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CONFIG: add patches for ParaView Catalyst

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- resolve problem with working directory:

    https://develop.openfoam.com/Community/catalyst/issues/4
    https://gitlab.kitware.com/paraview/paraview/merge_requests/2436
This commit is contained in:
Mark Olesen
2018-05-08 14:58:50 +02:00
parent 31ffa9c92c
commit 52ad71871c
3 changed files with 498 additions and 3 deletions
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480
etc/patches/paraview-5.5.0
View File

@ -18,3 +18,483 @@
version_matches "${version_string}")
if(CMAKE_MATCH_0)
set(full ${CMAKE_MATCH_0})
--- ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPProcessor.cxx.orig 2018-04-06 22:03:33.000000000 +0200
+++ ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPProcessor.cxx 2018-05-11 12:02:26.894772713 +0200
@@ -38,6 +38,7 @@
#include "vtkStringArray.h"
#include <list>
+#include <vtksys/SystemTools.hxx>
struct vtkCPProcessorInternals
{
@@ -47,12 +48,13 @@
};
vtkStandardNewMacro(vtkCPProcessor);
-vtkMultiProcessController* vtkCPProcessor::Controller = NULL;
+vtkMultiProcessController* vtkCPProcessor::Controller = nullptr;
//----------------------------------------------------------------------------
vtkCPProcessor::vtkCPProcessor()
{
this->Internal = new vtkCPProcessorInternals;
- this->InitializationHelper = NULL;
+ this->InitializationHelper = nullptr;
+ this->WorkingDirectory = nullptr;
}
//----------------------------------------------------------------------------
@@ -61,14 +63,15 @@
if (this->Internal)
{
delete this->Internal;
- this->Internal = NULL;
+ this->Internal = nullptr;
}
if (this->InitializationHelper)
{
this->InitializationHelper->Delete();
- this->InitializationHelper = NULL;
+ this->InitializationHelper = nullptr;
}
+ this->SetWorkingDirectory(nullptr);
}
//----------------------------------------------------------------------------
@@ -95,7 +98,7 @@
{
if (which < 0 || which >= this->GetNumberOfPipelines())
{
- return NULL;
+ return nullptr;
}
int counter = 0;
vtkCPProcessorInternals::PipelineListIterator iter = this->Internal->Pipelines.begin();
@@ -108,7 +111,7 @@
counter++;
iter++;
}
- return NULL;
+ return nullptr;
}
//----------------------------------------------------------------------------
@@ -130,17 +133,41 @@
}
//----------------------------------------------------------------------------
-int vtkCPProcessor::Initialize()
+int vtkCPProcessor::Initialize(const char* workingDirectory)
{
- if (this->InitializationHelper == NULL)
+ if (this->InitializationHelper == nullptr)
{
this->InitializationHelper = this->NewInitializationHelper();
}
+ // make sure the directory exists here so that we only do it once
+ if (workingDirectory)
+ {
+ vtkMultiProcessController* controller = vtkMultiProcessController::GetGlobalController();
+ int success = 1;
+ if (controller == nullptr || controller->GetLocalProcessId() == 0)
+ {
+ success = vtksys::SystemTools::MakeDirectory(workingDirectory) == true ? 1 : 0;
+ if (success == 0)
+ {
+ vtkWarningMacro("Could not make "
+ << workingDirectory << " directory. "
+ << "Results will be generated in current working directory instead.");
+ }
+ }
+ if (controller)
+ {
+ controller->Broadcast(&success, 1, 0);
+ }
+ if (success)
+ {
+ this->SetWorkingDirectory(workingDirectory);
+ }
+ }
return 1;
}
//----------------------------------------------------------------------------
-int vtkCPProcessor::Initialize(vtkMPICommunicatorOpaqueComm& comm)
+int vtkCPProcessor::Initialize(vtkMPICommunicatorOpaqueComm& comm, const char* workingDirectory)
{
