From b52cb92c3326241db722a728e49bd7de0f53f2ac Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 6 Mar 2014 13:20:46 -0500
Subject: [PATCH 01/43] added dashboard configuration

---
 src/CMakeLists.txt    |  4 ++--
 src/CTestConfig.cmake | 13 +++++++++++++
 2 files changed, 15 insertions(+), 2 deletions(-)
 create mode 100644 src/CTestConfig.cmake

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 40b76a08be..c0a2563784 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -220,8 +220,8 @@ endif()
 # Regression tests
 #===============================================================================
 
-# This allows mpi test to work
-enable_testing()
+# This allows for dashboard configuration
+include(CTest)
 
 # Get a list of all the tests to run
 file(GLOB_RECURSE TESTS ${CMAKE_CURRENT_SOURCE_DIR}/../tests/test_*.py)
diff --git a/src/CTestConfig.cmake b/src/CTestConfig.cmake
new file mode 100644
index 0000000000..fa3c21d29a
--- /dev/null
+++ b/src/CTestConfig.cmake
@@ -0,0 +1,13 @@
+## This file should be placed in the root directory of your project.
+## Then modify the CMakeLists.txt file in the root directory of your
+## project to incorporate the testing dashboard.
+## # The following are required to uses Dart and the Cdash dashboard
+##   ENABLE_TESTING()
+##   INCLUDE(CTest)
+set(CTEST_PROJECT_NAME "OpenMC")
+set(CTEST_NIGHTLY_START_TIME "05:00:00 UTC")
+
+set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_SITE "neutronbalance.mit.edu")
+set(CTEST_DROP_LOCATION "/CDash/submit.php?project=OpenMC")
+set(CTEST_DROP_SITE_CDASH TRUE)

From 19f04b56d0fbac0fd9dbdffca6c2a8667ca3a566 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 6 Mar 2014 14:19:40 -0500
Subject: [PATCH 02/43] added nightly test script for CDash integration

---
 tests/run_nightly_tests.py | 133 +++++++++++++++++++++++++++++++++++++
 1 file changed, 133 insertions(+)
 create mode 100755 tests/run_nightly_tests.py

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
new file mode 100755
index 0000000000..94f458e17c
--- /dev/null
+++ b/tests/run_nightly_tests.py
@@ -0,0 +1,133 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import os
+import sys
+import shutil
+from subprocess import call 
+from collections import OrderedDict
+
+# Compiler paths
+FC_DEFAULT='gfortran'
+MPI_DIR='/opt/mpich/3.0.4-gnu'
+HDF5_DIR='/opt/hdf5/1.8.12-gnu'
+PHDF5_DIR='/opt/phdf5/1.8.12-gnu'
+PETSC_DIR='/opt/petsc/3.4.3-gnu'
+
+# CTest script template
+ctest_str = """set (CTEST_SOURCE_DIRECTORY "{source_dir}")
+set (CTEST_BINARY_DIRECTORY "{build_dir}")
+
+set(CTEST_SITE "{host_name}")
+set (CTEST_BUILD_NAME "{build_name}")
+set (CTEST_CMAKE_GENERATOR "Unix Makefiles")
+set (CTEST_BUILD_OPTIONS "{build_opts}")
+
+set(CTEST_CONFIGURE_COMMAND "${{CMAKE_COMMAND}} -H${{CTEST_SOURCE_DIRECTORY}} -B${{CTEST_BINARY_DIRECTORY}} ${{CTEST_BUILD_OPTIONS}}")
+set(CTEST_MEMORYCHECK_COMMAND "/usr/bin/valgrind")
+set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "--tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes --track-origins=yes")
+
+ctest_start("Nightly")
+ctest_configure()
+ctest_build()
+ctest_test()
+ctest_submit()"""
+
+# Define test data structure
+tests = OrderedDict()
+
+class Test(object):
+    def __init__(self, name, debug=False, optimize=False, mpi=False, openmp=False,
+                 hdf5=False, petsc=False, valgrind=False):
+        self.name = name
+        self.debug = debug
+        self.optimize = optimize
+        self.mpi = mpi
+        self.openmp = openmp
+        self.hdf5 = hdf5
+        self.petsc = petsc
+        self.valgrind = valgrind
+
+    def get_build_name(self):
+        self.build_name = self.name
+        return self.build_name
+
+    def get_build_opts(self):
+        build_str = ""
+        if self.debug:
+            build_str += "-Ddebug=ON "
+        if self.optimize:
+            build_str += "-Doptimize=ON "
+        if self.openmp:
+            build_str += "-Dopenmp=ON "
+        if self.petsc:
+            build_str += "-Dpetsc=ON "
+        self.build_opts = build_str
+        return self.build_opts
+
+    def run_ctest(self, ctest_vars):
+        with open('ctestscript.run', 'w') as fh:
+            fh.write(ctest_str.format(**ctest_vars))
+
+def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
+             hdf5=False, petsc=False, valgrind=False):
+    tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, valgrind)})
+
+# List of tests
+#add_test('basic-normal')
+add_test('basic-debug', debug=True)
+#add_test('basic-optimize', optimize=True)
+#add_test('omp-normal', openmp=True)
+#add_test('omp-debug', openmp=True, debug=True)
+#add_test('omp-optimize', openmp=True, optimize=True)
+#add_test('hdf5-normal', hdf5=True)
+#add_test('hdf5-debug', hdf5=True, debug=True)
+#add_test('hdf5-optimize', hdf5=True, optimize=True)
+#add_test('omp-hdf5-normal', openmp=True, hdf5=True)
+#add_test('omp-hdf5-debug', openmp=True, hdf5=True, debug=True)
+#add_test('omp-hdf5-optimize', openmp=True, hdf5=True, optimize=True)
+#add_test('mpi-normal', mpi=True)
+#add_test('mpi-debug', mpi=True, debug=True)
+#add_test('mpi-optimize', mpi=True, optimize=True)
+#add_test('mpi-omp-normal', mpi=True, openmp=True)
+#add_test('mpi-omp-debug', mpi=True, openmp=True, debug=True)
+#add_test('mpi-omp-optimize', mpi=True, openmp=True, optimize=True)
+#add_test('phdf5-normal', mpi=True, hdf5=True)
+#add_test('phdf5-debug', mpi=True, hdf5=True, debug=True)
+#add_test('phdf5-optimize', mpi=True, hdf5=True, optimize=True)
+#add_test('phdf5-omp-normal', mpi=True, hdf5=True, openmp=True)
+#add_test('phdf5-omp-debug', mpi=True, hdf5=True, openmp=True, debug=True)
+#add_test('phdf5-omp-optimize', mpi=True, hdf5=True, openmp=True, optimize=True)
+#add_test('petsc-normal', petsc=True, mpi=True)
+#add_test('petsc-debug', petsc=True, mpi=True, debug=True)
+#add_test('petsc-optimize', petsc=True, mpi=True, optimize=True)
+#add_test('phdf5-petsc-normal', mpi=True, hdf5=True, petsc=True)
+#add_test('phdf5-petsc-debug', mpi=True, hdf5=True, petsc=True, debug=True)
+#add_test('phdf5-petsc-optimize', mpi=True, hdf5=True, petsc=True, optimize=True)
+#add_test('omp-phdf5-petsc-normal', openmp=True, mpi=True, hdf5=True, petsc=True)
+#add_test('omp-phdf5-petsc-debug', openmp=True, mpi=True, hdf5=True, petsc=True, debug=True)
+#add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=True, optimize=True)
+
+# Setup CTest vars
+pwd = os.environ['PWD']
+ctest_vars = {
+'source_dir' : pwd + '/../src',
+'build_dir' :  pwd + '/build',
+'host_name' : 'bryan laptop'
+}
+
+# Begin testing
+call(['rm', '-rf', 'build'])
+for key in iter(tests):
+    test = tests[key]
+
+    # Set test specific CTest vars
+    ctest_vars.update({'build_name' : test.get_build_name()})
+    ctest_vars.update({'build_opts' : test.get_build_opts()})
+
+    # Run test
+    test.run_ctest(ctest_vars)
+
+    # Clear build directory
+    call(['rm', '-rf', 'build'])

From 7c34f5c109cb404706e6a709dd2e5946b336ac11 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 6 Mar 2014 14:23:19 -0500
Subject: [PATCH 03/43] only run test basic for now

---
 tests/run_nightly_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 94f458e17c..25725c09ad 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -31,7 +31,7 @@ set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "--tool=memcheck --leak-check=yes --show-r
 ctest_start("Nightly")
 ctest_configure()
 ctest_build()
-ctest_test()
+ctest_test(INCLUDE test_basic)
 ctest_submit()"""
 
 # Define test data structure

From 160569cced5be73befe00c3752590bde5e8c8b49 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 6 Mar 2014 14:30:51 -0500
Subject: [PATCH 04/43] ctest script executed from python script

---
 tests/run_nightly_tests.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 25725c09ad..44e62b14ba 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -66,10 +66,13 @@ class Test(object):
         self.build_opts = build_str
         return self.build_opts
 
-    def run_ctest(self, ctest_vars):
+    def create_ctest_script(self, ctest_vars):
         with open('ctestscript.run', 'w') as fh:
             fh.write(ctest_str.format(**ctest_vars))
 
+    def run_ctest(self):
+        call(['ctest', '-S', 'ctestscript.run','-V'])
+
 def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
              hdf5=False, petsc=False, valgrind=False):
     tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, valgrind)})
@@ -126,8 +129,11 @@ for key in iter(tests):
     ctest_vars.update({'build_name' : test.get_build_name()})
     ctest_vars.update({'build_opts' : test.get_build_opts()})
 
+    # Create ctest script
+    test.create_ctest_script(ctest_vars)
+
     # Run test
-    test.run_ctest(ctest_vars)
+    test.run_ctest()
 
     # Clear build directory
     call(['rm', '-rf', 'build'])

From c074268ba1aaf551addbfb9c8b743c70d39fa014 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 6 Mar 2014 15:23:18 -0500
Subject: [PATCH 05/43] implemented valgrind test option

---
 src/CMakeLists.txt         | 35 +++++++++++++++++++++++------------
 tests/run_nightly_tests.py | 12 ++++++++++--
 2 files changed, 33 insertions(+), 14 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c0a2563784..21609a4d9a 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -241,22 +241,33 @@ foreach(test ${TESTS})
   get_filename_component(TEST_NAME ${test} NAME)
   get_filename_component(TEST_PATH ${test} PATH) 
 
-  # Check serial/parallel
-  if (${MPI_ENABLED})
+  if(NOT $ENV{MEM_CHECK})
 
-    # Preform a parallel test
-    add_test(NAME ${TEST_NAME} 
-      WORKING_DIRECTORY ${TEST_PATH} 
-      COMMAND ${PYTHON_EXECUTABLE} ${TEST_NAME} --exe $<TARGET_FILE:openmc>
-      --mpi_exec $ENV{MPI_DIR}/bin/mpiexec)
+    # Check serial/parallel
+    if (${MPI_ENABLED})
 
-  else(${MPI_ENABLED})
+      # Preform a parallel test
+      add_test(NAME ${TEST_NAME} 
+        WORKING_DIRECTORY ${TEST_PATH} 
+        COMMAND ${PYTHON_EXECUTABLE} ${TEST_NAME} --exe $<TARGET_FILE:openmc>
+        --mpi_exec $ENV{MPI_DIR}/bin/mpiexec)
 
-    # Perform a serial test
-    add_test(NAME ${TEST_NAME} 
+    else(${MPI_ENABLED})
+
+      # Perform a serial test
+      add_test(NAME ${TEST_NAME} 
+        WORKING_DIRECTORY ${TEST_PATH}
+        COMMAND ${PYTHON_EXECUTABLE} ${TEST_NAME} --exe $<TARGET_FILE:openmc>)
+
+    endif(${MPI_ENABLED})
+
+  else(NOT $ENV{MEM_CHECK})
+
+    # Perform serial valgrind test
+    add_test(NAME ${TEST_NAME}
       WORKING_DIRECTORY ${TEST_PATH}
-      COMMAND ${PYTHON_EXECUTABLE} ${TEST_NAME} --exe $<TARGET_FILE:openmc>)
+      COMMAND $<TARGET_FILE:openmc> ${TEST_PATH})
 
-  endif(${MPI_ENABLED})
+  endif(NOT $ENV{MEM_CHECK})
 
 endforeach(test)
diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 44e62b14ba..51d3ce8562 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -28,10 +28,16 @@ set(CTEST_CONFIGURE_COMMAND "${{CMAKE_COMMAND}} -H${{CTEST_SOURCE_DIRECTORY}} -B
 set(CTEST_MEMORYCHECK_COMMAND "/usr/bin/valgrind")
 set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "--tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes --track-origins=yes")
 
+set(MEM_CHECK {mem_check})
+set(ENV{{MEM_CHECK}} ${{MEM_CHECK}})
+
 ctest_start("Nightly")
 ctest_configure()
 ctest_build()
 ctest_test(INCLUDE test_basic)
+if(MEM_CHECK)
+ctest_memcheck(INCLUDE test_basic)
+endif(MEM_CHECK)
 ctest_submit()"""
 
 # Define test data structure
@@ -78,8 +84,8 @@ def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
     tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, valgrind)})
 
 # List of tests
-#add_test('basic-normal')
-add_test('basic-debug', debug=True)
+add_test('basic-normal')
+#add_test('basic-debug', debug=True)
 #add_test('basic-optimize', optimize=True)
 #add_test('omp-normal', openmp=True)
 #add_test('omp-debug', openmp=True, debug=True)
@@ -111,6 +117,7 @@ add_test('basic-debug', debug=True)
 #add_test('omp-phdf5-petsc-normal', openmp=True, mpi=True, hdf5=True, petsc=True)
 #add_test('omp-phdf5-petsc-debug', openmp=True, mpi=True, hdf5=True, petsc=True, debug=True)
 #add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=True, optimize=True)
+add_test('basic-debug_valgrind', debug=True, valgrind=True)
 
 # Setup CTest vars
 pwd = os.environ['PWD']
@@ -128,6 +135,7 @@ for key in iter(tests):
     # Set test specific CTest vars
     ctest_vars.update({'build_name' : test.get_build_name()})
     ctest_vars.update({'build_opts' : test.get_build_opts()})
+    ctest_vars.update({'mem_check'  : test.valgrind})
 
     # Create ctest script
     test.create_ctest_script(ctest_vars)

From c5dfca63eed9520ab5ec57d45b42d21d6c1aa210 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 6 Mar 2014 16:46:19 -0500
Subject: [PATCH 06/43] added coverage options with gcov

---
 src/CMakeLists.txt         | 11 ++++++++---
 tests/run_nightly_tests.py | 27 +++++++++++++++++++--------
 2 files changed, 27 insertions(+), 11 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 21609a4d9a..11f48f1f38 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -17,6 +17,7 @@ option(petsc    "Enable PETSC for use in CMFD acceleration"      OFF)
 option(debug    "Compile with debug flags"                       OFF)
 option(optimize "Turn on all compiler optimization flags"        OFF)
 option(verbose  "Create verbose Makefiles"                       OFF)
+option(coverage "Compile with flags"                             OFF)
 
 if (verbose)
   set(CMAKE_VERBOSE_MAKEFILE on)
@@ -62,6 +63,10 @@ if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
     set(f90flags  "-fopenmp ${f90flags}")
     set(ldflags   "-fopenmp ${ldflags}")
   endif()
+  if(coverage)
+    set(f90flags "-coverage ${f90flags}")
+    set(ldflags  "-coverage ${ldflags}")
+  endif()
 
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
   # Intel Fortran compiler options
@@ -241,7 +246,7 @@ foreach(test ${TESTS})
   get_filename_component(TEST_NAME ${test} NAME)
   get_filename_component(TEST_PATH ${test} PATH) 
 
-  if(NOT $ENV{MEM_CHECK})
+  if(NOT $ENV{MEM_CHECK} AND NOT $ENV{COVERAGE})
 
     # Check serial/parallel
     if (${MPI_ENABLED})
@@ -261,13 +266,13 @@ foreach(test ${TESTS})
 
     endif(${MPI_ENABLED})
 
-  else(NOT $ENV{MEM_CHECK})
+  else(NOT $ENV{MEM_CHECK} AND NOT $ENV{COVERAGE})
 
     # Perform serial valgrind test
     add_test(NAME ${TEST_NAME}
       WORKING_DIRECTORY ${TEST_PATH}
       COMMAND $<TARGET_FILE:openmc> ${TEST_PATH})
 
