database_init()
@@ -545,7 +546,7 @@ else:
database_load()
for i in range(0,test_count):
- os.system('/home/mytherin/bin/flushcache')
+ #os.system(drop_cache)
start = time.time()
database_execute()
end = time.time()
@@ -666,16 +667,16 @@ AS $$
import monetdb.sql
for i in range(0, max_retries):
try:
- connection = monetdb.sql.connect(username="monetdb",
password="monetdb", hostname="localhost",port=port,database="demo")
+ conn = monetdb.sql.connect(username="monetdb",
password="monetdb", hostname="localhost",port=port,database="demo")
break
except:
time.sleep(1)
- connection = None
+ conn = None
- if connection is None:
+ if conn is None:
print("Failed to connect to MonetDB Server (mserver5) in " +
str(max_retries) + " attempts.")
sys.exit(1)
- c = connection.cursor()
+ c = conn.cursor()
def monetdb_init():
return None
@@ -712,9 +713,75 @@ AS $$
conn.close()
execute_test(input_type, monetdb_init, monetdb_load, monetdb_execute,
monetdb_clear, monetdb_final)
+ elif str(args_input_database).lower() == "psycopg2":
+ dbname = os.environ["POSTGRES_DB_NAME"]
+ initdb = os.environ["POSTGRES_CREATEDB_COMMAND"]
+ dropdb = os.environ["POSTGRES_DROPDB_COMMAND"]
+ os.system(initdb)
+ import psycopg2
+ conn = psycopg2.connect("dbname=%s host=/tmp/" % dbname)
+ c = conn.cursor()
+ def psycopg2_init():
+ return None
+ def psycopg2_load():
+ c.execute("CREATE TABLE integers(i integer);")
+ c.execute("COPY integers FROM '%s' DELIMITER ',' CSV;" %
input_file)
+
+
+ def psycopg2_execute():
+ c.execute("SELECT * FROM integers;")
+ result = c.fetchall()
+ print function(numpy.array(result, dtype=numpy.int32))
+
+ def psycopg2_clear():
+ c.execute("DROP TABLE integers;")
+
+ def psycopg2_final():
+ os.system(dropdb)
+ conn.close()
+ os.remove(input_file)
+
+ execute_test(input_type, psycopg2_init, psycopg2_load,
psycopg2_execute, psycopg2_clear, psycopg2_final)
elif str(args_input_database).lower() == "pytables":
- print("Not implemented")
+ import tables
+ import csv
+
+ table_file = 'testfile.h5'
+
+ description = dict()
+ description['i'] = tables.Int32Col()
+
+ def pytables_init():
+ return None
+
+ def pytables_load():
+ file = tables.open_file(table_file, mode='w', title='test file')
+ group = file.create_group('/', 'integers', 'integer_data')
+ table = file.create_table(group, 'values', description, "example")
+ values = table.row
+ with open(input_file, 'rb') as csvfile:
+ reader = csv.reader(csvfile)
+ result = [x for x in reader]
+ for x in result:
+ values['i'] = int(x[0])
+ values.append()
+ table.flush()
+ file.close()
+
+ def pytables_execute():
+ file = tables.open_file(table_file, mode='r')
+ table = file.root.integers.values
+ result = [x['i'] for x in table.iterrows()]
+ function(numpy.array(result, dtype=numpy.int32))
+
+ def pytables_clear():
+ os.remove('testfile.h5')
+
+ def pytables_final():
+ os.remove(input_file)
+
+ execute_test(input_type, pytables_init, pytables_load,
pytables_execute, pytables_clear, pytables_final)
elif str(args_input_database).lower() == "csv":
import csv
def csv_init():
@@ -726,7 +793,7 @@ AS $$
def csv_execute():
with open(input_file, 'rb') as csvfile:
reader = csv.reader(csvfile)
- result = [x for x in reader]
+ result = [int(x[0]) for x in reader]
function(numpy.array(result, dtype=numpy.int32))