#ifdef PARAVIEW_USE_MPI
if (vtkCPProcessor::Controller)
@@ -148,7 +175,7 @@
vtkErrorMacro("Can only initialize with a communicator once per process.");
return 0;
}
- if (this->InitializationHelper == NULL)
+ if (this->InitializationHelper == nullptr)
{
vtkMPICommunicator* communicator = vtkMPICommunicator::New();
communicator->InitializeExternal(&comm);
@@ -157,12 +184,12 @@
this->Controller = controller;
this->Controller->SetGlobalController(controller);
communicator->Delete();
- return this->Initialize();
+ return this->Initialize(workingDirectory);
}
return 1;
#else
static_cast<void>(&comm); // get rid of variable not used warning
- return this->Initialize();
+ return this->Initialize(workingDirectory);
#endif
}
@@ -225,6 +252,13 @@
input->GetFieldData()->AddArray(catalystChannel);
}
}
+
+ std::string originalWorkingDirectory;
+ if (this->WorkingDirectory)
+ {
+ originalWorkingDirectory = vtksys::SystemTools::GetCurrentWorkingDirectory();
+ vtksys::SystemTools::ChangeDirectory(this->WorkingDirectory);
+ }
for (vtkCPProcessorInternals::PipelineListIterator iter = this->Internal->Pipelines.begin();
iter != this->Internal->Pipelines.end(); iter++)
{
@@ -248,6 +282,10 @@
}
}
}
+ if (originalWorkingDirectory.empty() == false)
+ {
+ vtksys::SystemTools::ChangeDirectory(originalWorkingDirectory);
+ }
// we want to reset everything here to make sure that new information
// is properly passed in the next time.
dataDescription->ResetAll();
@@ -259,7 +297,7 @@
{
if (this->Controller)
{
- this->Controller->SetGlobalController(NULL);
+ this->Controller->SetGlobalController(nullptr);
this->Controller->Finalize(1);
this->Controller->Delete();
}
--- ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPProcessor.h.orig 2018-04-06 22:03:33.000000000 +0200
+++ ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPProcessor.h 2018-05-11 12:02:26.894772713 +0200
@@ -76,14 +76,16 @@
virtual void RemoveAllPipelines();
/// Initialize the co-processor. Returns 1 if successful and 0
- /// otherwise.
/// otherwise. If Catalyst is built with MPI then Initialize()
/// can also be called with a specific MPI communicator if
/// MPI_COMM_WORLD isn't the proper one. Catalyst is initialized
- /// to use MPI_COMM_WORLD by default.
- virtual int Initialize();
+ /// to use MPI_COMM_WORLD by default. Both methods have an optional
+ /// workingDirectory argument which will set *WorkingDirectory* so
+ /// that files will be put relative to this directory.
+ virtual int Initialize(const char* workingDirectory = nullptr);
#ifndef __WRAP__
- virtual int Initialize(vtkMPICommunicatorOpaqueComm& comm);
+ virtual int Initialize(
+ vtkMPICommunicatorOpaqueComm& comm, const char* workingDirectory = nullptr);
#endif
/// The Catalyst input field data string array name. This array will
@@ -111,6 +113,13 @@
/// implementation an opportunity to clean up, before it is destroyed.
virtual int Finalize();
+ /// Get the current working directory for outputting Catalyst files.
+ /// If not set then Catalyst output files will be relative to the
+ /// current working directory. This will not affect where Catalyst
+ /// looks for Python scripts. *WorkingDirectory* gets set through
+ /// the *Initialize()* methods.
+ vtkGetStringMacro(WorkingDirectory);
+
protected:
vtkCPProcessor();
virtual ~vtkCPProcessor();
@@ -118,6 +127,11 @@
/// Create a new instance of the InitializationHelper.
virtual vtkObject* NewInitializationHelper();
+ /// Set the current working directory for outputting Catalyst files.
+ /// This is a protected method since simulation code adaptors should
+ /// set this through the *Initialize()* methods.