-  endif(NOT $ENV{MEM_CHECK})
+  endif(NOT $ENV{MEM_CHECK} AND NOT $ENV{COVERAGE})
 
 endforeach(test)
diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 51d3ce8562..8a1bc4e1d8 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -27,17 +27,23 @@ set (CTEST_BUILD_OPTIONS "{build_opts}")
 set(CTEST_CONFIGURE_COMMAND "${{CMAKE_COMMAND}} -H${{CTEST_SOURCE_DIRECTORY}} -B${{CTEST_BINARY_DIRECTORY}} ${{CTEST_BUILD_OPTIONS}}")
 set(CTEST_MEMORYCHECK_COMMAND "/usr/bin/valgrind")
 set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "--tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes --track-origins=yes")
-
 set(MEM_CHECK {mem_check})
 set(ENV{{MEM_CHECK}} ${{MEM_CHECK}})
 
+set(CTEST_COVERAGE_COMMAND "/usr/bin/gcov")
+set(COVERAGE {coverage})
+set(ENV{{COVERAGE}} ${{COVERAGE}})
+
 ctest_start("Nightly")
 ctest_configure()
 ctest_build()
-ctest_test(INCLUDE test_basic)
+ctest_test()
 if(MEM_CHECK)
 ctest_memcheck(INCLUDE test_basic)
 endif(MEM_CHECK)
+if(COVERAGE)
+ctest_coverage()
+endif(COVERAGE)
 ctest_submit()"""
 
 # Define test data structure
@@ -45,7 +51,7 @@ tests = OrderedDict()
 
 class Test(object):
     def __init__(self, name, debug=False, optimize=False, mpi=False, openmp=False,
-                 hdf5=False, petsc=False, valgrind=False):
+                 hdf5=False, petsc=False, valgrind=False, coverage=False):
         self.name = name
         self.debug = debug
         self.optimize = optimize
@@ -54,6 +60,7 @@ class Test(object):
         self.hdf5 = hdf5
         self.petsc = petsc
         self.valgrind = valgrind
+        self.coverage = coverage
 
     def get_build_name(self):
         self.build_name = self.name
@@ -69,6 +76,8 @@ class Test(object):
             build_str += "-Dopenmp=ON "
         if self.petsc:
             build_str += "-Dpetsc=ON "
+        if self.coverage:
+            build_str += "-Dcoverage=ON "
         self.build_opts = build_str
         return self.build_opts
 
@@ -80,11 +89,11 @@ class Test(object):
         call(['ctest', '-S', 'ctestscript.run','-V'])
 
 def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
-             hdf5=False, petsc=False, valgrind=False):
-    tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, valgrind)})
+             hdf5=False, petsc=False, valgrind=False, coverage=False):
+    tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, valgrind, coverage)})
 
 # List of tests
-add_test('basic-normal')
+#add_test('basic-normal')
 #add_test('basic-debug', debug=True)
 #add_test('basic-optimize', optimize=True)
 #add_test('omp-normal', openmp=True)
@@ -117,7 +126,8 @@ add_test('basic-normal')
 #add_test('omp-phdf5-petsc-normal', openmp=True, mpi=True, hdf5=True, petsc=True)
 #add_test('omp-phdf5-petsc-debug', openmp=True, mpi=True, hdf5=True, petsc=True, debug=True)
 #add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=True, optimize=True)
-add_test('basic-debug_valgrind', debug=True, valgrind=True)
+#add_test('basic-debug_valgrind', debug=True, valgrind=True)
+add_test('basic-normal_coverage', coverage=True)
 
 # Setup CTest vars
 pwd = os.environ['PWD']
@@ -136,6 +146,7 @@ for key in iter(tests):
     ctest_vars.update({'build_name' : test.get_build_name()})
     ctest_vars.update({'build_opts' : test.get_build_opts()})
     ctest_vars.update({'mem_check'  : test.valgrind})
+    ctest_vars.update({'coverage'  : test.coverage})
 
     # Create ctest script
     test.create_ctest_script(ctest_vars)
@@ -144,4 +155,4 @@ for key in iter(tests):
     test.run_ctest()
 
     # Clear build directory
-    call(['rm', '-rf', 'build'])
+#   call(['rm', '-rf', 'build'])

From 5391e922a51d6e4e82000b46ff5fd67146042206 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 6 Mar 2014 17:02:31 -0500
Subject: [PATCH 07/43] added compiler options

---
 tests/run_nightly_tests.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 8a1bc4e1d8..318f07233b 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -62,6 +62,17 @@ class Test(object):
         self.valgrind = valgrind
         self.coverage = coverage
 
+        # Check for MPI/HDF5
+        if self.mpi and not self.hdf5:
+            self.fc = MPI_DIR+'/bin/mpif90'
+        elif not self.mpi and self.hdf5:
+            self.fc = HDF5_DIR+'/bin/h5fc'
+        elif self.mpi and self.hdf5:
+            self.fc = PHDF5_DIR+'/bin/h5pfc'
+        else:
+            self.fc = FC_DEFAULT
+        os.environ['FC'] = self.fc
+
     def get_build_name(self):
         self.build_name = self.name
         return self.build_name

From 529d89b1291aa47e83f81f22e12d9279f51b0c44 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 11 Mar 2014 19:01:04 -0400
Subject: [PATCH 08/43] cdash nightly run script active

---
 tests/run_nightly_tests.py | 105 ++++++++++++++++++++++---------------
 1 file changed, 63 insertions(+), 42 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 318f07233b..ab5d4d586c 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -7,6 +7,7 @@ import sys
 import shutil
 from subprocess import call 
 from collections import OrderedDict
+from optparse import OptionParser
 
 # Compiler paths
 FC_DEFAULT='gfortran'
@@ -15,6 +16,14 @@ HDF5_DIR='/opt/hdf5/1.8.12-gnu'
 PHDF5_DIR='/opt/phdf5/1.8.12-gnu'
 PETSC_DIR='/opt/petsc/3.4.3-gnu'
 
+# Command line parsing
+parser = OptionParser()
+parser.add_option("-b", "--branch", dest="branch", default="",
+                  help="branch name for build")
+parser.add_option("-D", "--dashboard", dest="dash", default="Experimental",
+                  help="Dash name -- Experimental, Nightly, Continuous")
+(options, args) = parser.parse_args()
+
 # CTest script template
 ctest_str = """set (CTEST_SOURCE_DIRECTORY "{source_dir}")
 set (CTEST_BINARY_DIRECTORY "{build_dir}")
@@ -26,7 +35,7 @@ set (CTEST_BUILD_OPTIONS "{build_opts}")
 
 set(CTEST_CONFIGURE_COMMAND "${{CMAKE_COMMAND}} -H${{CTEST_SOURCE_DIRECTORY}} -B${{CTEST_BINARY_DIRECTORY}} ${{CTEST_BUILD_OPTIONS}}")
 set(CTEST_MEMORYCHECK_COMMAND "/usr/bin/valgrind")
-set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "--tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes --track-origins=yes")
+set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "--tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes")
 set(MEM_CHECK {mem_check})
 set(ENV{{MEM_CHECK}} ${{MEM_CHECK}})
 
@@ -34,12 +43,14 @@ set(CTEST_COVERAGE_COMMAND "/usr/bin/gcov")
 set(COVERAGE {coverage})
 set(ENV{{COVERAGE}} ${{COVERAGE}})
 
-ctest_start("Nightly")
+ctest_start("{dashboard}")
 ctest_configure()
 ctest_build()
-ctest_test()
 if(MEM_CHECK)
-ctest_memcheck(INCLUDE test_basic)
+ctest_test(START 1 END 67 STRIDE 5 PARALLEL_LEVEL 4)
+ctest_memcheck(START 1 END 67 STRIDE 5)
+else(MEM_CHECK)
+ctest_test(PARALLEL_LEVEL 4)
 endif(MEM_CHECK)
 if(COVERAGE)
 ctest_coverage()
@@ -71,10 +82,9 @@ class Test(object):
             self.fc = PHDF5_DIR+'/bin/h5pfc'
         else:
             self.fc = FC_DEFAULT
-        os.environ['FC'] = self.fc
 
     def get_build_name(self):
-        self.build_name = self.name
+        self.build_name =  options.branch + '_' + self.name
         return self.build_name
 
     def get_build_opts(self):
@@ -97,6 +107,11 @@ class Test(object):
             fh.write(ctest_str.format(**ctest_vars))
 
     def run_ctest(self):
+        os.environ['FC'] = self.fc
+        if self.petsc:
+            os.environ['PETSC_DIR'] = PETSC_DIR
+        if self.mpi:
+            os.environ['MPI_DIR'] = MPI_DIR
         call(['ctest', '-S', 'ctestscript.run','-V'])
 
 def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
@@ -104,48 +119,54 @@ def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
     tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, valgrind, coverage)})
 
 # List of tests
-#add_test('basic-normal')
-#add_test('basic-debug', debug=True)
-#add_test('basic-optimize', optimize=True)
-#add_test('omp-normal', openmp=True)
-#add_test('omp-debug', openmp=True, debug=True)
-#add_test('omp-optimize', openmp=True, optimize=True)
-#add_test('hdf5-normal', hdf5=True)
-#add_test('hdf5-debug', hdf5=True, debug=True)
-#add_test('hdf5-optimize', hdf5=True, optimize=True)
-#add_test('omp-hdf5-normal', openmp=True, hdf5=True)
-#add_test('omp-hdf5-debug', openmp=True, hdf5=True, debug=True)
-#add_test('omp-hdf5-optimize', openmp=True, hdf5=True, optimize=True)
-#add_test('mpi-normal', mpi=True)
-#add_test('mpi-debug', mpi=True, debug=True)
-#add_test('mpi-optimize', mpi=True, optimize=True)
-#add_test('mpi-omp-normal', mpi=True, openmp=True)
-#add_test('mpi-omp-debug', mpi=True, openmp=True, debug=True)
-#add_test('mpi-omp-optimize', mpi=True, openmp=True, optimize=True)
-#add_test('phdf5-normal', mpi=True, hdf5=True)
-#add_test('phdf5-debug', mpi=True, hdf5=True, debug=True)
-#add_test('phdf5-optimize', mpi=True, hdf5=True, optimize=True)
-#add_test('phdf5-omp-normal', mpi=True, hdf5=True, openmp=True)
-#add_test('phdf5-omp-debug', mpi=True, hdf5=True, openmp=True, debug=True)
-#add_test('phdf5-omp-optimize', mpi=True, hdf5=True, openmp=True, optimize=True)
-#add_test('petsc-normal', petsc=True, mpi=True)
-#add_test('petsc-debug', petsc=True, mpi=True, debug=True)
-#add_test('petsc-optimize', petsc=True, mpi=True, optimize=True)
-#add_test('phdf5-petsc-normal', mpi=True, hdf5=True, petsc=True)
-#add_test('phdf5-petsc-debug', mpi=True, hdf5=True, petsc=True, debug=True)
-#add_test('phdf5-petsc-optimize', mpi=True, hdf5=True, petsc=True, optimize=True)
-#add_test('omp-phdf5-petsc-normal', openmp=True, mpi=True, hdf5=True, petsc=True)
-#add_test('omp-phdf5-petsc-debug', openmp=True, mpi=True, hdf5=True, petsc=True, debug=True)
-#add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=True, optimize=True)
-#add_test('basic-debug_valgrind', debug=True, valgrind=True)
+add_test('basic-normal')
+add_test('basic-debug', debug=True)
+add_test('basic-optimize', optimize=True)
+add_test('omp-normal', openmp=True)
+add_test('omp-debug', openmp=True, debug=True)
+add_test('omp-optimize', openmp=True, optimize=True)
+add_test('hdf5-normal', hdf5=True)
+add_test('hdf5-debug', hdf5=True, debug=True)
+add_test('hdf5-optimize', hdf5=True, optimize=True)
+add_test('omp-hdf5-normal', openmp=True, hdf5=True)
+add_test('omp-hdf5-debug', openmp=True, hdf5=True, debug=True)
+add_test('omp-hdf5-optimize', openmp=True, hdf5=True, optimize=True)
+add_test('mpi-normal', mpi=True)
+add_test('mpi-debug', mpi=True, debug=True)
+add_test('mpi-optimize', mpi=True, optimize=True)
+add_test('mpi-omp-normal', mpi=True, openmp=True)
+add_test('mpi-omp-debug', mpi=True, openmp=True, debug=True)
+add_test('mpi-omp-optimize', mpi=True, openmp=True, optimize=True)
+add_test('phdf5-normal', mpi=True, hdf5=True)
+add_test('phdf5-debug', mpi=True, hdf5=True, debug=True)
+add_test('phdf5-optimize', mpi=True, hdf5=True, optimize=True)
+add_test('phdf5-omp-normal', mpi=True, hdf5=True, openmp=True)
+add_test('phdf5-omp-debug', mpi=True, hdf5=True, openmp=True, debug=True)
+add_test('phdf5-omp-optimize', mpi=True, hdf5=True, openmp=True, optimize=True)
+add_test('petsc-normal', petsc=True, mpi=True)
+add_test('petsc-debug', petsc=True, mpi=True, debug=True)
+add_test('petsc-optimize', petsc=True, mpi=True, optimize=True)
+add_test('phdf5-petsc-normal', mpi=True, hdf5=True, petsc=True)
+add_test('phdf5-petsc-debug', mpi=True, hdf5=True, petsc=True, debug=True)
+add_test('phdf5-petsc-optimize', mpi=True, hdf5=True, petsc=True, optimize=True)
+add_test('omp-phdf5-petsc-normal', openmp=True, mpi=True, hdf5=True, petsc=True)
+add_test('omp-phdf5-petsc-debug', openmp=True, mpi=True, hdf5=True, petsc=True, debug=True)
+add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=True, optimize=True)
+add_test('basic-debug_valgrind', debug=True, valgrind=True)
+add_test('hdf5-debug_valgrind', hdf5=True, debug=True, valgrind=True)
+add_test('petsc-debug_valgrind', petsc=True, debug=True, valgrind=True)
 add_test('basic-normal_coverage', coverage=True)
+add_test('hdf5-normal_coverage', hdf5=True, coverage=True)
+add_test('mpi-normal_coverage', mpi=True, coverage=True)
+add_test('petsc-normal_coverage', petsc=True, mpi=True, coverage=True)
 
 # Setup CTest vars
 pwd = os.environ['PWD']
 ctest_vars = {
 'source_dir' : pwd + '/../src',
 'build_dir' :  pwd + '/build',
-'host_name' : 'bryan laptop'
+'host_name' : 'neutronbalance',
+'dashboard' : options.dash
 }
 
 # Begin testing
@@ -166,4 +187,4 @@ for key in iter(tests):
     test.run_ctest()
 
     # Clear build directory
-#   call(['rm', '-rf', 'build'])
+    call(['rm', '-rf', 'build'])

From 7de662d92096e9852de1af389a3e23c2fa0b088c Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 11 Mar 2014 19:09:11 -0400
Subject: [PATCH 09/43] Updated run nightly tests with cleanup script

---
 src/CTestConfig.cmake      | 2 +-
 tests/run_nightly_tests.py | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/CTestConfig.cmake b/src/CTestConfig.cmake
index fa3c21d29a..f8aa74b7d4 100644
--- a/src/CTestConfig.cmake
+++ b/src/CTestConfig.cmake
@@ -5,7 +5,7 @@
 ##   ENABLE_TESTING()
 ##   INCLUDE(CTest)
 set(CTEST_PROJECT_NAME "OpenMC")
-set(CTEST_NIGHTLY_START_TIME "05:00:00 UTC")
+set(CTEST_NIGHTLY_START_TIME "03:00:00 UTC")
 
 set(CTEST_DROP_METHOD "http")
 set(CTEST_DROP_SITE "neutronbalance.mit.edu")
diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index ab5d4d586c..8682209924 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -171,6 +171,8 @@ ctest_vars = {
 
 # Begin testing
 call(['rm', '-rf', 'build'])
+call(['rm', '-rf', 'ctestscript.run'])
+call(['./cleanup'])
 for key in iter(tests):
     test = tests[key]
 
@@ -188,3 +190,5 @@ for key in iter(tests):
 
     # Clear build directory
     call(['rm', '-rf', 'build'])
+    call(['rm', '-rf', 'ctestscript.run'])
+    call(['./cleanup'])

From f31051c63e2b837b85a82e9d12956bbb71d664f3 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Wed, 12 Mar 2014 09:59:41 -0400
Subject: [PATCH 10/43] CTest now updates from github repo

---
 tests/run_nightly_tests.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 8682209924..4162545b12 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -33,6 +33,8 @@ set (CTEST_BUILD_NAME "{build_name}")
 set (CTEST_CMAKE_GENERATOR "Unix Makefiles")
 set (CTEST_BUILD_OPTIONS "{build_opts}")
 