def csv_clear():
@@ -745,7 +812,7 @@ AS $$
def numpy_load():
with open(input_file, 'rb') as csvfile:
reader = csv.reader(csvfile)
- result = [x for x in reader]
+ result = [int(x[0]) for x in reader]
numpy_array = numpy.array(result, dtype=numpy.int32)
numpy.save(numpy_binary, numpy_array)
@@ -762,7 +829,31 @@ AS $$
execute_test(input_type, numpy_init, numpy_load, numpy_execute,
numpy_clear, numpy_final)
elif str(args_input_database).lower() == "castra":
- print("Not implemented")
+ import castra, csv, shutil, pandas as pd
+ castra_binary = 'data.castra'
+ def castra_init():
+ return None
+
+ def castra_load():
+ with open(input_file, 'rb') as csvfile:
+ reader = csv.reader(csvfile)
+ result = [int(x[0]) for x in reader]
+ numpy_array = numpy.array(result, dtype=numpy.int32)
+ A = pd.DataFrame({'i': numpy_array})
+ c = castra.Castra(castra_binary, template=A)
+ c.extend(A)
+
+ def castra_execute():
+ c = castra.Castra(castra_binary, readonly=True)
+ print function(c[:, 'i'].values)
+
+ def castra_clear():
+ shutil.rmtree(castra_binary)
+
+ def castra_final():
+ os.remove(input_file)
+
+ execute_test(input_type, castra_init, castra_load, castra_execute,
castra_clear, castra_final)
elif str(args_input_database).lower() == "numpymemorymap":
import csv, numpy
numpy_binary = 'tempfile.npy'
@@ -772,7 +863,7 @@ AS $$
def numpy_load():
with open(input_file, 'rb') as csvfile:
reader = csv.reader(csvfile)
- result = [x for x in reader]
+ result = [int(x[0]) for x in reader]
numpy_array = numpy.array(result, dtype=numpy.int32)
numpy.save(numpy_binary, numpy_array)
diff --git a/monetdb5/extras/pyapi/Benchmarks/pyapi_test.sh
b/monetdb5/extras/pyapi/Benchmarks/pyapi_test.sh
--- a/monetdb5/extras/pyapi/Benchmarks/pyapi_test.sh
+++ b/monetdb5/extras/pyapi/Benchmarks/pyapi_test.sh
@@ -1,7 +1,7 @@
# The base directory of testing, a new folder is created in this base
directory [$PYAPI_TEST_DIR], and everything is done in that new folder
-export PYAPI_BASE_DIR=/home/mytherin
+export PYAPI_BASE_DIR=/export/scratch1/raasveld
# The terminal to start mserver with, examples are gnome-terminal, xterm,
konsole
export TERMINAL=x-terminal-emulator
# Port used by the MSERVER
@@ -214,7 +214,7 @@ function postgres_run_single_test() {
# start server
setsid $POSTGRES_SERVER_COMMAND > /dev/null && sleep 5
# call python test script
- python "$PYAPI_TESTFILE" POSTGRES $1 $2 $3 $MSERVER_PORT $4
+ python "$PYAPI_TESTFILE" $5 $1 $2 $3 $MSERVER_PORT $4
# finish testing, kill postgres
killall postgres
}
@@ -515,16 +515,14 @@ function postgres_test() {
postgres_run_tests
}
+export DROP_CACHE_COMMAND='echo 3 | sudo /usr/bin/tee /proc/sys/vm/drop_caches'
+
export IDENTITY_NTESTS=3
export IDENTITY_SIZES="100"
function postgres_run_tests() {
- if [ ! -d $PYAPI_OUTPUT_DIR ]; then
- mkdir $PYAPI_OUTPUT_DIR
- fi
- cd $PYAPI_OUTPUT_DIR
- postgres_run_single_test IDENTITY postgres_identity $IDENTITY_NTESTS
"$IDENTITY_SIZES"
- postgres_run_single_test SQROOT postgres_sqroot $IDENTITY_NTESTS
"$IDENTITY_SIZES"
+ postgres_run_single_test IDENTITY postgres_identity $IDENTITY_NTESTS
"$IDENTITY_SIZES" POSTGRES
+ postgres_run_single_test SQROOT postgres_sqroot $IDENTITY_NTESTS
"$IDENTITY_SIZES" POSTGRES
}
function sqlite_test() {
@@ -577,11 +575,33 @@ function monetdbrapi_test() {