+ vtkSetStringMacro(WorkingDirectory);
+
private:
vtkCPProcessor(const vtkCPProcessor&) = delete;
void operator=(const vtkCPProcessor&) = delete;
@@ -125,6 +139,7 @@
vtkCPProcessorInternals* Internal;
vtkObject* InitializationHelper;
static vtkMultiProcessController* Controller;
+ char* WorkingDirectory;
};
#endif
--- ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPXMLPWriterPipeline.cxx.orig 2018-04-06 22:03:33.000000000 +0200
+++ ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPXMLPWriterPipeline.cxx 2018-05-11 12:02:26.894772713 +0200
@@ -31,6 +31,7 @@
#include <vtkSmartPointer.h>
#include <vtkUnstructuredGrid.h>
+#include <algorithm>
#include <sstream>
#include <string>
@@ -174,7 +175,7 @@
for (unsigned int i = 0; i < dataDescription->GetNumberOfInputDescriptions(); i++)
{
- const char* inputName = dataDescription->GetInputDescriptionName(i);
+ std::string inputName = dataDescription->GetInputDescriptionName(i);
vtkCPInputDataDescription* idd = dataDescription->GetInputDescription(i);
vtkDataObject* grid = idd->GetGrid();
if (grid == nullptr)
@@ -206,6 +207,8 @@
vtkSMStringVectorProperty* fileName =
vtkSMStringVectorProperty::SafeDownCast(writer->GetProperty("FileName"));
+ // If we have a / in the channel name we take it out of the filename we're going to write to
+ inputName.erase(std::remove(inputName.begin(), inputName.end(), '/'), inputName.end());
std::ostringstream o;
if (this->Path.empty() == false)
{
--- ParaView-v5.5.0/Wrapping/Python/paraview/coprocessing.py.orig 2018-04-06 22:03:33.000000000 +0200
+++ ParaView-v5.5.0/Wrapping/Python/paraview/coprocessing.py 2018-05-11 12:02:27.038772408 +0200
@@ -11,22 +11,12 @@
from paraview.vtk.vtkPVVTKExtensionsCore import *
import math
-# -----------------------------------------------------------------------------
-def IsInModulo(timestep, frequencyArray):
- """
- Return True if the given timestep is in one of the provided frequency.
- This can be interpreted as follow::
-
- isFM = IsInModulo(timestep, [2,3,7])
-
- is similar to::
+# If the user created a filename in a location that doesn't exist by default we'll
+# make the directory for them. This can be changed though by setting createDirectoriesIfNeeded
+# to False.
+createDirectoriesIfNeeded = True
- isFM = (timestep % 2 == 0) or (timestep % 3 == 0) or (timestep % 7 == 0)
- """
- for frequency in frequencyArray:
- if frequency > 0 and (timestep % frequency == 0):
- return True
- return False
+# -----------------------------------------------------------------------------
class CoProcessor(object):
"""Base class for co-processing Pipelines.
@@ -68,6 +58,9 @@
self.__CinemaTracks = {}
self.__InitialFrequencies = {}
self.__PrintEnsightFormatString = False
+ self.__TimeStepToStartOutputAt=0
+ self.__ForceOutputAtFirstCall=False
+ self.__FirstTimeStepIndex = None
def SetPrintEnsightFormatString(self, enable):
"""If outputting ExodusII files with the purpose of reading them into
@@ -87,6 +80,17 @@
"Incorrect argument type: %s, must be a dict" % type(frequencies))
self.__InitialFrequencies = frequencies
+ def SetInitialOutputOptions(self, timeStepToStartOutputAt, forceOutputAtFirstCall):
+ """Set the frequencies at which the pipeline needs to be updated.
+ Typically, this is called by the subclass once it has determined what
+ timesteps co-processing will be needed to be done.
+ frequencies is a map, with key->string name of for the simulation
+ input, and value is a list of frequencies.
+ """
+
+ self.__TimeStepToStartOutputAt=timeStepToStartOutputAt
+ self.__ForceOutputAtFirstCall=forceOutputAtFirstCall
+
def EnableLiveVisualization(self, enable, frequency = 1):
"""Call this method to enable live-visualization. When enabled,
DoLiveVisualization() will communicate with ParaView server if possible
@@ -115,7 +119,7 @@
# if this is a time step to do live then all of the inputs
# must be made available. note that we want the pipeline built
# before we do the actual first live connection.
- if self.__EnableLiveVisualization and timestep % self.__LiveVisualizationFrequency == 0 \
+ if self.__EnableLiveVisualization and self.NeedToOutput(timestep, self.__LiveVisualizationFrequency) \
and self.__LiveVisualizationLink:
if self.__LiveVisualizationLink.Initialize(servermanager.ActiveConnection.Session.GetSessionProxyManager()):
num_inputs = datadescription.GetNumberOfInputDescriptions()