+set(CTEST_UPDATE_COMMAND "git")
+
 set(CTEST_CONFIGURE_COMMAND "${{CMAKE_COMMAND}} -H${{CTEST_SOURCE_DIRECTORY}} -B${{CTEST_BINARY_DIRECTORY}} ${{CTEST_BUILD_OPTIONS}}")
 set(CTEST_MEMORYCHECK_COMMAND "/usr/bin/valgrind")
 set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "--tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes")
@@ -45,6 +47,7 @@ set(ENV{{COVERAGE}} ${{COVERAGE}})
 
 ctest_start("{dashboard}")
 ctest_configure()
+ctest_update()
 ctest_build()
 if(MEM_CHECK)
 ctest_test(START 1 END 67 STRIDE 5 PARALLEL_LEVEL 4)

From b9f96e6fa2533a3b2b5483a234c983e73763c0e9 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Wed, 12 Mar 2014 14:50:50 -0400
Subject: [PATCH 11/43] MEM_CHECK and COVERAGE env vars are now checked before
 using

---
 src/CMakeLists.txt | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index a57fdaa4d3..8da7f0a2dc 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -236,6 +236,18 @@ if (NOT ${PETSC_ENABLED})
   endforeach(cmfd_test)
 endif(NOT ${PETSC_ENABLED})
 
+# Check for MEM_CHECK and COVERAGE variables
+if (DEFINED $ENV{MEM_CHECK})
+  set(MEM_CHECK $ENV{MEM_CHECK})
+else(DEFINED $ENV{MEM_CHECK})
+  set(MEM_CHECK FALSE)
+endif(DEFINED $ENV{MEM_CHECK})
+if (DEFINED $ENV{COVERAGE})
+  set(COVERAGE $ENV{COVERAGE})
+else(DEFINED $ENV{COVERAGE})
+  set(COVERAGE FALSE)
+endif(DEFINED $ENV{COVERAGE})
+
 # Loop through all the tests
 foreach(test ${TESTS})
 
@@ -243,7 +255,7 @@ foreach(test ${TESTS})
   get_filename_component(TEST_NAME ${test} NAME)
   get_filename_component(TEST_PATH ${test} PATH) 
 
-  if(NOT $ENV{MEM_CHECK} AND NOT $ENV{COVERAGE})
+  if(NOT ${MEM_CHECK} AND NOT ${COVERAGE})
 
     # Check serial/parallel
     if (${MPI_ENABLED})
@@ -263,13 +275,13 @@ foreach(test ${TESTS})
 
     endif(${MPI_ENABLED})
 
-  else(NOT $ENV{MEM_CHECK} AND NOT $ENV{COVERAGE})
+  else(NOT ${MEM_CHECK} AND NOT ${COVERAGE})
 
     # Perform serial valgrind test
     add_test(NAME ${TEST_NAME}
       WORKING_DIRECTORY ${TEST_PATH}
       COMMAND $<TARGET_FILE:openmc> ${TEST_PATH})
 
-  endif(NOT $ENV{MEM_CHECK} AND NOT $ENV{COVERAGE})
+  endif(NOT ${MEM_CHECK} AND NOT ${COVERAGE})
 
 endforeach(test)

From b9063468636841838ef51a9cbe7e5ea81aeeeb83 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Wed, 12 Mar 2014 16:43:59 -0400
Subject: [PATCH 12/43] fixed checking environmental vars for valgrind or
 coverage runs

---
 src/CMakeLists.txt | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 8da7f0a2dc..0b33a9ce0f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -237,16 +237,16 @@ if (NOT ${PETSC_ENABLED})
 endif(NOT ${PETSC_ENABLED})
 
 # Check for MEM_CHECK and COVERAGE variables
-if (DEFINED $ENV{MEM_CHECK})
+if (DEFINED ENV{MEM_CHECK})
   set(MEM_CHECK $ENV{MEM_CHECK})
-else(DEFINED $ENV{MEM_CHECK})
+else(DEFINED ENV{MEM_CHECK})
   set(MEM_CHECK FALSE)
-endif(DEFINED $ENV{MEM_CHECK})
-if (DEFINED $ENV{COVERAGE})
+endif(DEFINED ENV{MEM_CHECK})
+if (DEFINED ENV{COVERAGE})
   set(COVERAGE $ENV{COVERAGE})
-else(DEFINED $ENV{COVERAGE})
+else(DEFINED ENV{COVERAGE})
   set(COVERAGE FALSE)
-endif(DEFINED $ENV{COVERAGE})
+endif(DEFINED ENV{COVERAGE})
 
 # Loop through all the tests
 foreach(test ${TESTS})

From 3a91c11c6b6009167b3f2a46a41db37ba7e767ef Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Wed, 12 Mar 2014 16:44:56 -0400
Subject: [PATCH 13/43] specified tests to be executed for memcheck

---
 tests/run_nightly_tests.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 4162545b12..59dfa321cc 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -45,13 +45,15 @@ set(CTEST_COVERAGE_COMMAND "/usr/bin/gcov")
 set(COVERAGE {coverage})
 set(ENV{{COVERAGE}} ${{COVERAGE}})
 
+set(INCLUDED_TESTS "basic|cmfd_feed|confidence_intervals|density_atombcm|eigenvalue_genperbatch|energy_grid|entropy|filter_cell|lattice_multiple|output|reflective_plane|rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono|sourcepoint_batch|statepoint_interval|survival_biasing|tally_assumesep|translation|uniform_fs|universe|void")
+
 ctest_start("{dashboard}")
 ctest_configure()
 ctest_update()
 ctest_build()
 if(MEM_CHECK)
-ctest_test(START 1 END 67 STRIDE 5 PARALLEL_LEVEL 4)
-ctest_memcheck(START 1 END 67 STRIDE 5)
+ctest_test(INCLUDE ${{INCLUDED_TESTS}} PARALLEL_LEVEL 4)
+ctest_memcheck(INCLUDE ${{INCLUDED_TESTS}})
 else(MEM_CHECK)
 ctest_test(PARALLEL_LEVEL 4)
 endif(MEM_CHECK)

From e09530a8778f7fadf3c6288ced8ba096e41d1899 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 13 Mar 2014 09:52:35 -0400
Subject: [PATCH 14/43] petsc valgrind test needs mpi true

---
 tests/run_nightly_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 59dfa321cc..f5ca64adc9 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -159,7 +159,7 @@ add_test('omp-phdf5-petsc-debug', openmp=True, mpi=True, hdf5=True, petsc=True,
 add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=True, optimize=True)
 add_test('basic-debug_valgrind', debug=True, valgrind=True)
 add_test('hdf5-debug_valgrind', hdf5=True, debug=True, valgrind=True)
-add_test('petsc-debug_valgrind', petsc=True, debug=True, valgrind=True)
+add_test('petsc-debug_valgrind', petsc=True, mpi=True, debug=True, valgrind=True)
 add_test('basic-normal_coverage', coverage=True)
 add_test('hdf5-normal_coverage', hdf5=True, coverage=True)
 add_test('mpi-normal_coverage', mpi=True, coverage=True)

From 85804eca295172f9002e9f725fa81fccc447347d Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 1 Apr 2014 17:38:20 -0400
Subject: [PATCH 15/43] coverage tests are performed in debug mode

---
 tests/run_nightly_tests.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index f5ca64adc9..fdeeb26972 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -160,10 +160,10 @@ add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=Tru
 add_test('basic-debug_valgrind', debug=True, valgrind=True)
 add_test('hdf5-debug_valgrind', hdf5=True, debug=True, valgrind=True)
 add_test('petsc-debug_valgrind', petsc=True, mpi=True, debug=True, valgrind=True)
-add_test('basic-normal_coverage', coverage=True)
-add_test('hdf5-normal_coverage', hdf5=True, coverage=True)
-add_test('mpi-normal_coverage', mpi=True, coverage=True)
-add_test('petsc-normal_coverage', petsc=True, mpi=True, coverage=True)
+add_test('basic-debug_coverage', debug=True, coverage=True)
+add_test('hdf5-debug_coverage', debug=True, hdf5=True, coverage=True)
+add_test('mpi-debug_coverage', debug=True, mpi=True, coverage=True)
+add_test('petsc-debug_coverage', debug=True, petsc=True, mpi=True, coverage=True)
 
 # Setup CTest vars
 pwd = os.environ['PWD']

From 5c284be28bdda20dd1bf28feb47221435697d8b6 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Wed, 2 Apr 2014 08:31:16 -0400
Subject: [PATCH 16/43] raised limit of output data to show on CDash

---
 src/CTestConfig.cmake | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/CTestConfig.cmake b/src/CTestConfig.cmake
index f8aa74b7d4..6ae35bae56 100644
--- a/src/CTestConfig.cmake
+++ b/src/CTestConfig.cmake
@@ -11,3 +11,5 @@ set(CTEST_DROP_METHOD "http")
 set(CTEST_DROP_SITE "neutronbalance.mit.edu")
 set(CTEST_DROP_LOCATION "/CDash/submit.php?project=OpenMC")
 set(CTEST_DROP_SITE_CDASH TRUE)
+SET(CTEST_CUSTOM_MAXIMUM_FAILED_TEST_OUTPUT_SIZE "20000")
+SET(CTEST_CUSTOM_MAXIMUM_PASSED_TEST_OUTPUT_SIZE "20000")

From e215dc2107fac4d344257e585c5f8c1861026ec2 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Wed, 2 Apr 2014 16:01:56 -0400
Subject: [PATCH 17/43] added special case for plot tests and restart tests

---
 src/CMakeLists.txt         | 72 +++++++++++++++++++++++++++++++++++---
 tests/run_nightly_tests.py |  2 +-
 2 files changed, 69 insertions(+), 5 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 0b33a9ce0f..45e98f7beb 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -28,6 +28,7 @@ endif()
 #===============================================================================
 
 set(MPI_ENABLED FALSE)
+set(HDF5_ENABLED FALSE)
 if($ENV{FC} MATCHES "mpi.*")
   message("-- Detected MPI wrapper: $ENV{FC}")
   add_definitions(-DMPI)
@@ -35,10 +36,12 @@ if($ENV{FC} MATCHES "mpi.*")
 elseif($ENV{FC} MATCHES "h5fc$")
   message("-- Detected HDF5 wrapper: $ENV{FC}")
   add_definitions(-DHDF5)
+  set(HDF5_ENABLED TRUE)
 elseif($ENV{FC} MATCHES "h5pfc$")
   message("-- Detected parallel HDF5 wrapper: $ENV{FC}")
   add_definitions(-DMPI -DHDF5)
   set(MPI_ENABLED TRUE)
+  set(HDF5_ENABLED TRUE)
 endif()
 
 #===============================================================================
@@ -255,6 +258,7 @@ foreach(test ${TESTS})
   get_filename_component(TEST_NAME ${test} NAME)
   get_filename_component(TEST_PATH ${test} PATH) 
 
+  # Check for running standard tests (no valgrind, no gcov)
   if(NOT ${MEM_CHECK} AND NOT ${COVERAGE})
 
     # Check serial/parallel
@@ -275,12 +279,72 @@ foreach(test ${TESTS})
 
     endif(${MPI_ENABLED})
 
+  # Handle special case for valgrind and gcov (run openmc directly, no python)
   else(NOT ${MEM_CHECK} AND NOT ${COVERAGE})
 
-    # Perform serial valgrind test
-    add_test(NAME ${TEST_NAME}
-      WORKING_DIRECTORY ${TEST_PATH}
-      COMMAND $<TARGET_FILE:openmc> ${TEST_PATH})
+    # If a plot test is encountered, run with "-p"
+    if (${test} MATCHES "test_plot")
+
+      # Perform serial valgrind and coverage test with plot flag
+      add_test(NAME ${TEST_NAME}
+        WORKING_DIRECTORY ${TEST_PATH}
+        COMMAND $<TARGET_FILE:openmc> -p ${TEST_PATH})
+
+    # If a restart test is encounted, need to run with -r and restart file(s)
+    elseif(${test} MATCHES "restart")
+
+      # Set restart file names
+      if (${HDF5_ENABLED})
+
+        # Handle restart tests separately
+        if(${test} MATCHES "test_statepoint_restart")
+          set(RESTART_FILE statepoint.7.h5)
+        elseif(${test} MATCHES "test_sourcepoint_restart")
+          set(RESTART_FILE statepoint.7.h5 sourcepoint.7.h5)
+        elseif(${test} MATCHES "test_particle_restart")
+          set(RESTART_FILE particle_10_394.h5)
+        else(${test} MATCHES "test_statepoint_restart")
+          message(FATAL_ERROR "Restart test ${test} not recognized")
+        endif(${test} MATCHES "test_statepoint_restart")
+
+      else(${HDF5_ENABLED})
+
+        # Handle restart tests separately
+        if(${test} MATCHES "test_statepoint_restart")
+          set(RESTART_FILE statepoint.7.binary)
+        elseif(${test} MATCHES "test_sourcepoint_restart")
+          set(RESTART_FILE statepoint.7.binary source.7.binary)
+        elseif(${test} MATCHES "test_particle_restart")
+          set(RESTART_FILE particle_10_394.binary)
+        else(${test} MATCHES "test_statepoint_restart")
+          message(FATAL_ERROR "Restart test ${test} not recognized")
+        endif(${test} MATCHES "test_statepoint_restart")
+
+      endif(${HDF5_ENABLED})
+
+      # Perform serial valgrind and coverage test
+      add_test(NAME ${TEST_NAME}
+        WORKING_DIRECTORY ${TEST_PATH}
+        COMMAND $<TARGET_FILE:openmc> ${TEST_PATH})
+
+      # Perform serial valgrind and coverage restart test
+      add_test(NAME ${TEST_NAME}_restart
+        WORKING_DIRECTORY ${TEST_PATH}
+        COMMAND $<TARGET_FILE:openmc> -r ${RESTART_FILE} ${TEST_PATH})
+
+      # Set test dependency
+      set_tests_properties(${TEST_NAME}_restart PROPERTIES DEPENDS ${TEST_NAME})
+
+
+    # Handle standard tests for valgrind and gcov
+    else(${test} MATCHES "test_plot")
+
+      # Perform serial valgrind and coverage test
+      add_test(NAME ${TEST_NAME}
+        WORKING_DIRECTORY ${TEST_PATH}
+        COMMAND $<TARGET_FILE:openmc> ${TEST_PATH})
+
+    endif(${test} MATCHES "test_plot")
 
   endif(NOT ${MEM_CHECK} AND NOT ${COVERAGE})
 
diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index fdeeb26972..bd6f5a779c 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -45,7 +45,7 @@ set(CTEST_COVERAGE_COMMAND "/usr/bin/gcov")
 set(COVERAGE {coverage})
 set(ENV{{COVERAGE}} ${{COVERAGE}})
 
-set(INCLUDED_TESTS "basic|cmfd_feed|confidence_intervals|density_atombcm|eigenvalue_genperbatch|energy_grid|entropy|filter_cell|lattice_multiple|output|reflective_plane|rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono|sourcepoint_batch|statepoint_interval|survival_biasing|tally_assumesep|translation|uniform_fs|universe|void")
+set(INCLUDED_TESTS "basic|cmfd_feed|confidence_intervals|density_atombcm|eigenvalue_genperbatch|energy_grid|entropy|filter_cell|lattice_multiple|output|plot_background|reflective_plane|rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono|sourcepoint_batch|statepoint_interval|survival_biasing|tally_assumesep|translation|uniform_fs|universe|void")
 
 ctest_start("{dashboard}")
 ctest_configure()

From 284ff606c9096856ce8236689d0d4ef1a5fbfd80 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 08:20:31 -0400
Subject: [PATCH 18/43] added ppm files for cleanup

---
 tests/cleanup | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/cleanup b/tests/cleanup
index 288c81025b..7b81d2d9dd 100755
--- a/tests/cleanup
+++ b/tests/cleanup
@@ -7,4 +7,4 @@
 # deleting left over binary files. This will
 # cause an assertion error in some of the 
 # tests.
-find . \( -name "*.binary" -o -name "*.h5" \) -exec rm -f {} \;
+find . \( -name "*.binary" -o -name "*.h5" -o -name "*.ppm" \) -exec rm -f {} \;

From bfd13779939a6ae7444382c204c0604eb80606c1 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 08:21:20 -0400
Subject: [PATCH 19/43] changed sourcepoint to source

---
 src/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 45e98f7beb..93832e8c69 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -300,7 +300,7 @@ foreach(test ${TESTS})
         if(${test} MATCHES "test_statepoint_restart")
           set(RESTART_FILE statepoint.7.h5)
         elseif(${test} MATCHES "test_sourcepoint_restart")
-          set(RESTART_FILE statepoint.7.h5 sourcepoint.7.h5)
+          set(RESTART_FILE statepoint.7.h5 source.7.h5)
         elseif(${test} MATCHES "test_particle_restart")
           set(RESTART_FILE particle_10_394.h5)
         else(${test} MATCHES "test_statepoint_restart")

