fixing runtime_profiler tests

Author: oesteban

docker/circleci/run_nosetests.sh

@@ -3,21 +3,35 @@ set -e
 set -x
 set -u
 
+PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
+
 # Create necessary directories
-mkdir -p /scratch/nose /scratch/crashfiles /scratch/logs/$1
+mkdir -p /scratch/nose /scratch/crashfiles /scratch/logs/py${PYTHON_VERSION}
 
 # Create a nipype config file
 mkdir -p /root/.nipype
 echo '[logging]' > /root/.nipype/nipype.cfg
 echo 'log_to_file = true' >> /root/.nipype/nipype.cfg
-echo "log_directory = /scratch/logs/$1" >> /root/.nipype/nipype.cfg
-echo '[execution]' >> /root/.nipype/nipype.cfg
-echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
+echo "log_directory = /scratch/logs/py${PYTHON_VERSION}" >> /root/.nipype/nipype.cfg
+
+# Enable profile_runtime tests only for python 2.7
+if [[ "${PYTHON_VERSION}" -lt "30" ]]; then
+    echo '[execution]' >> /root/.nipype/nipype.cfg
+    echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
+fi
 
 # Run tests
 cd /root/src/nipype/
 make clean
-nosetests -s nipype -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests_$1.xml" --cover-xml-file="/scratch/coverage_$1.xml"
+nosetests -s nipype -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}.xml"
+
+# Workaround: run here the profiler tests in python 3
+if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
+    echo '[execution]' >> /root/.nipype/nipype.cfg
+    echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
+    nosetests nipype/interfaces/tests/test_runtime_profiler.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_profiler.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_profiler.xml"
+    nosetests nipype/pipeline/plugins/tests/test_multiproc*.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_multiproc.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml"
+fi
 
 # Copy crashfiles to scratch
 for i in $(find /root/src/nipype/ -name "crash-*" ); do cp $i /scratch/crashfiles/; done

nipype/interfaces/tests/test_runtime_profiler.py

@@ -8,7 +8,7 @@
 """
 
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import open
+from builtins import open, str
 
 # Import packages
 import unittest
@@ -72,9 +72,17 @@ def _use_gb_ram(num_gb):
         '''
         Function to consume GB of memory
         '''
+        import sys
 
-        # Eat 1 GB of memory for 1 second
-        gb_str = ' ' * int(num_gb*1024.0**3)
+        # Getsize of one character string
+        bsize = sys.getsizeof('  ') - sys.getsizeof(' ')
+        boffset = sys.getsizeof('')
+
+        num_bytes = int(num_gb * (1024**3))
+        # Eat num_gb GB of memory for 1 second
+        gb_str = ' ' * ((num_bytes - boffset) // bsize)
+
+        assert sys.getsizeof(gb_str) == num_bytes
 
         # Spin CPU
         ctr = 0
@@ -143,7 +151,7 @@ def setUp(self):
         # Input number of sub-threads (not including parent threads)
         self.num_threads = 2
         # Acceptable percent error for memory profiled against input
-        self.mem_err_gb = 0.25
+        self.mem_err_gb = 0.3  # Increased to 30% for py2.7
 
     # ! Only used for benchmarking the profiler over a range of
     # ! RAM usage and number of threads