From 9fa2a2cba92ebc8b1abf9aca431a7ec9318dbd92 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franck=20P=C3=A9rignon?= <franck.perignon@imag.fr>
Date: Fri, 20 May 2016 11:58:30 +0200
Subject: [PATCH] - Set timeout for tests. - Update doc
---
CMakeLists.txt | 6 +++
cmake/HySoPTests.cmake | 6 ++-
docs/sphinx/devel/index.rst | 6 +--
docs/sphinx/devel/memo_sphinx.rst | 47 ++++++++++++++++++-
docs/sphinx/reference/index.rst | 14 +++---
docs/sphinx/users_guide/biblio.rst | 2 +-
docs/sphinx/users_guide/develnotes.rst | 14 ------
.../tests/test_multiresolution_filter.py | 45 +++++++++---------
8 files changed, 91 insertions(+), 49 deletions(-)
delete mode 100644 docs/sphinx/users_guide/develnotes.rst
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 12ab08b63..241dbd58a 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -48,6 +48,7 @@ option(WITH_MPI_TESTS "Enable mpi tests. Default = ON if USE_MPI is ON." ON)
option(WITH_GOOGLE_TESTS "Enable google tests (c++). Default = OFF." OFF)
option(FORTRAN_LAYOUT "Choose default data layout ('fortran', column-major or 'C' order, row-major) for arrays. Default = column-major." ON)
option(WITH_DOCUMENTATION "Build Documentation. Default = OFF" ON)
+option(ENABLE_LONG_TESTS "Enable tests that may run for long time with important memory print. Default = OFF." OFF)
# Set python install mode:
# - user --> behave as 'python setup.py install --user'
@@ -461,6 +462,11 @@ add_custom_target(pyclean COMMAND rm -f ${PYCFILES}
# ============= Tests =============
if(WITH_TESTS)
+ if(NOT ENABLE_LONG_TESTS)
+ set(TEST_TIMEOUT 4 CACHE STRING "Default value for test runtime limit (in seconds)")
+ else()
+ set(TEST_TIMEOUT 500 CACHE STRING "Default value for test runtime limit (in seconds)")
+ endif()
include(CTest)
# Number of mpi processes used to run tests.
include(ProcessorCount)
diff --git a/cmake/HySoPTests.cmake b/cmake/HySoPTests.cmake
index 8138a30b2..bf9948b98 100755
--- a/cmake/HySoPTests.cmake
+++ b/cmake/HySoPTests.cmake
@@ -10,6 +10,7 @@
# or a call to ctest.
enable_testing()
+
find_python_module(pytest REQUIRED)
# Declaration of python test
@@ -23,6 +24,8 @@ macro(add_python_test test_name test_file)
set_tests_properties(${test_name} PROPERTIES WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/dataForTests)
set_tests_properties(${test_name} PROPERTIES ENVIRONMENT "PYTHONPATH=$ENV{PYTHONPATH}:${HYSOP_BUILD_PYTHONPATH}")
set_tests_properties(${test_name} PROPERTIES ENVIRONMENT "PYTHONPATH=$ENV{PYTHONPATH}:${HYSOP_BUILD_PYTHONPATH},LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:${HYSOP_BUILD_PYTHONPATH}")
+ set_tests_properties(${test_name} PROPERTIES TIMEOUT ${TEST_TIMEOUT})
+
if(WITH_MPI_TESTS)
# Run the same test using mpi multi process run.
# The number of processes used is set with NBPROCS_FOR_TESTS variable (user option for cmake, default=8)
@@ -33,7 +36,8 @@ macro(add_python_test test_name test_file)
set_tests_properties(${test_name}_mpi PROPERTIES FAIL_REGULAR_EXPRESSION "FAILURE;Exception;[^x]failed;ERROR;Assertion")
set_tests_properties(${test_name}_mpi PROPERTIES WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/dataForTests)
set_tests_properties(${test_name}_mpi PROPERTIES ENVIRONMENT "PYTHONPATH=$ENV{PYTHONPATH}:${HYSOP_BUILD_PYTHONPATH},LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:${HYSOP_BUILD_PYTHONPATH}")
- endif()
+ set_tests_properties(${test_name}_mpi PROPERTIES TIMEOUT ${TEST_TIMEOUT})
+ endif()
endmacro()
diff --git a/docs/sphinx/devel/index.rst b/docs/sphinx/devel/index.rst
index 53bfc494e..660c46633 100644
--- a/docs/sphinx/devel/index.rst
+++ b/docs/sphinx/devel/index.rst
@@ -12,8 +12,6 @@ This part is for developers of Hysop and provides guidelines on the "proper" way
about_doc
coding_guidelines
- writing_tests
- develnotes
+ about_work_arrays
memo_sphinx
-
-
+ hysop_validation
diff --git a/docs/sphinx/devel/memo_sphinx.rst b/docs/sphinx/devel/memo_sphinx.rst
index ca787892b..0e0edf97f 100644
--- a/docs/sphinx/devel/memo_sphinx.rst
+++ b/docs/sphinx/devel/memo_sphinx.rst
@@ -3,6 +3,51 @@
Reminder for sphinx utilities
=============================
+Source code for this page::
+
+ To print source Code::
+
+ for i in xrange(3):
+ do un_truc()
+
+
+ Hyperlinks `HySoP Web`_.
