e7e32cc2d6
* paraview: adding variants to use external packages as internal do not compile * paraview: add latest paraview version * catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5 * catalyst: add latest catalyst version * catalyst: added ParaView_DIR env variable to catalyst module * add paraview, catalyst patches - https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2433 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2436 * - Handle updated library paths for catalyst. Versions 5.4 and old places libraries under a paraview subdirectory. Eg, "lib/paraview-5.4", they are now placed directly under "lib" - Minor code style cleanup * Handle update library and python paths for ParaView-5.5 * catalyst: added ParaView_DIR path to spack_env * BUG: applied the patch to the extracted catalyst source files * paraview: added missing self to a member variable * paraview: added Paraview_DIR to env * catalyst: added osmesa variant * of-catalyst: added new package * add (FOAM,WM)_PROJECT_DIR also to spack_env environment * depends on first openfoam release supporting catalyst * openfoam-com: added missing env variables to module generation * openfoam: fixed flake8 errors * of-catalyst: added full variant and openfoam version dependency * paraview: adding variants to use external packages as internal do not compile * catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5 * catalyst: added ParaView_DIR env variable to catalyst module * add paraview, catalyst patches - https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2433 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2436 * - Handle updated library paths for catalyst. Versions 5.4 and old places libraries under a paraview subdirectory. Eg, "lib/paraview-5.4", they are now placed directly under "lib" - Minor code style cleanup * Handle update library and python paths for ParaView-5.5 * catalyst: added ParaView_DIR path to spack_env * BUG: applied the patch to the extracted catalyst source files * of-catalyst: added new package * add (FOAM,WM)_PROJECT_DIR also to spack_env environment * depends on first openfoam release supporting catalyst * paraview: added missing self to a member variable * openfoam-com: added missing env variables to module generation * openfoam: fixed flake8 errors * paraview: added Paraview_DIR to env * catalyst: added osmesa variant * of-catalyst: added full variant and openfoam version dependency * paraview-catalyst: use always external expat and netcdf * of-catalyst: reformatted package description * paraview-catalyst: removed duplicated function * catalyst: fixed flake8 error * of-catalyst: fixed license header * of-catalyst: minor changes * of-catalyst: renamed gitrepo with git * of-catalyst: removed useless gitrepo parameter
511 lines
21 KiB
Diff
511 lines
21 KiB
Diff
# The VTK-m changes are slated for paraview-5.5.x
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#
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# The catalyst changes (the working directory for output) are slated for
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# paraview-5.6.
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# They are API-compatible with paraview-5.5 but not ABI compatible.
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#
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# https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
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# https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
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# https://gitlab.kitware.com/paraview/paraview/merge_requests/2436
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#
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--- ParaView-v5.5.0/VTK/ThirdParty/vtkm/vtk-m/CMake/VTKmDetermineVersion.cmake.orig 2018-04-06 22:03:33.000000000 +0200
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+++ ParaView-v5.5.0/VTK/ThirdParty/vtkm/vtk-m/CMake/VTKmDetermineVersion.cmake 2018-04-23 12:00:23.708544206 +0200
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@@ -51,6 +51,8 @@
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ERROR_QUIET
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OUTPUT_STRIP_TRAILING_WHITESPACE
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ERROR_STRIP_TRAILING_WHITESPACE)
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+ else()
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+ set(output)
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endif()
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else()
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set(result 0)
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@@ -75,7 +77,7 @@
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# Extracts components from a version string. See determine_version() for usage.