@@ -132,13 +136,13 @@
# hasn't been set up yet). If we don't have live enabled
# we know that the output frequencies aren't changed and can
# just use the initial frequencies.
- if self.__InitialFrequencies or not self.__EnableLiveVisualization:
+ if self.__ForceOutputAtFirstCall or self.__InitialFrequencies or not self.__EnableLiveVisualization:
num_inputs = datadescription.GetNumberOfInputDescriptions()
for cc in range(num_inputs):
input_name = datadescription.GetInputDescriptionName(cc)
freqs = self.__InitialFrequencies.get(input_name, [])
- if self.__EnableLiveVisualization or ( self and IsInModulo(timestep, freqs) ):
+ if self.__EnableLiveVisualization or ( self and self.IsInModulo(timestep, freqs) ):
datadescription.GetInputDescription(cc).AllFieldsOn()
datadescription.GetInputDescription(cc).GenerateMeshOn()
else:
@@ -149,15 +153,14 @@
for writer in self.__WritersList:
frequency = writer.parameters.GetProperty(
"WriteFrequency").GetElement(0)
- if (timestep % frequency) == 0 or \
- datadescription.GetForceOutput() == True:
+ if self.NeedToOutput(timestep, frequency) or datadescription.GetForceOutput() == True:
writerinputs = cpstate.locate_simulation_inputs(writer)
for writerinput in writerinputs:
datadescription.GetInputDescriptionByName(writerinput).AllFieldsOn()
datadescription.GetInputDescriptionByName(writerinput).GenerateMeshOn()
for view in self.__ViewsList:
- if (view.cpFrequency and timestep % view.cpFrequency == 0) or \
+ if (view.cpFrequency and self.NeedToOutput(timestep, view.cpFrequency)) or \
datadescription.GetForceOutput() == True:
viewinputs = cpstate.locate_simulation_inputs_for_view(view)
for viewinput in viewinputs:
@@ -192,8 +195,7 @@
for writer in self.__WritersList:
frequency = writer.parameters.GetProperty(
"WriteFrequency").GetElement(0)
- if (timestep % frequency) == 0 or \
- datadescription.GetForceOutput() == True:
+ if self.NeedToOutput(timestep, frequency) or datadescription.GetForceOutput() == True:
fileName = writer.parameters.GetProperty("FileName").GetElement(0)
paddingamount = writer.parameters.GetProperty("PaddingAmount").GetElement(0)
helperName = writer.GetXMLName()
@@ -203,6 +205,23 @@
else:
ts = str(timestep).rjust(paddingamount, '0')
writer.FileName = fileName.replace("%t", ts)
+ if '/' in writer.FileName and createDirectoriesIfNeeded:
+ oktowrite = [1.]
+ import vtk
+ comm = vtk.vtkMultiProcessController.GetGlobalController()
+ if comm.GetLocalProcessId() == 0:
+ import os
+ newDir = writer.FileName[0:writer.FileName.rfind('/')]
+ try:
+ os.makedirs(newDir)
+ except OSError:
+ if not os.path.isdir(newDir):
+ print ("ERROR: Cannot make directory for", writer.FileName, ". No data will be written.")
+ oktowrite[0] = 0.
+ comm.Broadcast(oktowrite, 1, 0)
+ if oktowrite[0] == 0:
+ # we can't make the directory so no reason to update the pipeline
+ return
writer.UpdatePipeline(datadescription.GetTime())
def WriteImages(self, datadescription, rescale_lookuptable=False,
@@ -240,7 +259,7 @@
cinema_dirs = []
for view in self.__ViewsList:
- if (view.cpFrequency and timestep % view.cpFrequency == 0) or \
+ if (view.cpFrequency and self.NeedToOutput(timestep, view.cpFrequency)) or \
datadescription.GetForceOutput() == True:
fname = view.cpFileName
ts = str(timestep).rjust(padding_amount, '0')
@@ -267,6 +286,24 @@
if dirname:
cinema_dirs.append(dirname)
else:
+ if '/' in fname and createDirectoriesIfNeeded:
+ oktowrite = [1.]