+
+
+ .. math::
+
+ \begin{eqnarray}
+ a &=& \frac{1}{2}\\
+ \alpha &=& 3 \times \nabla \omega
+ \end{eqnarray}
+
+ To print a link to some HySoP object:
+
+ .. currentmodule:: hysop.operator.discrete
+
+ An example of a discrete operator, :class:`stretching.Conservative`, used to represent the
+ stretching part of NS.
+
+ Reference to :ref:`forces`.
+
+
+ Links
+ -----
+
+ * rst :
+ http://sphinx-doc.org/rest.html
+
+ * math support
+ http://sphinx-doc.org/ext/math.html
+
+ * numpydoc :
+ https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
+
+ .. _Hysop Web: https://forge.imag.fr
+
+
+Which results in:
+
To print source Code::
for i in xrange(3):
@@ -29,7 +74,7 @@ Reference to :ref:`forces`.
Links
-=====
+-----
* rst :
http://sphinx-doc.org/rest.html
diff --git a/docs/sphinx/reference/index.rst b/docs/sphinx/reference/index.rst
index 6817069a8..6a3a027d2 100644
--- a/docs/sphinx/reference/index.rst
+++ b/docs/sphinx/reference/index.rst
@@ -1,12 +1,12 @@
-.. HySoP reference (auto generated) documentation
+.. _hysop_reference:
-Welcome to HySoP's documentation!
-==================================
-
-Contents:
+HySoP reference (auto generated) documentation
+==============================================
.. toctree::
- :maxdepth: 2
+ :maxdepth: 3
+
+ Python API <../apidoc/modules>
+ fortran_api
- modules
diff --git a/docs/sphinx/users_guide/biblio.rst b/docs/sphinx/users_guide/biblio.rst
index b6df74814..c83f5fde2 100644
--- a/docs/sphinx/users_guide/biblio.rst
+++ b/docs/sphinx/users_guide/biblio.rst
@@ -3,6 +3,6 @@
Bibliography
============
-.. bibliography:: hysop.bib
+.. bibliography:: ../hysop.bib
:cited:
:style: plain
diff --git a/docs/sphinx/users_guide/develnotes.rst b/docs/sphinx/users_guide/develnotes.rst
deleted file mode 100644
index b9a666066..000000000
--- a/docs/sphinx/users_guide/develnotes.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-.. _develnotes:
-
-Notes for developpers
-=====================
-
-Draft. Notes, remarks ... anything which may help developpers
-to write and understand HySoP software.
-
-Contents:
-
-.. toctree::
- :maxdepth: 2
-
- forces
diff --git a/hysop/operator/tests/test_multiresolution_filter.py b/hysop/operator/tests/test_multiresolution_filter.py
index 91febfd77..44e3e5e7e 100755
--- a/hysop/operator/tests/test_multiresolution_filter.py
+++ b/hysop/operator/tests/test_multiresolution_filter.py
@@ -14,6 +14,9 @@ L = [1., 1., 1.]
O = [0., 0., 0.]