monetdbmapi_run_single_test RAPI "--set gdk_nr_threads=1 --set
embedded_r=true" SQROOT monetdbrapi_sqroot $IDENTITY_NTESTS "$IDENTITY_SIZES"
}
-function psycopg_install() {
- wget http://initd.org/psycopg/tarballs/PSYCOPG-2-6/psycopg2-2.6.1.tar.gz
&& tar xvzf psycopg2-2.6.1.tar.gz && rm tar xvzf psycopg2-2.6.1.tar.gz && cd
psycopg2-2.6.1 && python setup.py install --user build_ext --pg-config
$POSTGRES_BUILD_DIR/bin/pg_config
+function psycopg2_install() {
+ wget http://initd.org/psycopg/tarballs/PSYCOPG-2-6/psycopg2-2.6.1.tar.gz
&& tar xvzf psycopg2-2.6.1.tar.gz && rm psycopg2-2.6.1.tar.gz && cd
psycopg2-2.6.1 && python setup.py install --user build_ext --pg-config
$POSTGRES_BUILD_DIR/bin/pg_config
+}
+
+function psycopg2_test() {
+ postgres_run_single_test IDENTITY psycopg2_identity $IDENTITY_NTESTS
"$IDENTITY_SIZES" PSYCOPG2
+}
+
+function cython_install() {
+ wget http://cython.org/release/Cython-0.23.1.tar.gz && tar xvzf
Cython-0.23.1.tar.gz && cd Cython-0.23.1 && python setup.py install --user
+}
+
+function pytables_install() {
+ wget https://github.com/PyTables/PyTables/archive/develop.zip && unzip
develop.zip && cd PyTables-develop && python setup.py install --user
+}
+
+function pytables_test() {
+ python_run_single_test PYTABLES IDENTITY pytables_identity
$IDENTITY_NTESTS "$IDENTITY_SIZES"
+ python_run_single_test PYTABLES SQROOT pytables_sqroot $IDENTITY_NTESTS
"$IDENTITY_SIZES"
}
function comparison_test() {
+ if [ ! -d $PYAPI_OUTPUT_DIR ]; then
+ mkdir $PYAPI_OUTPUT_DIR
+ fi
+ cd $PYAPI_OUTPUT_DIR
+
postgres_run_tests
sqlite_test
csv_test
@@ -592,8 +612,21 @@ function comparison_test() {
monetdbpyapi_test
monetdbpyapimap_test
monetdbrapi_test
+ psycopg2_test
+ pytables_test
+ castra_test
}
+function castra_install() {
+ wget https://github.com/blaze/castra/archive/master.zip && unzip
master.zip && cd castra-master && python setup.py install --user
+}
+
+function castra_test() {
+ python_run_single_test CASTRA IDENTITY castra_identity $IDENTITY_NTESTS
"$IDENTITY_SIZES"
+ python_run_single_test CASTRA SQROOT castra_sqroot $IDENTITY_NTESTS
"$IDENTITY_SIZES"
+}
+
+
function comparison_graph() {
python $PYAPI_GRAPHFILE "SAVE" "Identity" "postgres:postgres_identity.tsv"
"sqlitemem:sqlitemem_identity.tsv" "sqlitedb:sqlitedb_identity.tsv"
"csv:csv_identity.tsv" "numpy:numpy_identity.tsv"
"numpymmap:numpymmap_identity.tsv"
"monetdbembedded:monetdbembedded_identity.tsv"
"monetdbmapi:monetdbmapi_identity.tsv" "monetdbpyapi:monetdbpyapi_identity.tsv"
"monetdbpyapimap:monetdbpyapimap_identity.tsv"
"monetdbrapi:monetdbrapi_identity.tsv"
python $PYAPI_GRAPHFILE "SAVE" "Identity [Fast Only]"
"numpy:numpy_identity.tsv" "numpymmap:numpymmap_identity.tsv"
"monetdbembedded:monetdbembedded_identity.tsv"
"monetdbpyapi:monetdbpyapi_identity.tsv"
"monetdbpyapimap:monetdbpyapimap_identity.tsv"
"monetdbrapi:monetdbrapi_identity.tsv"
@@ -602,4 +635,3 @@ function comparison_graph() {
python $PYAPI_GRAPHFILE "SAVE" "Square Root [Fast Only]"
"numpy:numpy_sqroot.tsv" "numpymmap:numpymmap_sqroot.tsv"
"monetdbembedded:monetdbembedded_sqroot.tsv"
"monetdbpyapi:monetdbpyapi_sqroot.tsv"
"monetdbpyapimap:monetdbpyapimap_sqroot.tsv"
"monetdbrapi:monetdbrapi_sqroot.tsv"
}
-
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