+ import vtk
+ comm = vtk.vtkMultiProcessController.GetGlobalController()
+ if comm.GetLocalProcessId() == 0:
+ import os
+ newDir = fname[0:fname.rfind('/')]
+ try:
+ os.makedirs(newDir)
+ except OSError:
+ if not os.path.isdir(newDir):
+ print ("ERROR: Cannot make directory for", fname, ". No image will be output.")
+ oktowrite[0] = 0.
+ comm.Broadcast(oktowrite, 1, 0)
+ if oktowrite[0] == 0:
+ # we can't make the directory so no reason to update the pipeline
+ return
+
if image_quality is None and fname.endswith('png'):
# for png quality = 0 means no compression. compression can be a potentially
# very costly serial operation on process 0
@@ -307,7 +344,7 @@
timeStep = datadescription.GetTimeStep()
- if self.__EnableLiveVisualization and timeStep % self.__LiveVisualizationFrequency == 0:
+ if self.__EnableLiveVisualization and self.NeedToOutput(timeStep, self.__LiveVisualizationFrequency):
if not self.__LiveVisualizationLink.Initialize(servermanager.ActiveConnection.Session.GetSessionProxyManager()):
return
@@ -412,7 +449,7 @@
"""
controller = servermanager.ParaViewPipelineController()
# assume that a client only proxy with the same name as a writer
- # is available in "insitu_writer_paramters"
+ # is available in "insitu_writer_parameters"
# Since coprocessor sometimes pass writer as a custom object and not
# a proxy, we need to handle that. Just creating any arbitrary writer
@@ -666,3 +703,42 @@
#restore what we showed
pv_introspect.restore_visibility(pxystate)
return os.path.basename(vfname)
+
+ def IsInModulo(self, timestep, frequencies):
+ """
+ Return True if the given timestep is in one of the provided frequency.
+ This can be interpreted as follow::
+
+ isFM = IsInModulo(timestep-timeStepToStartOutputAt, [2,3,7])
+
+ is similar to::
+
+ isFM = (timestep-timeStepToStartOutputAt % 2 == 0) or (timestep-timeStepToStartOutputAt % 3 == 0) or (timestep-timeStepToStartOutputAt % 7 == 0)
+
+ The timeStepToStartOutputAt is the first timestep that will potentially be output.
+ """
+ if timestep < self.__TimeStepToStartOutputAt and not self.__ForceOutputAtFirstCall:
+ return False
+ for frequency in frequencies:
+ if frequency > 0 and self.NeedToOutput(timestep, frequency):
+ return True
+
+ return False
+
+
+ def NeedToOutput(self, timestep, frequency):
+ """
+ Return True if we need to output based on the input timestep and frequency. Checks based
+ __FirstTimeStepIndex, __FirstTimeStepIndex, __ForceOutputAtFirstCall and __TimeStepToStartOutputAt
+ member variables.
+ """
+ if self.__FirstTimeStepIndex == None:
+ self.__FirstTimeStepIndex = timestep
+
+ if self.__ForceOutputAtFirstCall and self.__FirstTimeStepIndex == timestep:
+ return True
+
+ if self.__TimeStepToStartOutputAt <= timestep and (timestep-self.__TimeStepToStartOutputAt) % frequency == 0:
+ return True
+
+ return False

1
makeParaView.example
View File

@ -7,6 +7,7 @@
# mesa=mesa-13.0.3
mesa=mesa-17.1.1
set -x
./makeParaView \
-mpi=0 \
-mesa-prefix $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$mesa \

20
makeVTK.example
View File

@ -2,15 +2,29 @@
# An example for building particular combinations of VTK with
# - mesa (off-screen only)
vtk=VTK-8.1.0
vtk=VTK-9.0.0
# mesa=mesa-11.2.2
# mesa=mesa-13.0.3
mesa=mesa-17.1.1
# Request building MPI modules
# VTK_Group_MPI=ON
#
# Request building vtkAcceleratorsVTKm
# Module_vtkAcceleratorsVTKm=OFF
#
# Request building vtkParallelMPI
# Module_vtkParallelMPI=ON
set -x
./makeVTK \
$vtk \
-mpi=0 \
-osmesa \
-mesa-prefix $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$mesa \
"$@"
$vtk "$@" \
VTK_Group_MPI=ON \
Module_vtkAcceleratorsVTKm=ON \
Module_vtkParallelMPI=ON
#------------------------------------------------------------------------------