simu = Simulation(tinit=0., tend=0.1, nbIter=1)
+# Warning : values too large for tests
+n_middle = 513
+n_large = 1025
def func_periodic_X(res, x, y, z, t=0):
res[0][...] = np.sin(2. * np.pi * x)
@@ -61,34 +64,34 @@ def filter(d_fine, d_coarse, func, method, atol=1e-8, rtol=1e-5):
def test_linear_X():
- b, e, err = filter(d_coarse=Discretization([513, 5, 5],
+ b, e, err = filter(d_coarse=Discretization([n_middle, 5, 5],
ghosts=[1, 1, 1]),
- d_fine=Discretization([1025, 5, 5]),
+ d_fine=Discretization([n_large, 5, 5]),
method={Remesh: Rmsh_Linear, },
func=func_periodic_X)
assert b, "max(|error|)=" + str(e) + " <= " + str(err)
def test_linear_Y():
- b, e, err = filter(d_coarse=Discretization([5, 513, 5],
+ b, e, err = filter(d_coarse=Discretization([5, n_middle, 5],
ghosts=[1, 1, 1]),
- d_fine=Discretization([5, 1025, 5]),
+ d_fine=Discretization([5, n_large, 5]),
method={Remesh: Rmsh_Linear, },
func=func_periodic_Y)
assert b, "max(|error|)=" + str(e) + " <= " + str(err)
def test_linear_Z():
- b, e, err = filter(d_coarse=Discretization([5, 5, 513],
+ b, e, err = filter(d_coarse=Discretization([5, 5, n_middle],
ghosts=[1, 1, 1]),
- d_fine=Discretization([5, 5, 1025]),
+ d_fine=Discretization([5, 5, n_large]),
method={Remesh: Rmsh_Linear, },
func=func_periodic_Z)
assert b, "max(|error|)=" + str(e) + " <= " + str(err)
def test_linear_XY():
- b, e, err = filter(d_coarse=Discretization([1025, 1025, 5],
+ b, e, err = filter(d_coarse=Discretization([n_large, n_large, 5],
ghosts=[1, 1, 1]),
d_fine=Discretization([2049, 2049, 5]),
func=func_periodic_XY,
@@ -111,34 +114,34 @@ def order_linear():
def test_L21_X():
- b, e, err = filter(d_coarse=Discretization([513, 5, 5],
+ b, e, err = filter(d_coarse=Discretization([n_middle, 5, 5],
ghosts=[2, 2, 2]),
- d_fine=Discretization([1025, 5, 5]),
- method={Remesh: L2_1, },
+ d_fine=Discretization([n_large, 5, 5]),
+ method={Remesh: L21, },
func=func_periodic_X)
assert b, "max(|error|)=" + str(e) + " <= " + str(err)
def test_L21_Y():
- b, e, err = filter(d_coarse=Discretization([5, 513, 5],
+ b, e, err = filter(d_coarse=Discretization([5, n_middle, 5],
ghosts=[2, 2, 2]),
- d_fine=Discretization([5, 1025, 5]),
- method={Remesh: L2_1, },
+ d_fine=Discretization([5, n_large, 5]),
+ method={Remesh: L21, },
func=func_periodic_X)
assert b, "max(|error|)=" + str(e) + " <= " + str(err)
def test_L21_Z():
- b, e, err = filter(d_coarse=Discretization([5, 5, 513],
+ b, e, err = filter(d_coarse=Discretization([5, 5, n_middle],
ghosts=[2, 2, 2]),
- d_fine=Discretization([5, 5, 1025]),
- method={Remesh: L2_1, },
+ d_fine=Discretization([5, 5, n_large]),
+ method={Remesh: L21, },
func=func_periodic_X)
assert b, "max(|error|)=" + str(e) + " <= " + str(err)
def test_L21_XY():
- b, e, err = filter(d_coarse=Discretization([1025, 1025, 5],
+ b, e, err = filter(d_coarse=Discretization([n_large, n_large, 5],
ghosts=[2, 2, 2]),
d_fine=Discretization([2049, 2049, 5]),
func=func_periodic_XY,
@@ -169,8 +172,8 @@ def func(res, x, y, z, t=0):
def test_filter_linear():
"""This test compares the GPU linear filter with python implementation"""
box = Box(length=L, origin=O)
- f = Field(box, formula=func, name='f0')
- d_fine = Discretization([513, 513, 513])
+ f = Field(box, formula=func, name='f1')
+ d_fine = Discretization([n_middle, n_middle, n_middle])
d_coarse = Discretization([257, 257, 257], ghosts=[1, 1, 1])
op = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
variables={f: d_coarse},
@@ -195,8 +198,8 @@ def test_filter_linear():
def test_filter_l2_1():
"""This test compares the GPU linear filter with python implementation"""
box = Box(length=L, origin=O)
- f = Field(box, formula=func, name='f0')
- d_fine = Discretization([513, 513, 513])
+ f = Field(box, formula=func, name='f1')
+ d_fine = Discretization([n_middle, n_middle, n_middle])
d_coarse = Discretization([257, 257, 257], ghosts=[2, 2, 2])
op = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
variables={f: d_coarse},
--
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