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function(extract_version_components version_string var_prefix)
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- string(REGEX MATCH "([0-9]+)\\.([0-9]+)\\.([0-9]+)[-]*(.*)"
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+ string(REGEX MATCH "^([0-9]+)\\.([0-9]+)\\.([0-9]+)[-]*(.*)$"
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version_matches "${version_string}")
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if(CMAKE_MATCH_0)
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set(full ${CMAKE_MATCH_0})
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--- ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPProcessor.cxx.orig 2018-04-06 22:03:33.000000000 +0200
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+++ ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPProcessor.cxx 2018-05-11 12:02:26.894772713 +0200
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@@ -38,6 +38,7 @@
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#include "vtkStringArray.h"
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#include <list>
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+#include <vtksys/SystemTools.hxx>
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struct vtkCPProcessorInternals
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{
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@@ -47,12 +48,13 @@
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};
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vtkStandardNewMacro(vtkCPProcessor);
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-vtkMultiProcessController* vtkCPProcessor::Controller = NULL;
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+vtkMultiProcessController* vtkCPProcessor::Controller = nullptr;
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//----------------------------------------------------------------------------
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vtkCPProcessor::vtkCPProcessor()
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{
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this->Internal = new vtkCPProcessorInternals;
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- this->InitializationHelper = NULL;
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+ this->InitializationHelper = nullptr;
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+ this->WorkingDirectory = nullptr;
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}
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//----------------------------------------------------------------------------
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@@ -61,14 +63,15 @@
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if (this->Internal)
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{
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delete this->Internal;
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- this->Internal = NULL;
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+ this->Internal = nullptr;
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}
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if (this->InitializationHelper)
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{
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this->InitializationHelper->Delete();
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- this->InitializationHelper = NULL;
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+ this->InitializationHelper = nullptr;
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}
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+ this->SetWorkingDirectory(nullptr);
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}
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//----------------------------------------------------------------------------
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@@ -95,7 +98,7 @@
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{
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if (which < 0 || which >= this->GetNumberOfPipelines())
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{
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- return NULL;
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+ return nullptr;
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}
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int counter = 0;
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vtkCPProcessorInternals::PipelineListIterator iter = this->Internal->Pipelines.begin();
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@@ -108,7 +111,7 @@
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counter++;
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iter++;
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}
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- return NULL;
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+ return nullptr;
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}
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//----------------------------------------------------------------------------
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@@ -130,17 +133,41 @@
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}
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//----------------------------------------------------------------------------
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-int vtkCPProcessor::Initialize()
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+int vtkCPProcessor::Initialize(const char* workingDirectory)
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{
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- if (this->InitializationHelper == NULL)
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+ if (this->InitializationHelper == nullptr)
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{
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this->InitializationHelper = this->NewInitializationHelper();
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}
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+ // make sure the directory exists here so that we only do it once
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+ if (workingDirectory)
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+ {
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+ vtkMultiProcessController* controller = vtkMultiProcessController::GetGlobalController();
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+ int success = 1;
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+ if (controller == nullptr || controller->GetLocalProcessId() == 0)
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+ {
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+ success = vtksys::SystemTools::MakeDirectory(workingDirectory) == true ? 1 : 0;
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+ if (success == 0)
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+ {
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+ vtkWarningMacro("Could not make "
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+ << workingDirectory << " directory. "
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+ << "Results will be generated in current working directory instead.");
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+ }
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+ }
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+ if (controller)
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+ {
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+ controller->Broadcast(&success, 1, 0);
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+ }
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+ if (success)
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+ {
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+ this->SetWorkingDirectory(workingDirectory);
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+ }
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+ }
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return 1;
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}
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//----------------------------------------------------------------------------
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-int vtkCPProcessor::Initialize(vtkMPICommunicatorOpaqueComm& comm)
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+int vtkCPProcessor::Initialize(vtkMPICommunicatorOpaqueComm& comm, const char* workingDirectory)
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{
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#ifdef PARAVIEW_USE_MPI
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if (vtkCPProcessor::Controller)
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@@ -148,7 +175,7 @@
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vtkErrorMacro("Can only initialize with a communicator once per process.");
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return 0;
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}
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- if (this->InitializationHelper == NULL)
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+ if (this->InitializationHelper == nullptr)
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{
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vtkMPICommunicator* communicator = vtkMPICommunicator::New();
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communicator->InitializeExternal(&comm);
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@@ -157,12 +184,12 @@
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this->Controller = controller;
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this->Controller->SetGlobalController(controller);
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communicator->Delete();
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- return this->Initialize();
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+ return this->Initialize(workingDirectory);
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}
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return 1;
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#else
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static_cast<void>(&comm); // get rid of variable not used warning
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- return this->Initialize();
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+ return this->Initialize(workingDirectory);
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#endif
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}
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@@ -225,6 +252,13 @@
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input->GetFieldData()->AddArray(catalystChannel);
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}
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}
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+
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+ std::string originalWorkingDirectory;
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+ if (this->WorkingDirectory)
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+ {
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+ originalWorkingDirectory = vtksys::SystemTools::GetCurrentWorkingDirectory();
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+ vtksys::SystemTools::ChangeDirectory(this->WorkingDirectory);
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+ }
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for (vtkCPProcessorInternals::PipelineListIterator iter = this->Internal->Pipelines.begin();
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iter != this->Internal->Pipelines.end(); iter++)
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{
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@@ -248,6 +282,10 @@
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}
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}
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}
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+ if (originalWorkingDirectory.empty() == false)
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+ {
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+ vtksys::SystemTools::ChangeDirectory(originalWorkingDirectory);
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+ }
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// we want to reset everything here to make sure that new information
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// is properly passed in the next time.