From 2f9c6a8ae82eccc41667806784fcf7cb40345df4 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 22:16:20 -0400
Subject: [PATCH 20/43] added more command line control

---
 tests/run_nightly_tests.py | 78 ++++++++++++++++++++++++++++++++------
 1 file changed, 67 insertions(+), 11 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index bd6f5a779c..0f84a535c9 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -3,8 +3,8 @@
 from __future__ import print_function
 
 import os
-import sys
 import shutil
+import re
 from subprocess import call 
 from collections import OrderedDict
 from optparse import OptionParser
@@ -18,6 +18,20 @@ PETSC_DIR='/opt/petsc/3.4.3-gnu'
 
 # Command line parsing
 parser = OptionParser()
+parser.add_option('-j', '--parallel', dest='n_procs', default='1',
+                  help="Number of parallel jobs.")
+parser.add_option('-R', '--tests-regex', dest='regex_tests',
+                  help="Run tests matching regular expression. \
+                  Test names are the directories present in tests folder.\
+                  This uses standard regex syntax to select tests.")
+parser.add_option('-C', '--build-config', dest='build_config',
+                  help="Build configurations matching regular expression. \
+                        Specific build configurations can be printed out with \
+                        optional argument -p, --print. This uses standard \
+                        regex syntax to select build configurations.")
+parser.add_option('-p', '--print', action="store_true", 
+                  dest="print_build_configs", default=False,
+                  help="Print out build configurations.")
 parser.add_option("-b", "--branch", dest="branch", default="",
                   help="branch name for build")
 parser.add_option("-D", "--dashboard", dest="dash", default="Experimental",
@@ -45,17 +59,15 @@ set(CTEST_COVERAGE_COMMAND "/usr/bin/gcov")
 set(COVERAGE {coverage})
 set(ENV{{COVERAGE}} ${{COVERAGE}})
 
-set(INCLUDED_TESTS "basic|cmfd_feed|confidence_intervals|density_atombcm|eigenvalue_genperbatch|energy_grid|entropy|filter_cell|lattice_multiple|output|plot_background|reflective_plane|rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono|sourcepoint_batch|statepoint_interval|survival_biasing|tally_assumesep|translation|uniform_fs|universe|void")
-
 ctest_start("{dashboard}")
 ctest_configure()
 ctest_update()
 ctest_build()
 if(MEM_CHECK)
-ctest_test(INCLUDE ${{INCLUDED_TESTS}} PARALLEL_LEVEL 4)
-ctest_memcheck(INCLUDE ${{INCLUDED_TESTS}})
+ctest_test({tests} PARALLEL_LEVEL {n_procs})
+ctest_memcheck({tests})
 else(MEM_CHECK)
-ctest_test(PARALLEL_LEVEL 4)
+ctest_test({tests} PARALLEL_LEVEL {n_procs})
 endif(MEM_CHECK)
 if(COVERAGE)
 ctest_coverage()
@@ -165,18 +177,48 @@ add_test('hdf5-debug_coverage', debug=True, hdf5=True, coverage=True)
 add_test('mpi-debug_coverage', debug=True, mpi=True, coverage=True)
 add_test('petsc-debug_coverage', debug=True, petsc=True, mpi=True, coverage=True)
 
+# Check to see if we are to just print build configuratinos
+if options.print_build_configs:
+    for key in tests:
+        print('Configuration Name: {0}'.format(key))
+        print('  Debug Flags:..........{0}'.format(tests[key].debug))
+        print('  Optimization Flags:...{0}'.format(tests[key].optimize))
+        print('  HDF5 Active:..........{0}'.format(tests[key].hdf5))
+        print('  MPI Active:...........{0}'.format(tests[key].mpi))
+        print('  OpenMP Active:........{0}'.format(tests[key].openmp))
+        print('  PETSc Active:.........{0}'.format(tests[key].petsc))
+        print('  Valgrind Test:........{0}'.format(tests[key].valgrind))
+        print('  Coverage Test:........{0}\n'.format(tests[key].coverage))
+    exit()
+
+# Delete items of dictionary that don't match regular expression
+if options.build_config is not None:
+    for key in tests:
+        if not re.search(options.build_config, key):
+            del tests[key]
+
 # Setup CTest vars
 pwd = os.environ['PWD']
 ctest_vars = {
 'source_dir' : pwd + '/../src',
 'build_dir' :  pwd + '/build',
 'host_name' : 'neutronbalance',
-'dashboard' : options.dash
+'dashboard' : options.dash,
+'n_procs'   : options.n_procs
 }
 
+# Set up default valgrind tests
+# Currently takes too long to run all the tests with valgrind
+valgrind_default_tests = "basic|cmfd_feed|confidence_intervals| \
+    density_atombcm|eigenvalue_genperbatch|energy_grid|entropy| \
+    filter_cell|lattice_multiple|output|plot_background|reflective_plane| \
+    rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono| \
+    sourcepoint_batch|statepoint_interval|survival_biasing| \
+    tally_assumesep|translation|uniform_fs|universe|void"
+
 # Begin testing
-call(['rm', '-rf', 'build'])
-call(['rm', '-rf', 'ctestscript.run'])
+shutils.rmtree('build', ignore_errors=True)
+os.remove('ctestscript.run')
 call(['./cleanup'])
 for key in iter(tests):
     test = tests[key]
@@ -187,6 +229,20 @@ for key in iter(tests):
     ctest_vars.update({'mem_check'  : test.valgrind})
     ctest_vars.update({'coverage'  : test.coverage})
 
+    # Check for user custom tests
+    # INCLUDE is a CTest command that allows for a subset
+    # of tests to be executed.
+    if options.regex_tests is None:
+        ctest_vars.update({'tests' : ''})
+
+        # No user tests, use default valgrind tests
+        if test.valgrind:
+            ctest_vars.update({'tests' : 'INCLUDE {0}'.
+                              format(valgrind_default_tests)})
+    else:
+        ctest_vars.update({'tests' : 'INCLUDE {0}'.
+                          format(options.regex_tests)})
+
     # Create ctest script
     test.create_ctest_script(ctest_vars)
 
@@ -194,6 +250,6 @@ for key in iter(tests):
     test.run_ctest()
 
     # Clear build directory
-    call(['rm', '-rf', 'build'])
-    call(['rm', '-rf', 'ctestscript.run'])
+    shutils.rmtree('build', ignore_errors=True)
+    os.remove('ctestscript.run')
     call(['./cleanup'])

From a8e046e896100aac1d17fddef790ce0273b81a39 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 22:17:05 -0400
Subject: [PATCH 21/43] changed shutils to shutil

---
 tests/run_nightly_tests.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 0f84a535c9..91dbdabfd4 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -217,7 +217,7 @@ valgrind_default_tests = "basic|cmfd_feed|confidence_intervals| \
     tally_assumesep|translation|uniform_fs|universe|void"
 
 # Begin testing
-shutils.rmtree('build', ignore_errors=True)
+shutil.rmtree('build', ignore_errors=True)
 os.remove('ctestscript.run')
 call(['./cleanup'])
 for key in iter(tests):
@@ -250,6 +250,6 @@ for key in iter(tests):
     test.run_ctest()
 
     # Clear build directory
-    shutils.rmtree('build', ignore_errors=True)
+    shutil.rmtree('build', ignore_errors=True)
     os.remove('ctestscript.run')
     call(['./cleanup'])

From a786082f7650ff9c2b010ad66212c40086afe3d4 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 22:20:44 -0400
Subject: [PATCH 22/43] dont need to remove ctest script at the beginning

---
 tests/run_nightly_tests.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 91dbdabfd4..4170521ae7 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -218,7 +218,6 @@ valgrind_default_tests = "basic|cmfd_feed|confidence_intervals| \
 
 # Begin testing
 shutil.rmtree('build', ignore_errors=True)
-os.remove('ctestscript.run')
 call(['./cleanup'])
 for key in iter(tests):
     test = tests[key]

From 0538a48fd0653631f6de8d8a16ef4f18c60d0d96 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 22:22:09 -0400
Subject: [PATCH 23/43] removed spaces in valgrind default tests

---
 tests/run_nightly_tests.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 4170521ae7..50ee0e75bc 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -210,11 +210,11 @@ ctest_vars = {
 # Set up default valgrind tests
 # Currently takes too long to run all the tests with valgrind
 valgrind_default_tests = "basic|cmfd_feed|confidence_intervals| \
-    density_atombcm|eigenvalue_genperbatch|energy_grid|entropy| \
-    filter_cell|lattice_multiple|output|plot_background|reflective_plane| \
-    rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono| \
-    sourcepoint_batch|statepoint_interval|survival_biasing| \
-    tally_assumesep|translation|uniform_fs|universe|void"
+density_atombcm|eigenvalue_genperbatch|energy_grid|entropy| \
+filter_cell|lattice_multiple|output|plot_background|reflective_plane| \
+rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono| \
+sourcepoint_batch|statepoint_interval|survival_biasing| \
+tally_assumesep|translation|uniform_fs|universe|void"
 
 # Begin testing
 shutil.rmtree('build', ignore_errors=True)

From 67a4092495536d09b6d688a242a89e86cfba4395 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 22:23:28 -0400
Subject: [PATCH 24/43] removed more spaces in valgrind default tests

---
 tests/run_nightly_tests.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 50ee0e75bc..f9d376da54 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -209,11 +209,11 @@ ctest_vars = {
 
 # Set up default valgrind tests
 # Currently takes too long to run all the tests with valgrind
-valgrind_default_tests = "basic|cmfd_feed|confidence_intervals| \
-density_atombcm|eigenvalue_genperbatch|energy_grid|entropy| \
-filter_cell|lattice_multiple|output|plot_background|reflective_plane| \
-rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono| \
-sourcepoint_batch|statepoint_interval|survival_biasing| \
+valgrind_default_tests = "basic|cmfd_feed|confidence_intervals|\
+density_atombcm|eigenvalue_genperbatch|energy_grid|entropy|\
+filter_cell|lattice_multiple|output|plot_background|reflective_plane|\
+rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono|\
+sourcepoint_batch|statepoint_interval|survival_biasing|\
 tally_assumesep|translation|uniform_fs|universe|void"
 
 # Begin testing

From 3fd2b1269510f4d50e0e9acb9c68cb5f1ac28080 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 22:24:55 -0400
Subject: [PATCH 25/43] removed redundant ctest call

---
 tests/run_nightly_tests.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index f9d376da54..b401271a04 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -63,11 +63,9 @@ ctest_start("{dashboard}")
 ctest_configure()
 ctest_update()
 ctest_build()
+ctest_test({tests} PARALLEL_LEVEL {n_procs})
 if(MEM_CHECK)
-ctest_test({tests} PARALLEL_LEVEL {n_procs})
 ctest_memcheck({tests})
-else(MEM_CHECK)
-ctest_test({tests} PARALLEL_LEVEL {n_procs})
 endif(MEM_CHECK)
 if(COVERAGE)
 ctest_coverage()

From ee7e099ef5c6a837a8985ef4e974e37994451c2b Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 22:38:11 -0400
Subject: [PATCH 26/43] added default option to not submit tests to CDash
 server

---
 tests/run_nightly_tests.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index b401271a04..597c0e9da3 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -34,7 +34,7 @@ parser.add_option('-p', '--print', action="store_true",
                   help="Print out build configurations.")
 parser.add_option("-b", "--branch", dest="branch", default="",
                   help="branch name for build")
-parser.add_option("-D", "--dashboard", dest="dash", default="Experimental",
+parser.add_option("-D", "--dashboard", dest="dash",
                   help="Dash name -- Experimental, Nightly, Continuous")
 (options, args) = parser.parse_args()
 
@@ -70,7 +70,7 @@ endif(MEM_CHECK)
 if(COVERAGE)
 ctest_coverage()
 endif(COVERAGE)
-ctest_submit()"""
+{submit}"""
 
 # Define test data structure
 tests = OrderedDict()
@@ -195,13 +195,22 @@ if options.build_config is not None:
         if not re.search(options.build_config, key):
             del tests[key]
 
+# Check for dashboard and determine whether to push results to server
+if options.dash is None:
+    dash = 'Experimental'
+    submit = ''
+else
+    dash = options.dash
+    submit = 'ctest_submit()'
+
 # Setup CTest vars
 pwd = os.environ['PWD']
 ctest_vars = {
 'source_dir' : pwd + '/../src',
 'build_dir' :  pwd + '/build',
 'host_name' : 'neutronbalance',
-'dashboard' : options.dash,
+'dashboard' : dash,
+'submit'    : submit,
 'n_procs'   : options.n_procs
 }
 

From f6ffb8e42f0bb8ac36525a76cbbab3765d545f4a Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 3 Apr 2014 22:38:50 -0400
Subject: [PATCH 27/43] fixed python syntax

---
 tests/run_nightly_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 597c0e9da3..c78c6763fa 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -199,7 +199,7 @@ if options.build_config is not None:
 if options.dash is None:
     dash = 'Experimental'
     submit = ''
-else
+else:
     dash = options.dash
     submit = 'ctest_submit()'
 

From a1de0675feb1b9a5e6bf26e4a2d6cd242349c3a4 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 8 Apr 2014 14:33:12 -0400
Subject: [PATCH 28/43] added environ vars

---
 tests/run_nightly_tests.py | 28 +++++++++++++++++++++-------
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index c78c6763fa..c025dd5e18 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -9,13 +9,6 @@ from subprocess import call
 from collections import OrderedDict
 from optparse import OptionParser
 
-# Compiler paths
-FC_DEFAULT='gfortran'
-MPI_DIR='/opt/mpich/3.0.4-gnu'
-HDF5_DIR='/opt/hdf5/1.8.12-gnu'
-PHDF5_DIR='/opt/phdf5/1.8.12-gnu'
-PETSC_DIR='/opt/petsc/3.4.3-gnu'
-
 # Command line parsing
 parser = OptionParser()
 parser.add_option('-j', '--parallel', dest='n_procs', default='1',
@@ -38,6 +31,27 @@ parser.add_option("-D", "--dashboard", dest="dash",
                   help="Dash name -- Experimental, Nightly, Continuous")
 (options, args) = parser.parse_args()
 
+# Compiler paths
+FC_DEFAULT='gfortran'
+MPI_DIR='/opt/mpich/3.0.4-gnu'
+HDF5_DIR='/opt/hdf5/1.8.12-gnu'
+PHDF5_DIR='/opt/phdf5/1.8.12-gnu'
+PETSC_DIR='/opt/petsc/3.4.3-gnu'
+
+# Override default compiler paths if environmental vars are found
+if os.environ.has_key('FC'):
+    FC = os.environ['FC']
+    if FC is not 'gfortran':
+        print('NOTE: Test suite only verifed for gfortran compiler.')
+if os.environ.has_key('MPI_DIR'):
+    MPI_DIR = os.environ['MPI_DIR']
+if os.environ.has_key('HDF5_DIR'):
+    HDF5_DIR = os.environ['HDF5_DIR']
+if os.environ.has_key('PHDF5_DIR'):
+    PHDF5_DIR = os.environ['PHDF5_DIR']
+if os.environ.has_key('PETSC_DIR'):
+    PETSC_DIR = os.environ['PETSC_DIR']
+
 # CTest script template
 ctest_str = """set (CTEST_SOURCE_DIRECTORY "{source_dir}")
 set (CTEST_BINARY_DIRECTORY "{build_dir}")

From 549a05f62ee382858bb6a066c97decfdfa007edd Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 8 Apr 2014 14:40:25 -0400
Subject: [PATCH 29/43] added option for updating repo

---
 tests/run_nightly_tests.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index c025dd5e18..dcd4636a8b 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -29,6 +29,9 @@ parser.add_option("-b", "--branch", dest="branch", default="",
                   help="branch name for build")
 parser.add_option("-D", "--dashboard", dest="dash",
                   help="Dash name -- Experimental, Nightly, Continuous")
+parser.add_option("-u", "--update", action="store_true", dest="update",
+                  help="Allow CTest to update repo. (WARNING: may overwrite\
+                        changes that were not pushed.")
 (options, args) = parser.parse_args()
 
 # Compiler paths
@@ -75,7 +78,7 @@ set(ENV{{COVERAGE}} ${{COVERAGE}})
 
 ctest_start("{dashboard}")
 ctest_configure()
-ctest_update()
+{update}
 ctest_build()
 ctest_test({tests} PARALLEL_LEVEL {n_procs})
 if(MEM_CHECK)
@@ -217,6 +220,12 @@ else:
     dash = options.dash
     submit = 'ctest_submit()'
 
+# Check for update command
+if options.update:
+    update = 'ctest_update()'
+else:
+    update = ''
+
 # Setup CTest vars
 pwd = os.environ['PWD']
 ctest_vars = {
@@ -225,6 +234,7 @@ ctest_vars = {
 'host_name' : 'neutronbalance',
 'dashboard' : dash,
 'submit'    : submit,
+'update'    : update,
 'n_procs'   : options.n_procs
 }
 

From 66107d89a02e9ded934cbd0208bac11545214358 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 8 Apr 2014 14:56:06 -0400
Subject: [PATCH 30/43] changed FC_DEFAULT to FC

---
 tests/run_nightly_tests.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index dcd4636a8b..2a27732eb4 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -35,7 +35,7 @@ parser.add_option("-u", "--update", action="store_true", dest="update",
 (options, args) = parser.parse_args()
 
 # Compiler paths
-FC_DEFAULT='gfortran'
+FC='gfortran'
 MPI_DIR='/opt/mpich/3.0.4-gnu'
 HDF5_DIR='/opt/hdf5/1.8.12-gnu'
 PHDF5_DIR='/opt/phdf5/1.8.12-gnu'
@@ -113,7 +113,7 @@ class Test(object):
         elif self.mpi and self.hdf5:
             self.fc = PHDF5_DIR+'/bin/h5pfc'
         else:
-            self.fc = FC_DEFAULT
+            self.fc = FC
 
     def get_build_name(self):
         self.build_name =  options.branch + '_' + self.name

From 3e060d5793fd459cd9dd8a9ecc244463fcb850f2 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 8 Apr 2014 15:26:22 -0400
Subject: [PATCH 31/43] always save log file

---
 tests/run_nightly_tests.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 2a27732eb4..6121856425 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -5,6 +5,7 @@ from __future__ import print_function
 import os
 import shutil
 import re
+import glob
 from subprocess import call 
 from collections import OrderedDict
 from optparse import OptionParser
@@ -279,6 +280,10 @@ for key in iter(tests):
     # Run test
     test.run_ctest()
 
+    # Copy over log file
+    logfile = glob.glob('build/Testing/Temporary/LastTest*.log')
+    shutil.copy(logfile[0], 'LastTest_{0}.log'.format(test.name))
+
     # Clear build directory
     shutil.rmtree('build', ignore_errors=True)
     os.remove('ctestscript.run')

From 0ac10fbc1e9275a48304f64c3bb3adba4d02e876 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 8 Apr 2014 15:30:16 -0400
Subject: [PATCH 32/43] added better regex for log file

---
 tests/run_nightly_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 6121856425..7fe8b8199f 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -281,7 +281,7 @@ for key in iter(tests):
     test.run_ctest()
 
     # Copy over log file
-    logfile = glob.glob('build/Testing/Temporary/LastTest*.log')
+    logfile = glob.glob('build/Testing/Temporary/LastTest_*.log')
     shutil.copy(logfile[0], 'LastTest_{0}.log'.format(test.name))
 
     # Clear build directory

From b7dcf9f1b3ebc7829b8314f89ad0559d4fcda0f6 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 8 Apr 2014 15:44:26 -0400
Subject: [PATCH 33/43] keep timestamp on logfile name

---
 tests/run_nightly_tests.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 7fe8b8199f..bff745b815 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -282,7 +282,10 @@ for key in iter(tests):
 
     # Copy over log file
     logfile = glob.glob('build/Testing/Temporary/LastTest_*.log')
-    shutil.copy(logfile[0], 'LastTest_{0}.log'.format(test.name))
+    logfilename = os.path.split(logfile[0])[1]
+    logfilename = os.path.splitext(logfilename)[0]
+    logfilename = logfilename + '_{0}.log'.format(test.name)
+    shutil.copy(logfile[0], logfilename)
 
     # Clear build directory
     shutil.rmtree('build', ignore_errors=True)

From e57453c0988fcda992acde10638f182f71dce65e Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 10 Apr 2014 16:35:10 -0400
Subject: [PATCH 34/43] hostname now set by socket

---
 tests/run_nightly_tests.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index bff745b815..661104c352 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -6,6 +6,7 @@ import os
 import shutil
 import re
 import glob
+import socket
 from subprocess import call 
 from collections import OrderedDict
 from optparse import OptionParser
@@ -232,7 +233,7 @@ pwd = os.environ['PWD']
 ctest_vars = {
 'source_dir' : pwd + '/../src',
 'build_dir' :  pwd + '/build',
-'host_name' : 'neutronbalance',
+'host_name' : socket.gethostname(),
 'dashboard' : dash,
 'submit'    : submit,
 'update'    : update,

From f02f077d6341307f7d52b06cd056b9c7e823f1ed Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Fri, 25 Apr 2014 10:04:08 -0400
Subject: [PATCH 35/43] changed restart particles in CMakeLists

---
 src/CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 82da9e878a..d1e88abb42 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -310,7 +310,7 @@ foreach(test ${TESTS})
         elseif(${test} MATCHES "test_sourcepoint_restart")
           set(RESTART_FILE statepoint.7.h5 source.7.h5)
         elseif(${test} MATCHES "test_particle_restart")
-          set(RESTART_FILE particle_10_394.h5)
+          set(RESTART_FILE particle_12_192.h5)
         else(${test} MATCHES "test_statepoint_restart")
           message(FATAL_ERROR "Restart test ${test} not recognized")
         endif(${test} MATCHES "test_statepoint_restart")
@@ -323,7 +323,7 @@ foreach(test ${TESTS})
         elseif(${test} MATCHES "test_sourcepoint_restart")
           set(RESTART_FILE statepoint.7.binary source.7.binary)
         elseif(${test} MATCHES "test_particle_restart")
-          set(RESTART_FILE particle_10_394.binary)
+          set(RESTART_FILE particle_12_192.binary)
         else(${test} MATCHES "test_statepoint_restart")
           message(FATAL_ERROR "Restart test ${test} not recognized")
         endif(${test} MATCHES "test_statepoint_restart")

From a83d50c8496ae1d4c6142fa66d2aea1e091a4222 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Mon, 28 Apr 2014 23:15:54 -0400
Subject: [PATCH 36/43] merged run_tests into run_nightly tests

---
 tests/run_nightly_tests.py | 162 +++++++++++++++++++++++++++++++++++--
 1 file changed, 154 insertions(+), 8 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index 661104c352..cf8e3cf228 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -3,6 +3,7 @@
 from __future__ import print_function
 
 import os
+import sys
 import shutil
 import re
 import glob
@@ -34,6 +35,9 @@ parser.add_option("-D", "--dashboard", dest="dash",
 parser.add_option("-u", "--update", action="store_true", dest="update",
                   help="Allow CTest to update repo. (WARNING: may overwrite\
                         changes that were not pushed.")
+parser.add_option("-s", "--script", action="store_true", dest="script",
+                  help="Activate CTest scripting mode for coverage, valgrind\
+                        and dashboard capability.")
 (options, args) = parser.parse_args()
 
 # Compiler paths
@@ -43,6 +47,9 @@ HDF5_DIR='/opt/hdf5/1.8.12-gnu'
 PHDF5_DIR='/opt/phdf5/1.8.12-gnu'
 PETSC_DIR='/opt/petsc/3.4.3-gnu'
 
+# Script mode for extra capability
+script_mode = False
+
 # Override default compiler paths if environmental vars are found
 if os.environ.has_key('FC'):
     FC = os.environ['FC']
@@ -106,6 +113,9 @@ class Test(object):
         self.petsc = petsc
         self.valgrind = valgrind
         self.coverage = coverage
+        self.success = True
+        self.msg = None
+        self.cmake = ['cmake', '-H../src', '-Bbuild']
 
         # Check for MPI/HDF5
         if self.mpi and not self.hdf5:
@@ -140,13 +150,79 @@ class Test(object):
         with open('ctestscript.run', 'w') as fh:
             fh.write(ctest_str.format(**ctest_vars))
 
-    def run_ctest(self):
+    def run_ctest_script(self):
         os.environ['FC'] = self.fc
         if self.petsc:
             os.environ['PETSC_DIR'] = PETSC_DIR
         if self.mpi:
             os.environ['MPI_DIR'] = MPI_DIR
-        call(['ctest', '-S', 'ctestscript.run','-V'])
+        rc = call(['ctest', '-S', 'ctestscript.run','-V'])
+        if rc != 0:
+            self.success = False
+            self.msg = 'Failed on ctest script.'
+
+    def run_cmake(self):
+        os.environ['FC'] = self.fc
+        build_opts = self.build_opts.split()
+        self.cmake += build_opts
+        rc = call(self.cmake)
+        if rc != 0:
+            self.success = False
+            self.msg = 'Failed on cmake.'
+
+    def run_make(self):
+        if not self.success:
+            return
+
+        # Default make string
+        make_list = ['make','-s']
+
+        # Check for parallel
+        if options.n_procs is not None:
+            make_list.append('-j')
+            make_list.append(options.n_procs)
+
+        # Run make
+        rc = call(make_list)
+        if rc != 0:
+            self.success = False
+            self.msg = 'Failed on make.'
+
+    def run_ctests(self):
+        if not self.success:
+            return
+
+        # Default ctest string
+        ctest_list = ['ctest']
+
+        # Check for parallel
+        if options.n_procs is not None:
+            ctest_list.append('-j')
+            ctest_list.append(options.n_procs)
+
+        # Check for subset of tests
+        if options.regex_tests is not None:
+            ctest_list.append('-R')
+            ctest_list.append(options.regex_tests)
+
+        # Run ctests
+        rc = call(ctest_list)
+        if rc != 0:
+            self.success = False
+            self.msg = 'Failed on testing.'
+
+    # Checks to see if file exists in PWD or PATH
+    def check_compiler(self):
+        result = False
+        if os.path.isfile(self.fc):
+            result = True
+        for path in os.environ["PATH"].split(":"):
+            if os.path.isfile(os.path.join(path, self.fc)):
+                result = True
+        if not result: 
+            raise Exception("Compiler path '{0}' does not exist."
+                           .format(self.fc)+
+                           "Please set appropriate environmental variable(s).")
 
 def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
              hdf5=False, petsc=False, valgrind=False, coverage=False):
@@ -228,6 +304,12 @@ if options.update:
 else:
     update = ''
 
+# Check for CTest scipts mode
+if not options.dash is None or options.script:
+    script_mode = True
+else:
+    script_mode = False
+
 # Setup CTest vars
 pwd = os.environ['PWD']
 ctest_vars = {
@@ -255,6 +337,23 @@ call(['./cleanup'])
 for key in iter(tests):
     test = tests[key]
 
+    # No valgrind or coverage if not in CTest script mode
+    if not script_mode:
+        if test.valgrind:
+            continue
+        if test.coverage:
+            continue
+
+    # Extra display if not in script mode
+    if not script_mode:
+        print('-'*(len(key) + 6))
+        print(key + ' tests')
+        print('-'*(len(key) + 6))
+        sys.stdout.flush()
+
+    # Verify fortran compiler exists
+    test.check_compiler()
+
     # Set test specific CTest vars
     ctest_vars.update({'build_name' : test.get_build_name()})
     ctest_vars.update({'build_opts' : test.get_build_opts()})
@@ -275,14 +374,37 @@ for key in iter(tests):
         ctest_vars.update({'tests' : 'INCLUDE {0}'.
                           format(options.regex_tests)})
 
-    # Create ctest script
-    test.create_ctest_script(ctest_vars)
+    # Script mode
+    if script_mode:
 
-    # Run test
-    test.run_ctest()
+        # Create ctest script
+        test.create_ctest_script(ctest_vars)
+
+        # Run test
+        test.run_ctest_script()
+
+    else:
+
+        # Run CMAKE to configure build
+        test.run_cmake()
+
+        # Go into build directory
+        os.chdir('build')
+
+        # Build OpenMC
+        test.run_make()
+
+        # Run tests
+        test.run_ctests()
+
+        # Leave build directory
+        os.chdir('..')
 
     # Copy over log file
-    logfile = glob.glob('build/Testing/Temporary/LastTest_*.log')
+    if script_mode:
+        logfile = glob.glob('build/Testing/Temporary/LastTest_*.log')
+    else:
+        logfile = glob.glob('build/Testing/Temporary/LastTest.log')
     logfilename = os.path.split(logfile[0])[1]
     logfilename = os.path.splitext(logfilename)[0]
     logfilename = logfilename + '_{0}.log'.format(test.name)
@@ -290,5 +412,29 @@ for key in iter(tests):
 
     # Clear build directory
     shutil.rmtree('build', ignore_errors=True)
-    os.remove('ctestscript.run')
+    if script_mode:
+        os.remove('ctestscript.run')
     call(['./cleanup'])
+
+# Print out summary of results
+print('\n' + '='*54)
+print('Summary of Compilation Option Testing:\n')
+
+if sys.stdout.isatty():
+    OK = '\033[92m'
+    FAIL = '\033[91m'
+    ENDC = '\033[0m'
+    BOLD = '\033[1m'
+else:
+    OK = ''
+    FAIL = ''
+    ENDC = ''
+    BOLD = ''
+
+for test in tests:
+    print(test + '.'*(50 - len(test)), end='')
+    if tests[test].success:
+        print(BOLD + OK + '[OK]' + ENDC)
+    else:
+        print(BOLD + FAIL + '[FAILED]' + ENDC)
+        print(' '*len(test)+tests[test].msg)

From 265c25574625a3fdc9a3189a82ce1f8900de43bc Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 29 Apr 2014 10:40:40 -0400
Subject: [PATCH 37/43] added more comments, only copy logfile if found, remove
 gfortran warning

---
 tests/run_nightly_tests.py | 53 ++++++++++++++++++++++++++------------
 1 file changed, 36 insertions(+), 17 deletions(-)

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
index cf8e3cf228..4d2e0876b3 100755
--- a/tests/run_nightly_tests.py
+++ b/tests/run_nightly_tests.py
@@ -53,8 +53,6 @@ script_mode = False
 # Override default compiler paths if environmental vars are found
 if os.environ.has_key('FC'):
     FC = os.environ['FC']
-    if FC is not 'gfortran':
-        print('NOTE: Test suite only verifed for gfortran compiler.')
 if os.environ.has_key('MPI_DIR'):
     MPI_DIR = os.environ['MPI_DIR']
 if os.environ.has_key('HDF5_DIR'):
@@ -127,10 +125,13 @@ class Test(object):
         else:
             self.fc = FC
 
+    # Sets the build name that will show up on the CDash
     def get_build_name(self):
         self.build_name =  options.branch + '_' + self.name
         return self.build_name
 
+    # Sets up build options for various tests. It is used both
+    # in script and non-script modes
     def get_build_opts(self):
         build_str = ""
         if self.debug:
@@ -146,10 +147,12 @@ class Test(object):
         self.build_opts = build_str
         return self.build_opts
 
+    # Write out the ctest script to tests directory
     def create_ctest_script(self, ctest_vars):
         with open('ctestscript.run', 'w') as fh:
             fh.write(ctest_str.format(**ctest_vars))
 
+    # Runs the ctest script which performs all the cmake/ctest/cdash
     def run_ctest_script(self):
         os.environ['FC'] = self.fc
         if self.petsc:
@@ -161,6 +164,7 @@ class Test(object):
             self.success = False
             self.msg = 'Failed on ctest script.'
 
+    # Runs cmake when in non-script mode
     def run_cmake(self):
         os.environ['FC'] = self.fc
         build_opts = self.build_opts.split()
@@ -170,6 +174,7 @@ class Test(object):
             self.success = False
             self.msg = 'Failed on cmake.'
 
+    # Runs make when in non-script mode
     def run_make(self):
         if not self.success:
             return
@@ -188,6 +193,7 @@ class Test(object):
             self.success = False
             self.msg = 'Failed on make.'
 
+    # Runs ctest when in non-script mode
     def run_ctests(self):
         if not self.success:
             return
@@ -224,11 +230,14 @@ class Test(object):
                            .format(self.fc)+
                            "Please set appropriate environmental variable(s).")
 