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dataDescription->ResetAll();
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@@ -259,7 +297,7 @@
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{
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if (this->Controller)
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{
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- this->Controller->SetGlobalController(NULL);
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+ this->Controller->SetGlobalController(nullptr);
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this->Controller->Finalize(1);
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this->Controller->Delete();
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}
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--- ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPProcessor.h.orig 2018-04-06 22:03:33.000000000 +0200
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+++ ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPProcessor.h 2018-05-11 12:02:26.894772713 +0200
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@@ -76,14 +76,16 @@
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virtual void RemoveAllPipelines();
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/// Initialize the co-processor. Returns 1 if successful and 0
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- /// otherwise.
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/// otherwise. If Catalyst is built with MPI then Initialize()
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/// can also be called with a specific MPI communicator if
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/// MPI_COMM_WORLD isn't the proper one. Catalyst is initialized
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- /// to use MPI_COMM_WORLD by default.
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- virtual int Initialize();
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+ /// to use MPI_COMM_WORLD by default. Both methods have an optional
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+ /// workingDirectory argument which will set *WorkingDirectory* so
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+ /// that files will be put relative to this directory.
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+ virtual int Initialize(const char* workingDirectory = nullptr);
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#ifndef __WRAP__
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- virtual int Initialize(vtkMPICommunicatorOpaqueComm& comm);
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+ virtual int Initialize(
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+ vtkMPICommunicatorOpaqueComm& comm, const char* workingDirectory = nullptr);
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#endif
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/// The Catalyst input field data string array name. This array will
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@@ -111,6 +113,13 @@
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/// implementation an opportunity to clean up, before it is destroyed.
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virtual int Finalize();
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+ /// Get the current working directory for outputting Catalyst files.
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+ /// If not set then Catalyst output files will be relative to the
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+ /// current working directory. This will not affect where Catalyst
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+ /// looks for Python scripts. *WorkingDirectory* gets set through
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+ /// the *Initialize()* methods.
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+ vtkGetStringMacro(WorkingDirectory);
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+
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protected:
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vtkCPProcessor();
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virtual ~vtkCPProcessor();
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@@ -118,6 +127,11 @@
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/// Create a new instance of the InitializationHelper.
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virtual vtkObject* NewInitializationHelper();
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+ /// Set the current working directory for outputting Catalyst files.
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+ /// This is a protected method since simulation code adaptors should
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+ /// set this through the *Initialize()* methods.