+# Simple function to add a test to the global tests dictionary
 def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
              hdf5=False, petsc=False, valgrind=False, coverage=False):
-    tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, valgrind, coverage)})
+    tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, 
+    valgrind, coverage)})
 
-# List of tests
+# List of all tests that may be run. User can add -C to command line to specify
+# a subset of these configurations
 add_test('basic-normal')
 add_test('basic-debug', debug=True)
 add_test('basic-optimize', optimize=True)
@@ -270,7 +279,7 @@ add_test('hdf5-debug_coverage', debug=True, hdf5=True, coverage=True)
 add_test('mpi-debug_coverage', debug=True, mpi=True, coverage=True)
 add_test('petsc-debug_coverage', debug=True, petsc=True, mpi=True, coverage=True)
 
-# Check to see if we are to just print build configuratinos
+# Check to see if we should just print build configuration information to user
 if options.print_build_configs:
     for key in tests:
         print('Configuration Name: {0}'.format(key))
@@ -291,6 +300,10 @@ if options.build_config is not None:
             del tests[key]
 
 # Check for dashboard and determine whether to push results to server
+# Note that there are only 3 basic dashboards: 
+# Experimental, Nightly, Continuous. On the CDash end, these can be
+# reorganized into groups when a hostname, dashboard and build name
+# are matched.
 if options.dash is None:
     dash = 'Experimental'
     submit = ''
@@ -298,19 +311,22 @@ else:
     dash = options.dash
     submit = 'ctest_submit()'
 
-# Check for update command
+# Check for update command, which will run git fetch/merge and will delete
+# any changes to repo that were not pushed to remote origin
 if options.update:
     update = 'ctest_update()'
 else:
     update = ''
 
 # Check for CTest scipts mode
+# Sets up whether we should use just the basic ctest command or use 
+# CTest scripting to perform tests.
 if not options.dash is None or options.script:
     script_mode = True
 else:
     script_mode = False
 
-# Setup CTest vars
+# Setup CTest script vars. Not used in non-script mode
 pwd = os.environ['PWD']
 ctest_vars = {
 'source_dir' : pwd + '/../src',
@@ -322,8 +338,9 @@ ctest_vars = {
 'n_procs'   : options.n_procs
 }
 
-# Set up default valgrind tests
+# Set up default valgrind tests (subset of all tests)
 # Currently takes too long to run all the tests with valgrind
+# Only used in script mode
 valgrind_default_tests = "basic|cmfd_feed|confidence_intervals|\
 density_atombcm|eigenvalue_genperbatch|energy_grid|entropy|\
 filter_cell|lattice_multiple|output|plot_background|reflective_plane|\
@@ -333,7 +350,7 @@ tally_assumesep|translation|uniform_fs|universe|void"
 
 # Begin testing
 shutil.rmtree('build', ignore_errors=True)
-call(['./cleanup'])
+call(['./cleanup']) # removes all binary and hdf5 output files from tests
 for key in iter(tests):
     test = tests[key]
 
@@ -354,7 +371,7 @@ for key in iter(tests):
     # Verify fortran compiler exists
     test.check_compiler()
 
-    # Set test specific CTest vars
+    # Set test specific CTest script vars. Not used in non-script mode
     ctest_vars.update({'build_name' : test.get_build_name()})
     ctest_vars.update({'build_opts' : test.get_build_opts()})
     ctest_vars.update({'mem_check'  : test.valgrind})
@@ -362,7 +379,7 @@ for key in iter(tests):
 
     # Check for user custom tests
     # INCLUDE is a CTest command that allows for a subset
-    # of tests to be executed.
+    # of tests to be executed. Only used in script mode.
     if options.regex_tests is None:
         ctest_vars.update({'tests' : ''})
 
@@ -374,7 +391,8 @@ for key in iter(tests):
         ctest_vars.update({'tests' : 'INCLUDE {0}'.
                           format(options.regex_tests)})
 
-    # Script mode
+    # Main part of code that does the ctest execution.
+    # It is broken up by two modes, script and non-script
     if script_mode:
 
         # Create ctest script
@@ -405,12 +423,13 @@ for key in iter(tests):
         logfile = glob.glob('build/Testing/Temporary/LastTest_*.log')
     else:
         logfile = glob.glob('build/Testing/Temporary/LastTest.log')
-    logfilename = os.path.split(logfile[0])[1]
-    logfilename = os.path.splitext(logfilename)[0]
-    logfilename = logfilename + '_{0}.log'.format(test.name)
-    shutil.copy(logfile[0], logfilename)
+    if len(logfile) > 0:
+        logfilename = os.path.split(logfile[0])[1]
+        logfilename = os.path.splitext(logfilename)[0]
+        logfilename = logfilename + '_{0}.log'.format(test.name)
+        shutil.copy(logfile[0], logfilename)
 
-    # Clear build directory
+    # Clear build directory and remove binary and hdf5 files
     shutil.rmtree('build', ignore_errors=True)
     if script_mode:
         os.remove('ctestscript.run')

From 96cda14fb9acf8f1f9e393a8264a8bbdc64d6137 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 29 Apr 2014 10:41:32 -0400
Subject: [PATCH 38/43] merged run nightly tests and run tests into one common
 script

---
 tests/run_nightly_tests.py | 459 -------------------------------------
 tests/run_tests.py         | 318 +++++++++++++++++++------
 2 files changed, 254 insertions(+), 523 deletions(-)
 delete mode 100755 tests/run_nightly_tests.py

diff --git a/tests/run_nightly_tests.py b/tests/run_nightly_tests.py
deleted file mode 100755
index 4d2e0876b3..0000000000
--- a/tests/run_nightly_tests.py
+++ /dev/null
@@ -1,459 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-
-import os
-import sys
-import shutil
-import re
-import glob
-import socket
-from subprocess import call 
-from collections import OrderedDict
-from optparse import OptionParser
-
-# Command line parsing
-parser = OptionParser()
-parser.add_option('-j', '--parallel', dest='n_procs', default='1',
-                  help="Number of parallel jobs.")
-parser.add_option('-R', '--tests-regex', dest='regex_tests',
-                  help="Run tests matching regular expression. \
-                  Test names are the directories present in tests folder.\
-                  This uses standard regex syntax to select tests.")
-parser.add_option('-C', '--build-config', dest='build_config',
-                  help="Build configurations matching regular expression. \
-                        Specific build configurations can be printed out with \
-                        optional argument -p, --print. This uses standard \
-                        regex syntax to select build configurations.")
-parser.add_option('-p', '--print', action="store_true", 
-                  dest="print_build_configs", default=False,
-                  help="Print out build configurations.")
-parser.add_option("-b", "--branch", dest="branch", default="",
-                  help="branch name for build")
-parser.add_option("-D", "--dashboard", dest="dash",
-                  help="Dash name -- Experimental, Nightly, Continuous")
-parser.add_option("-u", "--update", action="store_true", dest="update",
-                  help="Allow CTest to update repo. (WARNING: may overwrite\
-                        changes that were not pushed.")
-parser.add_option("-s", "--script", action="store_true", dest="script",
-                  help="Activate CTest scripting mode for coverage, valgrind\
-                        and dashboard capability.")
-(options, args) = parser.parse_args()
-
-# Compiler paths
-FC='gfortran'
-MPI_DIR='/opt/mpich/3.0.4-gnu'
-HDF5_DIR='/opt/hdf5/1.8.12-gnu'
-PHDF5_DIR='/opt/phdf5/1.8.12-gnu'
-PETSC_DIR='/opt/petsc/3.4.3-gnu'
-
-# Script mode for extra capability
-script_mode = False
-
-# Override default compiler paths if environmental vars are found
-if os.environ.has_key('FC'):
-    FC = os.environ['FC']
-if os.environ.has_key('MPI_DIR'):
-    MPI_DIR = os.environ['MPI_DIR']
-if os.environ.has_key('HDF5_DIR'):
-    HDF5_DIR = os.environ['HDF5_DIR']
-if os.environ.has_key('PHDF5_DIR'):
-    PHDF5_DIR = os.environ['PHDF5_DIR']
-if os.environ.has_key('PETSC_DIR'):
-    PETSC_DIR = os.environ['PETSC_DIR']
-
-# CTest script template
-ctest_str = """set (CTEST_SOURCE_DIRECTORY "{source_dir}")
-set (CTEST_BINARY_DIRECTORY "{build_dir}")
-
-set(CTEST_SITE "{host_name}")
-set (CTEST_BUILD_NAME "{build_name}")
-set (CTEST_CMAKE_GENERATOR "Unix Makefiles")
-set (CTEST_BUILD_OPTIONS "{build_opts}")
-
-set(CTEST_UPDATE_COMMAND "git")
-
-set(CTEST_CONFIGURE_COMMAND "${{CMAKE_COMMAND}} -H${{CTEST_SOURCE_DIRECTORY}} -B${{CTEST_BINARY_DIRECTORY}} ${{CTEST_BUILD_OPTIONS}}")
-set(CTEST_MEMORYCHECK_COMMAND "/usr/bin/valgrind")
-set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "--tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes")
-set(MEM_CHECK {mem_check})
-set(ENV{{MEM_CHECK}} ${{MEM_CHECK}})
-
-set(CTEST_COVERAGE_COMMAND "/usr/bin/gcov")
-set(COVERAGE {coverage})
-set(ENV{{COVERAGE}} ${{COVERAGE}})
-
-ctest_start("{dashboard}")
-ctest_configure()
-{update}
-ctest_build()
-ctest_test({tests} PARALLEL_LEVEL {n_procs})
-if(MEM_CHECK)
-ctest_memcheck({tests})
-endif(MEM_CHECK)
-if(COVERAGE)
-ctest_coverage()
-endif(COVERAGE)
-{submit}"""
-
-# Define test data structure
-tests = OrderedDict()
-
-class Test(object):
-    def __init__(self, name, debug=False, optimize=False, mpi=False, openmp=False,
-                 hdf5=False, petsc=False, valgrind=False, coverage=False):
-        self.name = name
-        self.debug = debug
-        self.optimize = optimize
-        self.mpi = mpi
-        self.openmp = openmp
-        self.hdf5 = hdf5
-        self.petsc = petsc
-        self.valgrind = valgrind
-        self.coverage = coverage
-        self.success = True
-        self.msg = None
-        self.cmake = ['cmake', '-H../src', '-Bbuild']
-
-        # Check for MPI/HDF5
-        if self.mpi and not self.hdf5:
-            self.fc = MPI_DIR+'/bin/mpif90'
-        elif not self.mpi and self.hdf5:
-            self.fc = HDF5_DIR+'/bin/h5fc'
-        elif self.mpi and self.hdf5:
-            self.fc = PHDF5_DIR+'/bin/h5pfc'
-        else:
-            self.fc = FC
-
-    # Sets the build name that will show up on the CDash
-    def get_build_name(self):
-        self.build_name =  options.branch + '_' + self.name
-        return self.build_name
-
-    # Sets up build options for various tests. It is used both
-    # in script and non-script modes
-    def get_build_opts(self):
-        build_str = ""
-        if self.debug:
-            build_str += "-Ddebug=ON "
-        if self.optimize:
-            build_str += "-Doptimize=ON "
-        if self.openmp:
-            build_str += "-Dopenmp=ON "
-        if self.petsc:
-            build_str += "-Dpetsc=ON "
-        if self.coverage:
-            build_str += "-Dcoverage=ON "
-        self.build_opts = build_str
-        return self.build_opts
-
-    # Write out the ctest script to tests directory
-    def create_ctest_script(self, ctest_vars):
-        with open('ctestscript.run', 'w') as fh:
-            fh.write(ctest_str.format(**ctest_vars))
-
-    # Runs the ctest script which performs all the cmake/ctest/cdash
-    def run_ctest_script(self):
-        os.environ['FC'] = self.fc
-        if self.petsc:
-            os.environ['PETSC_DIR'] = PETSC_DIR
-        if self.mpi:
-            os.environ['MPI_DIR'] = MPI_DIR
-        rc = call(['ctest', '-S', 'ctestscript.run','-V'])
-        if rc != 0:
-            self.success = False
-            self.msg = 'Failed on ctest script.'
-
-    # Runs cmake when in non-script mode
-    def run_cmake(self):
-        os.environ['FC'] = self.fc
-        build_opts = self.build_opts.split()
-        self.cmake += build_opts
-        rc = call(self.cmake)
-        if rc != 0:
-            self.success = False
-            self.msg = 'Failed on cmake.'
-
-    # Runs make when in non-script mode
-    def run_make(self):
-        if not self.success:
-            return
-
-        # Default make string
-        make_list = ['make','-s']
-
-        # Check for parallel
-        if options.n_procs is not None:
-            make_list.append('-j')
-            make_list.append(options.n_procs)
-
-        # Run make
-        rc = call(make_list)
-        if rc != 0:
-            self.success = False
-            self.msg = 'Failed on make.'
-
-    # Runs ctest when in non-script mode
-    def run_ctests(self):
-        if not self.success:
-            return
-
-        # Default ctest string
-        ctest_list = ['ctest']
-
-        # Check for parallel
-        if options.n_procs is not None:
-            ctest_list.append('-j')
-            ctest_list.append(options.n_procs)
-
-        # Check for subset of tests
-        if options.regex_tests is not None:
-            ctest_list.append('-R')
-            ctest_list.append(options.regex_tests)
-
-        # Run ctests
-        rc = call(ctest_list)
-        if rc != 0:
-            self.success = False
-            self.msg = 'Failed on testing.'
-
-    # Checks to see if file exists in PWD or PATH
-    def check_compiler(self):
-        result = False
-        if os.path.isfile(self.fc):
-            result = True
-        for path in os.environ["PATH"].split(":"):
-            if os.path.isfile(os.path.join(path, self.fc)):
-                result = True
-        if not result: 
-            raise Exception("Compiler path '{0}' does not exist."
-                           .format(self.fc)+
-                           "Please set appropriate environmental variable(s).")
-
-# Simple function to add a test to the global tests dictionary
-def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
-             hdf5=False, petsc=False, valgrind=False, coverage=False):
-    tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, 
-    valgrind, coverage)})
-
-# List of all tests that may be run. User can add -C to command line to specify
-# a subset of these configurations
-add_test('basic-normal')
-add_test('basic-debug', debug=True)
-add_test('basic-optimize', optimize=True)
-add_test('omp-normal', openmp=True)
-add_test('omp-debug', openmp=True, debug=True)
-add_test('omp-optimize', openmp=True, optimize=True)
-add_test('hdf5-normal', hdf5=True)
-add_test('hdf5-debug', hdf5=True, debug=True)
-add_test('hdf5-optimize', hdf5=True, optimize=True)
-add_test('omp-hdf5-normal', openmp=True, hdf5=True)
-add_test('omp-hdf5-debug', openmp=True, hdf5=True, debug=True)
-add_test('omp-hdf5-optimize', openmp=True, hdf5=True, optimize=True)
-add_test('mpi-normal', mpi=True)
-add_test('mpi-debug', mpi=True, debug=True)
-add_test('mpi-optimize', mpi=True, optimize=True)
-add_test('mpi-omp-normal', mpi=True, openmp=True)
-add_test('mpi-omp-debug', mpi=True, openmp=True, debug=True)
-add_test('mpi-omp-optimize', mpi=True, openmp=True, optimize=True)
-add_test('phdf5-normal', mpi=True, hdf5=True)
-add_test('phdf5-debug', mpi=True, hdf5=True, debug=True)
-add_test('phdf5-optimize', mpi=True, hdf5=True, optimize=True)
-add_test('phdf5-omp-normal', mpi=True, hdf5=True, openmp=True)
-add_test('phdf5-omp-debug', mpi=True, hdf5=True, openmp=True, debug=True)
-add_test('phdf5-omp-optimize', mpi=True, hdf5=True, openmp=True, optimize=True)
-add_test('petsc-normal', petsc=True, mpi=True)
-add_test('petsc-debug', petsc=True, mpi=True, debug=True)
-add_test('petsc-optimize', petsc=True, mpi=True, optimize=True)
-add_test('phdf5-petsc-normal', mpi=True, hdf5=True, petsc=True)
-add_test('phdf5-petsc-debug', mpi=True, hdf5=True, petsc=True, debug=True)
-add_test('phdf5-petsc-optimize', mpi=True, hdf5=True, petsc=True, optimize=True)
-add_test('omp-phdf5-petsc-normal', openmp=True, mpi=True, hdf5=True, petsc=True)
-add_test('omp-phdf5-petsc-debug', openmp=True, mpi=True, hdf5=True, petsc=True, debug=True)
-add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=True, optimize=True)
-add_test('basic-debug_valgrind', debug=True, valgrind=True)
-add_test('hdf5-debug_valgrind', hdf5=True, debug=True, valgrind=True)
-add_test('petsc-debug_valgrind', petsc=True, mpi=True, debug=True, valgrind=True)
-add_test('basic-debug_coverage', debug=True, coverage=True)
-add_test('hdf5-debug_coverage', debug=True, hdf5=True, coverage=True)
-add_test('mpi-debug_coverage', debug=True, mpi=True, coverage=True)
-add_test('petsc-debug_coverage', debug=True, petsc=True, mpi=True, coverage=True)
-
-# Check to see if we should just print build configuration information to user
-if options.print_build_configs:
-    for key in tests:
-        print('Configuration Name: {0}'.format(key))
-        print('  Debug Flags:..........{0}'.format(tests[key].debug))
-        print('  Optimization Flags:...{0}'.format(tests[key].optimize))
-        print('  HDF5 Active:..........{0}'.format(tests[key].hdf5))
-        print('  MPI Active:...........{0}'.format(tests[key].mpi))
-        print('  OpenMP Active:........{0}'.format(tests[key].openmp))
-        print('  PETSc Active:.........{0}'.format(tests[key].petsc))
-        print('  Valgrind Test:........{0}'.format(tests[key].valgrind))
-        print('  Coverage Test:........{0}\n'.format(tests[key].coverage))
-    exit()
-
-# Delete items of dictionary that don't match regular expression
-if options.build_config is not None:
-    for key in tests:
-        if not re.search(options.build_config, key):
-            del tests[key]
-
-# Check for dashboard and determine whether to push results to server
-# Note that there are only 3 basic dashboards: 
-# Experimental, Nightly, Continuous. On the CDash end, these can be
-# reorganized into groups when a hostname, dashboard and build name
-# are matched.
-if options.dash is None:
-    dash = 'Experimental'
-    submit = ''
-else:
-    dash = options.dash
-    submit = 'ctest_submit()'
-
-# Check for update command, which will run git fetch/merge and will delete
-# any changes to repo that were not pushed to remote origin
-if options.update:
-    update = 'ctest_update()'
-else:
-    update = ''
-
-# Check for CTest scipts mode
-# Sets up whether we should use just the basic ctest command or use 
-# CTest scripting to perform tests.
-if not options.dash is None or options.script:
-    script_mode = True
-else:
-    script_mode = False
-
-# Setup CTest script vars. Not used in non-script mode
-pwd = os.environ['PWD']
-ctest_vars = {
-'source_dir' : pwd + '/../src',
-'build_dir' :  pwd + '/build',
-'host_name' : socket.gethostname(),
-'dashboard' : dash,
-'submit'    : submit,
-'update'    : update,
-'n_procs'   : options.n_procs
-}
-
-# Set up default valgrind tests (subset of all tests)
-# Currently takes too long to run all the tests with valgrind
-# Only used in script mode
-valgrind_default_tests = "basic|cmfd_feed|confidence_intervals|\
-density_atombcm|eigenvalue_genperbatch|energy_grid|entropy|\
-filter_cell|lattice_multiple|output|plot_background|reflective_plane|\
-rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono|\
-sourcepoint_batch|statepoint_interval|survival_biasing|\
-tally_assumesep|translation|uniform_fs|universe|void"
-
-# Begin testing
-shutil.rmtree('build', ignore_errors=True)
-call(['./cleanup']) # removes all binary and hdf5 output files from tests
-for key in iter(tests):
-    test = tests[key]
-
-    # No valgrind or coverage if not in CTest script mode
-    if not script_mode:
-        if test.valgrind:
-            continue
-        if test.coverage:
-            continue
-
-    # Extra display if not in script mode
-    if not script_mode:
-        print('-'*(len(key) + 6))
-        print(key + ' tests')
-        print('-'*(len(key) + 6))
-        sys.stdout.flush()
-
-    # Verify fortran compiler exists
-    test.check_compiler()
-
-    # Set test specific CTest script vars. Not used in non-script mode
-    ctest_vars.update({'build_name' : test.get_build_name()})
-    ctest_vars.update({'build_opts' : test.get_build_opts()})
-    ctest_vars.update({'mem_check'  : test.valgrind})
-    ctest_vars.update({'coverage'  : test.coverage})
-
-    # Check for user custom tests
-    # INCLUDE is a CTest command that allows for a subset
-    # of tests to be executed. Only used in script mode.
-    if options.regex_tests is None:
-        ctest_vars.update({'tests' : ''})
-
-        # No user tests, use default valgrind tests
-        if test.valgrind:
-            ctest_vars.update({'tests' : 'INCLUDE {0}'.
-                              format(valgrind_default_tests)})
-    else:
-        ctest_vars.update({'tests' : 'INCLUDE {0}'.
-                          format(options.regex_tests)})
-
-    # Main part of code that does the ctest execution.
-    # It is broken up by two modes, script and non-script
-    if script_mode:
-
-        # Create ctest script
-        test.create_ctest_script(ctest_vars)
-
-        # Run test
-        test.run_ctest_script()
-
-    else:
-
-        # Run CMAKE to configure build
-        test.run_cmake()
-
-        # Go into build directory
-        os.chdir('build')
-
-        # Build OpenMC
-        test.run_make()
-
-        # Run tests
-        test.run_ctests()
-
-        # Leave build directory
-        os.chdir('..')
-
-    # Copy over log file
-    if script_mode:
-        logfile = glob.glob('build/Testing/Temporary/LastTest_*.log')
-    else:
-        logfile = glob.glob('build/Testing/Temporary/LastTest.log')
-    if len(logfile) > 0:
-        logfilename = os.path.split(logfile[0])[1]
-        logfilename = os.path.splitext(logfilename)[0]
-        logfilename = logfilename + '_{0}.log'.format(test.name)
-        shutil.copy(logfile[0], logfilename)
-
-    # Clear build directory and remove binary and hdf5 files
-    shutil.rmtree('build', ignore_errors=True)
-    if script_mode:
-        os.remove('ctestscript.run')
-    call(['./cleanup'])
-
-# Print out summary of results
-print('\n' + '='*54)
-print('Summary of Compilation Option Testing:\n')
-
-if sys.stdout.isatty():
-    OK = '\033[92m'
-    FAIL = '\033[91m'
-    ENDC = '\033[0m'
-    BOLD = '\033[1m'
-else:
-    OK = ''
-    FAIL = ''
-    ENDC = ''
-    BOLD = ''
-
-for test in tests:
-    print(test + '.'*(50 - len(test)), end='')
-    if tests[test].success:
-        print(BOLD + OK + '[OK]' + ENDC)
-    else:
-        print(BOLD + FAIL + '[FAILED]' + ENDC)
-        print(' '*len(test)+tests[test].msg)
diff --git a/tests/run_tests.py b/tests/run_tests.py
index ce67f3ab7a..4d2e0876b3 100755
--- a/tests/run_tests.py
+++ b/tests/run_tests.py
@@ -3,15 +3,18 @@
 from __future__ import print_function
 
 import os
+import sys
 import shutil
 import re
-import sys
+import glob
+import socket
 from subprocess import call 
 from collections import OrderedDict
 from optparse import OptionParser
 
+# Command line parsing
 parser = OptionParser()
-parser.add_option('-j', '--parallel', dest='n_procs',
+parser.add_option('-j', '--parallel', dest='n_procs', default='1',
                   help="Number of parallel jobs.")
 parser.add_option('-R', '--tests-regex', dest='regex_tests',
                   help="Run tests matching regular expression. \
@@ -25,48 +28,92 @@ parser.add_option('-C', '--build-config', dest='build_config',
 parser.add_option('-p', '--print', action="store_true", 
                   dest="print_build_configs", default=False,
                   help="Print out build configurations.")
-(opts, args) = parser.parse_args()
+parser.add_option("-b", "--branch", dest="branch", default="",
+                  help="branch name for build")
+parser.add_option("-D", "--dashboard", dest="dash",
+                  help="Dash name -- Experimental, Nightly, Continuous")
+parser.add_option("-u", "--update", action="store_true", dest="update",
+                  help="Allow CTest to update repo. (WARNING: may overwrite\
+                        changes that were not pushed.")
+parser.add_option("-s", "--script", action="store_true", dest="script",
+                  help="Activate CTest scripting mode for coverage, valgrind\
+                        and dashboard capability.")
+(options, args) = parser.parse_args()
 
-# Default compiler paths
+# Compiler paths
 FC='gfortran'
-MPI_DIR='/opt/mpich/3.1-gnu'
+MPI_DIR='/opt/mpich/3.0.4-gnu'
 HDF5_DIR='/opt/hdf5/1.8.12-gnu'
 PHDF5_DIR='/opt/phdf5/1.8.12-gnu'
-PETSC_DIR='/opt/petsc/3.4.4-gnu'
+PETSC_DIR='/opt/petsc/3.4.3-gnu'
+
+# Script mode for extra capability
+script_mode = False
 
 # Override default compiler paths if environmental vars are found
-if 'FC' in os.environ:
+if os.environ.has_key('FC'):
     FC = os.environ['FC']
-    if FC is not 'gfortran':
-        print('NOTE: Test suite only verifed for gfortran compiler.')
-if 'MPI_DIR' in os.environ:
+if os.environ.has_key('MPI_DIR'):
     MPI_DIR = os.environ['MPI_DIR']
-if 'HDF5_DIR' in os.environ:
+if os.environ.has_key('HDF5_DIR'):
     HDF5_DIR = os.environ['HDF5_DIR']
-if 'PHDF5_DIR' in os.environ:
+if os.environ.has_key('PHDF5_DIR'):
     PHDF5_DIR = os.environ['PHDF5_DIR']
-if 'PETSC_DIR' in os.environ:
+if os.environ.has_key('PETSC_DIR'):
     PETSC_DIR = os.environ['PETSC_DIR']
 
+# CTest script template
+ctest_str = """set (CTEST_SOURCE_DIRECTORY "{source_dir}")
+set (CTEST_BINARY_DIRECTORY "{build_dir}")
+
+set(CTEST_SITE "{host_name}")
+set (CTEST_BUILD_NAME "{build_name}")
+set (CTEST_CMAKE_GENERATOR "Unix Makefiles")
+set (CTEST_BUILD_OPTIONS "{build_opts}")
+
+set(CTEST_UPDATE_COMMAND "git")
+
+set(CTEST_CONFIGURE_COMMAND "${{CMAKE_COMMAND}} -H${{CTEST_SOURCE_DIRECTORY}} -B${{CTEST_BINARY_DIRECTORY}} ${{CTEST_BUILD_OPTIONS}}")
+set(CTEST_MEMORYCHECK_COMMAND "/usr/bin/valgrind")
+set(CTEST_MEMORYCHECK_COMMAND_OPTIONS "--tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes")
+set(MEM_CHECK {mem_check})
+set(ENV{{MEM_CHECK}} ${{MEM_CHECK}})
+
+set(CTEST_COVERAGE_COMMAND "/usr/bin/gcov")
+set(COVERAGE {coverage})
+set(ENV{{COVERAGE}} ${{COVERAGE}})
+
+ctest_start("{dashboard}")
+ctest_configure()
+{update}
+ctest_build()
+ctest_test({tests} PARALLEL_LEVEL {n_procs})
+if(MEM_CHECK)
+ctest_memcheck({tests})
+endif(MEM_CHECK)
+if(COVERAGE)
+ctest_coverage()
+endif(COVERAGE)
+{submit}"""
+
 # Define test data structure
 tests = OrderedDict()
 
 class Test(object):
-    def __init__(self, debug=False, optimize=False, mpi=False, openmp=False,
-                 hdf5=False, petsc=False):
+    def __init__(self, name, debug=False, optimize=False, mpi=False, openmp=False,
+                 hdf5=False, petsc=False, valgrind=False, coverage=False):
+        self.name = name
         self.debug = debug
         self.optimize = optimize
         self.mpi = mpi
         self.openmp = openmp
         self.hdf5 = hdf5
         self.petsc = petsc
+        self.valgrind = valgrind
+        self.coverage = coverage
         self.success = True
         self.msg = None
-        self.setup_cmake()
-
-    def setup_cmake(self):
-        # Default cmake
-        self.cmake = ['cmake','-H../src','-Bbuild']
+        self.cmake = ['cmake', '-H../src', '-Bbuild']
 
         # Check for MPI/HDF5
         if self.mpi and not self.hdf5:
@@ -78,26 +125,56 @@ class Test(object):
         else:
             self.fc = FC
 
-        # Set rest of options
+    # Sets the build name that will show up on the CDash
+    def get_build_name(self):
+        self.build_name =  options.branch + '_' + self.name
+        return self.build_name
+
+    # Sets up build options for various tests. It is used both
+    # in script and non-script modes
+    def get_build_opts(self):
+        build_str = ""
         if self.debug:
-            self.cmake.append('-Ddebug=on')
+            build_str += "-Ddebug=ON "
         if self.optimize:
-            self.cmake.append('-Doptimize=on')
+            build_str += "-Doptimize=ON "
         if self.openmp:
-            self.cmake.append('-Dopenmp=on')
+            build_str += "-Dopenmp=ON "
+        if self.petsc:
+            build_str += "-Dpetsc=ON "
+        if self.coverage:
+            build_str += "-Dcoverage=ON "
+        self.build_opts = build_str
+        return self.build_opts
+
+    # Write out the ctest script to tests directory
+    def create_ctest_script(self, ctest_vars):
+        with open('ctestscript.run', 'w') as fh:
+            fh.write(ctest_str.format(**ctest_vars))
+
+    # Runs the ctest script which performs all the cmake/ctest/cdash
+    def run_ctest_script(self):
+        os.environ['FC'] = self.fc
         if self.petsc:
-            self.cmake.append('-Dpetsc=on')
             os.environ['PETSC_DIR'] = PETSC_DIR
         if self.mpi:
             os.environ['MPI_DIR'] = MPI_DIR
+        rc = call(['ctest', '-S', 'ctestscript.run','-V'])
+        if rc != 0:
+            self.success = False
+            self.msg = 'Failed on ctest script.'
 
+    # Runs cmake when in non-script mode
     def run_cmake(self):
         os.environ['FC'] = self.fc
+        build_opts = self.build_opts.split()
+        self.cmake += build_opts
         rc = call(self.cmake)
         if rc != 0:
             self.success = False
             self.msg = 'Failed on cmake.'
 
+    # Runs make when in non-script mode
     def run_make(self):
         if not self.success:
             return
@@ -106,9 +183,9 @@ class Test(object):
         make_list = ['make','-s']
 
         # Check for parallel
-        if opts.n_procs is not None:
+        if options.n_procs is not None:
             make_list.append('-j')
-            make_list.append(opts.n_procs)
+            make_list.append(options.n_procs)
 
         # Run make
         rc = call(make_list)
@@ -116,6 +193,7 @@ class Test(object):
             self.success = False
             self.msg = 'Failed on make.'
 
+    # Runs ctest when in non-script mode
     def run_ctests(self):
         if not self.success:
             return
@@ -124,14 +202,14 @@ class Test(object):
         ctest_list = ['ctest']
 
         # Check for parallel
-        if opts.n_procs is not None:
+        if options.n_procs is not None:
             ctest_list.append('-j')
-            ctest_list.append(opts.n_procs)
+            ctest_list.append(options.n_procs)
 
         # Check for subset of tests
-        if opts.regex_tests is not None:
+        if options.regex_tests is not None:
             ctest_list.append('-R')
-            ctest_list.append(opts.regex_tests)
+            ctest_list.append(options.regex_tests)
 
         # Run ctests
         rc = call(ctest_list)
@@ -152,11 +230,14 @@ class Test(object):
                            .format(self.fc)+
                            "Please set appropriate environmental variable(s).")
 
+# Simple function to add a test to the global tests dictionary
 def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
-             hdf5=False, petsc=False):
-    tests.update({name:Test(debug, optimize, mpi, openmp, hdf5, petsc)})
+             hdf5=False, petsc=False, valgrind=False, coverage=False):
+    tests.update({name:Test(name, debug, optimize, mpi, openmp, hdf5, petsc, 
+    valgrind, coverage)})
 
-# List of tests
+# List of all tests that may be run. User can add -C to command line to specify
+# a subset of these configurations
 add_test('basic-normal')
 add_test('basic-debug', debug=True)
 add_test('basic-optimize', optimize=True)
@@ -188,13 +269,18 @@ add_test('phdf5-petsc-normal', mpi=True, hdf5=True, petsc=True)
 add_test('phdf5-petsc-debug', mpi=True, hdf5=True, petsc=True, debug=True)
 add_test('phdf5-petsc-optimize', mpi=True, hdf5=True, petsc=True, optimize=True)
 add_test('omp-phdf5-petsc-normal', openmp=True, mpi=True, hdf5=True, petsc=True)
-add_test('omp-phdf5-petsc-debug', openmp=True, mpi=True, hdf5=True, petsc=True,
-                                  debug=True)
-add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=True,
-                                     optimize=True)
+add_test('omp-phdf5-petsc-debug', openmp=True, mpi=True, hdf5=True, petsc=True, debug=True)
+add_test('omp-phdf5-petsc-optimize', openmp=True, mpi=True, hdf5=True, petsc=True, optimize=True)
+add_test('basic-debug_valgrind', debug=True, valgrind=True)
+add_test('hdf5-debug_valgrind', hdf5=True, debug=True, valgrind=True)
+add_test('petsc-debug_valgrind', petsc=True, mpi=True, debug=True, valgrind=True)
+add_test('basic-debug_coverage', debug=True, coverage=True)
+add_test('hdf5-debug_coverage', debug=True, hdf5=True, coverage=True)
+add_test('mpi-debug_coverage', debug=True, mpi=True, coverage=True)
+add_test('petsc-debug_coverage', debug=True, petsc=True, mpi=True, coverage=True)
 
-# Check to see if we are to just print build configuratinos
-if opts.print_build_configs:
+# Check to see if we should just print build configuration information to user
+if options.print_build_configs:
     for key in tests:
         print('Configuration Name: {0}'.format(key))
         print('  Debug Flags:..........{0}'.format(tests[key].debug))
@@ -202,48 +288,152 @@ if opts.print_build_configs:
         print('  HDF5 Active:..........{0}'.format(tests[key].hdf5))
         print('  MPI Active:...........{0}'.format(tests[key].mpi))
         print('  OpenMP Active:........{0}'.format(tests[key].openmp))
-        print('  PETSc Active:.........{0}\n'.format(tests[key].petsc))
+        print('  PETSc Active:.........{0}'.format(tests[key].petsc))
+        print('  Valgrind Test:........{0}'.format(tests[key].valgrind))
+        print('  Coverage Test:........{0}\n'.format(tests[key].coverage))
     exit()
 
 # Delete items of dictionary that don't match regular expression
-if opts.build_config is not None:
+if options.build_config is not None:
     for key in tests:
-        if not re.search(opts.build_config, key):
+        if not re.search(options.build_config, key):
             del tests[key]
 
+# Check for dashboard and determine whether to push results to server
+# Note that there are only 3 basic dashboards: 
+# Experimental, Nightly, Continuous. On the CDash end, these can be
+# reorganized into groups when a hostname, dashboard and build name
+# are matched.
+if options.dash is None:
+    dash = 'Experimental'
+    submit = ''
+else:
+    dash = options.dash
+    submit = 'ctest_submit()'
+
+# Check for update command, which will run git fetch/merge and will delete
+# any changes to repo that were not pushed to remote origin
+if options.update:
+    update = 'ctest_update()'
+else:
+    update = ''
+
+# Check for CTest scipts mode
+# Sets up whether we should use just the basic ctest command or use 
+# CTest scripting to perform tests.
+if not options.dash is None or options.script:
+    script_mode = True
+else:
+    script_mode = False
+
+# Setup CTest script vars. Not used in non-script mode
+pwd = os.environ['PWD']
+ctest_vars = {
+'source_dir' : pwd + '/../src',
+'build_dir' :  pwd + '/build',
+'host_name' : socket.gethostname(),
+'dashboard' : dash,
+'submit'    : submit,
+'update'    : update,
+'n_procs'   : options.n_procs
+}
+
+# Set up default valgrind tests (subset of all tests)
+# Currently takes too long to run all the tests with valgrind
+# Only used in script mode
+valgrind_default_tests = "basic|cmfd_feed|confidence_intervals|\
+density_atombcm|eigenvalue_genperbatch|energy_grid|entropy|\
+filter_cell|lattice_multiple|output|plot_background|reflective_plane|\
+rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono|\
+sourcepoint_batch|statepoint_interval|survival_biasing|\
+tally_assumesep|translation|uniform_fs|universe|void"
+
 # Begin testing
 shutil.rmtree('build', ignore_errors=True)
-for test in tests:
-    print('-'*(len(test) + 6))
-    print(test + ' tests')
-    print('-'*(len(test) + 6))
-    sys.stdout.flush()
+call(['./cleanup']) # removes all binary and hdf5 output files from tests
+for key in iter(tests):
+    test = tests[key]
+
+    # No valgrind or coverage if not in CTest script mode
+    if not script_mode:
+        if test.valgrind:
+            continue
+        if test.coverage:
+            continue
+
+    # Extra display if not in script mode
+    if not script_mode:
+        print('-'*(len(key) + 6))
+        print(key + ' tests')
+        print('-'*(len(key) + 6))
+        sys.stdout.flush()
 
     # Verify fortran compiler exists
-    tests[test].check_compiler()
+    test.check_compiler()
 
-    # Run CMAKE to configure build
-    tests[test].run_cmake()
+    # Set test specific CTest script vars. Not used in non-script mode
+    ctest_vars.update({'build_name' : test.get_build_name()})
+    ctest_vars.update({'build_opts' : test.get_build_opts()})
+    ctest_vars.update({'mem_check'  : test.valgrind})
+    ctest_vars.update({'coverage'  : test.coverage})
 
-    # Go into build directory
-    os.chdir('build')
+    # Check for user custom tests
+    # INCLUDE is a CTest command that allows for a subset
+    # of tests to be executed. Only used in script mode.
+    if options.regex_tests is None:
+        ctest_vars.update({'tests' : ''})
 
-    # Build OpenMC
-    tests[test].run_make()
+        # No user tests, use default valgrind tests
+        if test.valgrind:
+            ctest_vars.update({'tests' : 'INCLUDE {0}'.
+                              format(valgrind_default_tests)})
+    else:
+        ctest_vars.update({'tests' : 'INCLUDE {0}'.
+                          format(options.regex_tests)})
 
-    # Run tests
-    tests[test].run_ctests()
+    # Main part of code that does the ctest execution.
+    # It is broken up by two modes, script and non-script
+    if script_mode:
 
-    # Leave build directory
-    os.chdir('..')
+        # Create ctest script
+        test.create_ctest_script(ctest_vars)
 
-    # Copy test log file if failed
-    if tests[test].msg == 'Failed on testing.':
-        shutil.copy('build/Testing/Temporary/LastTest.log',
-                    'LastTest_{0}.log'.format(test))
+        # Run test
+        test.run_ctest_script()
 
-    # Clean up build
+    else:
+
+        # Run CMAKE to configure build
+        test.run_cmake()
+
+        # Go into build directory
+        os.chdir('build')
+
+        # Build OpenMC
+        test.run_make()
+
+        # Run tests
+        test.run_ctests()
+
+        # Leave build directory
+        os.chdir('..')
+
+    # Copy over log file
+    if script_mode:
+        logfile = glob.glob('build/Testing/Temporary/LastTest_*.log')
+    else:
+        logfile = glob.glob('build/Testing/Temporary/LastTest.log')
+    if len(logfile) > 0:
+        logfilename = os.path.split(logfile[0])[1]
+        logfilename = os.path.splitext(logfilename)[0]
+        logfilename = logfilename + '_{0}.log'.format(test.name)
+        shutil.copy(logfile[0], logfilename)
+
+    # Clear build directory and remove binary and hdf5 files
     shutil.rmtree('build', ignore_errors=True)
+    if script_mode:
+        os.remove('ctestscript.run')
+    call(['./cleanup'])
 
 # Print out summary of results
 print('\n' + '='*54)

From 85f76c6a67f69ebe766a26a8febb2e49d8619ffc Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Tue, 29 Apr 2014 10:48:41 -0400
Subject: [PATCH 39/43] updated some python syntax

---
 tests/run_tests.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/run_tests.py b/tests/run_tests.py
index 4d2e0876b3..8d7c517d2a 100755
--- a/tests/run_tests.py
+++ b/tests/run_tests.py
@@ -40,26 +40,26 @@ parser.add_option("-s", "--script", action="store_true", dest="script",
                         and dashboard capability.")
 (options, args) = parser.parse_args()
 
-# Compiler paths
+# Default compiler paths
 FC='gfortran'
-MPI_DIR='/opt/mpich/3.0.4-gnu'
+MPI_DIR='/opt/mpich/3.1-gnu'
 HDF5_DIR='/opt/hdf5/1.8.12-gnu'
 PHDF5_DIR='/opt/phdf5/1.8.12-gnu'
-PETSC_DIR='/opt/petsc/3.4.3-gnu'
+PETSC_DIR='/opt/petsc/3.4.4-gnu'
 
 # Script mode for extra capability
 script_mode = False
 
 # Override default compiler paths if environmental vars are found
-if os.environ.has_key('FC'):
+if 'FC' in os.environ:
     FC = os.environ['FC']
-if os.environ.has_key('MPI_DIR'):
+if 'MPI_DIR' in os.environ:
     MPI_DIR = os.environ['MPI_DIR']
-if os.environ.has_key('HDF5_DIR'):
+if 'HDF5_DIR' in os.environ:
     HDF5_DIR = os.environ['HDF5_DIR']
-if os.environ.has_key('PHDF5_DIR'):
+if 'PHDF5_DIR' in os.environ:
     PHDF5_DIR = os.environ['PHDF5_DIR']
-if os.environ.has_key('PETSC_DIR'):
+if 'PETSC_DIR' in os.environ:
     PETSC_DIR = os.environ['PETSC_DIR']
 
 # CTest script template

From 4759892dcbcbc8fede7b88c954a5348673208557 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 1 May 2014 11:33:57 -0400
Subject: [PATCH 40/43] updated cdash drop site information

---
 src/CTestConfig.cmake | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/src/CTestConfig.cmake b/src/CTestConfig.cmake
index 6ae35bae56..77b7cec250 100644
--- a/src/CTestConfig.cmake
+++ b/src/CTestConfig.cmake
@@ -4,12 +4,22 @@
 ## # The following are required to uses Dart and the Cdash dashboard
 ##   ENABLE_TESTING()
 ##   INCLUDE(CTest)
+
+# Generic information about CDASH site
 set(CTEST_PROJECT_NAME "OpenMC")
 set(CTEST_NIGHTLY_START_TIME "03:00:00 UTC")
-
 set(CTEST_DROP_METHOD "http")
-set(CTEST_DROP_SITE "neutronbalance.mit.edu")
-set(CTEST_DROP_LOCATION "/CDash/submit.php?project=OpenMC")
+set(CTEST_DROP_SITE "54.83.201.173")
+set(CTEST_DROP_LOCATION "/cdash/submit.php?project=OpenMC")
 set(CTEST_DROP_SITE_CDASH TRUE)
-SET(CTEST_CUSTOM_MAXIMUM_FAILED_TEST_OUTPUT_SIZE "20000")
-SET(CTEST_CUSTOM_MAXIMUM_PASSED_TEST_OUTPUT_SIZE "20000")
+
+# Set file size larger to see more output
+set(CTEST_CUSTOM_MAXIMUM_FAILED_TEST_OUTPUT_SIZE "20000")
+set(CTEST_CUSTOM_MAXIMUM_PASSED_TEST_OUTPUT_SIZE "20000")
+
+# User/password to CDASH site
+# Please contact Nick Horelik <nhorelik@mit.edu> or
+# Bryan Herman <bherman@mit.edu> if you want to push
+# test suite information to our CDASH site.
+set(CTEST_DROP_SITE_USER "")
+set(CTEST_DROP_SITE_PASSWORD "")

From 336744a6c40c25c2492eb5321fc02a0aa6405233 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Thu, 1 May 2014 14:56:52 -0400
Subject: [PATCH 41/43] added subproject capability

---
 tests/run_tests.py | 25 ++++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/tests/run_tests.py b/tests/run_tests.py
index 8d7c517d2a..20161978b0 100755
--- a/tests/run_tests.py
+++ b/tests/run_tests.py
@@ -25,11 +25,11 @@ parser.add_option('-C', '--build-config', dest='build_config',
                         Specific build configurations can be printed out with \
                         optional argument -p, --print. This uses standard \
                         regex syntax to select build configurations.")
-parser.add_option('-p', '--print', action="store_true", 
-                  dest="print_build_configs", default=False,
-                  help="Print out build configurations.")
-parser.add_option("-b", "--branch", dest="branch", default="",
-                  help="branch name for build")
+parser.add_option('-l', '--list', action="store_true", 
+                  dest="list_build_configs", default=False,
+                  help="List out build configurations.")
+parser.add_option("-p", "--project", dest="project", default="",
+                  help="project name for build")
 parser.add_option("-D", "--dashboard", dest="dash",
                   help="Dash name -- Experimental, Nightly, Continuous")
 parser.add_option("-u", "--update", action="store_true", dest="update",
@@ -83,6 +83,8 @@ set(CTEST_COVERAGE_COMMAND "/usr/bin/gcov")
 set(COVERAGE {coverage})
 set(ENV{{COVERAGE}} ${{COVERAGE}})
 
+{subproject}
+
 ctest_start("{dashboard}")
 ctest_configure()
 {update}
@@ -127,7 +129,7 @@ class Test(object):
 
     # Sets the build name that will show up on the CDash
     def get_build_name(self):
-        self.build_name =  options.branch + '_' + self.name
+        self.build_name =  options.project + '_' + self.name
         return self.build_name
 
     # Sets up build options for various tests. It is used both
@@ -280,7 +282,7 @@ add_test('mpi-debug_coverage', debug=True, mpi=True, coverage=True)
 add_test('petsc-debug_coverage', debug=True, petsc=True, mpi=True, coverage=True)
 
 # Check to see if we should just print build configuration information to user
-if options.print_build_configs:
+if options.list_build_configs:
     for key in tests:
         print('Configuration Name: {0}'.format(key))
         print('  Debug Flags:..........{0}'.format(tests[key].debug))
@@ -338,6 +340,15 @@ ctest_vars = {
 'n_procs'   : options.n_procs
 }
 
+# Check project name
+subprop = """set_property(GLOBAL PROPERTY SubProject {0})"""
+if options.project == "" :
+    ctest_vars.update({'subproject':''})
+elif options.project == 'develop':
+    ctest_vars.update({'subproject':''})
+else:
+    ctest_vars.update({'subproject':subprop.format(options.project)})
+
 # Set up default valgrind tests (subset of all tests)
 # Currently takes too long to run all the tests with valgrind
 # Only used in script mode

From c9a21b29141869fc14c99b5a739bf32aacdd4a87 Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Mon, 5 May 2014 17:43:02 -0400
Subject: [PATCH 42/43] check compiler doesnt kill script

---
 tests/run_tests.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/tests/run_tests.py b/tests/run_tests.py
index 20161978b0..84587e5721 100755
--- a/tests/run_tests.py
+++ b/tests/run_tests.py
@@ -227,10 +227,11 @@ class Test(object):
         for path in os.environ["PATH"].split(":"):
             if os.path.isfile(os.path.join(path, self.fc)):
                 result = True
-        if not result: 
-            raise Exception("Compiler path '{0}' does not exist."
-                           .format(self.fc)+
-                           "Please set appropriate environmental variable(s).")
+        if not result:
+            self.msg = 'Compiler not found: {0}'.\
+                       format((os.path.join(path, self.fc)))
+            self.success = False
+        return self.success
 
 # Simple function to add a test to the global tests dictionary
 def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
@@ -380,7 +381,8 @@ for key in iter(tests):
         sys.stdout.flush()
 
     # Verify fortran compiler exists
-    test.check_compiler()
+    if not test.check_compiler():
+        continue
 
     # Set test specific CTest script vars. Not used in non-script mode
     ctest_vars.update({'build_name' : test.get_build_name()})

From 39ad55a2449124ac6feb942eb32959ae26fc2f3b Mon Sep 17 00:00:00 2001
From: Bryan Herman <bherman@mit.edu>
Date: Mon, 5 May 2014 18:09:12 -0400
Subject: [PATCH 43/43] exit script if no tests to run, check script mode for
 valgrind and coverage before test loop

---
 tests/run_tests.py | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/tests/run_tests.py b/tests/run_tests.py
index 84587e5721..f534c79333 100755
--- a/tests/run_tests.py
+++ b/tests/run_tests.py
@@ -115,6 +115,7 @@ class Test(object):
         self.coverage = coverage
         self.success = True
         self.msg = None
+        self.skipped = False
         self.cmake = ['cmake', '-H../src', '-Bbuild']
 
         # Check for MPI/HDF5
@@ -231,7 +232,6 @@ class Test(object):
             self.msg = 'Compiler not found: {0}'.\
                        format((os.path.join(path, self.fc)))
             self.success = False
-        return self.success
 
 # Simple function to add a test to the global tests dictionary
 def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
@@ -360,19 +360,23 @@ rotation|salphabeta_multiple|score_absorption|seed|source_energy_mono|\
 sourcepoint_batch|statepoint_interval|survival_biasing|\
 tally_assumesep|translation|uniform_fs|universe|void"
 
+# Delete items of dictionary if valgrind or coverage and not in script mode
+if not script_mode:
+    for key in tests:
+        if re.search('valgrind|coverage', key):
+            del tests[key]
+
+# Check if tests empty
+if len(tests.keys()) == 0:
+    print('No tests to run.')
+    exit()
+
 # Begin testing
 shutil.rmtree('build', ignore_errors=True)
 call(['./cleanup']) # removes all binary and hdf5 output files from tests
 for key in iter(tests):
     test = tests[key]
 
-    # No valgrind or coverage if not in CTest script mode
-    if not script_mode:
-        if test.valgrind:
-            continue
-        if test.coverage:
-            continue
-
     # Extra display if not in script mode
     if not script_mode:
         print('-'*(len(key) + 6))
@@ -381,7 +385,8 @@ for key in iter(tests):
         sys.stdout.flush()
 
     # Verify fortran compiler exists
-    if not test.check_compiler():
+    test.check_compiler()
+    if not test.success:
         continue
 
     # Set test specific CTest script vars. Not used in non-script mode