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+ vtkSetStringMacro(WorkingDirectory);
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+
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private:
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vtkCPProcessor(const vtkCPProcessor&) = delete;
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void operator=(const vtkCPProcessor&) = delete;
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@@ -125,6 +139,7 @@
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vtkCPProcessorInternals* Internal;
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vtkObject* InitializationHelper;
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static vtkMultiProcessController* Controller;
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+ char* WorkingDirectory;
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};
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#endif
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--- ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPXMLPWriterPipeline.cxx.orig 2018-04-06 22:03:33.000000000 +0200
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+++ ParaView-v5.5.0/CoProcessing/Catalyst/vtkCPXMLPWriterPipeline.cxx 2018-05-11 12:02:26.894772713 +0200
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@@ -31,6 +31,7 @@
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#include <vtkSmartPointer.h>
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#include <vtkUnstructuredGrid.h>
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+#include <algorithm>
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#include <sstream>
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#include <string>
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@@ -174,7 +175,7 @@
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for (unsigned int i = 0; i < dataDescription->GetNumberOfInputDescriptions(); i++)
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{
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- const char* inputName = dataDescription->GetInputDescriptionName(i);
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+ std::string inputName = dataDescription->GetInputDescriptionName(i);
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vtkCPInputDataDescription* idd = dataDescription->GetInputDescription(i);
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vtkDataObject* grid = idd->GetGrid();
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if (grid == nullptr)
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@@ -206,6 +207,8 @@
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vtkSMStringVectorProperty* fileName =
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vtkSMStringVectorProperty::SafeDownCast(writer->GetProperty("FileName"));
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+ // If we have a / in the channel name we take it out of the filename we're going to write to
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+ inputName.erase(std::remove(inputName.begin(), inputName.end(), '/'), inputName.end());
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std::ostringstream o;
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if (this->Path.empty() == false)
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{
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--- ParaView-v5.5.0/Wrapping/Python/paraview/coprocessing.py.orig 2018-04-06 22:03:33.000000000 +0200
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+++ ParaView-v5.5.0/Wrapping/Python/paraview/coprocessing.py 2018-05-11 12:02:27.038772408 +0200
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@@ -11,22 +11,12 @@
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from paraview.vtk.vtkPVVTKExtensionsCore import *
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import math
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-# -----------------------------------------------------------------------------
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-def IsInModulo(timestep, frequencyArray):
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- """
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- Return True if the given timestep is in one of the provided frequency.
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- This can be interpreted as follow::
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-
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- isFM = IsInModulo(timestep, [2,3,7])
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-
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- is similar to::
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+# If the user created a filename in a location that doesn't exist by default we'll
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+# make the directory for them. This can be changed though by setting createDirectoriesIfNeeded
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+# to False.
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+createDirectoriesIfNeeded = True
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- isFM = (timestep % 2 == 0) or (timestep % 3 == 0) or (timestep % 7 == 0)
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- """
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- for frequency in frequencyArray:
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- if frequency > 0 and (timestep % frequency == 0):
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- return True
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- return False
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+# -----------------------------------------------------------------------------
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class CoProcessor(object):
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"""Base class for co-processing Pipelines.
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@@ -68,6 +58,9 @@
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self.__CinemaTracks = {}
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self.__InitialFrequencies = {}
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self.__PrintEnsightFormatString = False
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+ self.__TimeStepToStartOutputAt=0
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+ self.__ForceOutputAtFirstCall=False
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+ self.__FirstTimeStepIndex = None
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def SetPrintEnsightFormatString(self, enable):
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"""If outputting ExodusII files with the purpose of reading them into
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@@ -87,6 +80,17 @@
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"Incorrect argument type: %s, must be a dict" % type(frequencies))
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self.__InitialFrequencies = frequencies
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+ def SetInitialOutputOptions(self, timeStepToStartOutputAt, forceOutputAtFirstCall):
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+ """Set the frequencies at which the pipeline needs to be updated.
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+ Typically, this is called by the subclass once it has determined what
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+ timesteps co-processing will be needed to be done.
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+ frequencies is a map, with key->string name of for the simulation
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+ input, and value is a list of frequencies.
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+ """
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+
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+ self.__TimeStepToStartOutputAt=timeStepToStartOutputAt
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+ self.__ForceOutputAtFirstCall=forceOutputAtFirstCall
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+
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def EnableLiveVisualization(self, enable, frequency = 1):
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"""Call this method to enable live-visualization. When enabled,
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DoLiveVisualization() will communicate with ParaView server if possible
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@@ -115,7 +119,7 @@
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# if this is a time step to do live then all of the inputs
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# must be made available. note that we want the pipeline built
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# before we do the actual first live connection.
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- if self.__EnableLiveVisualization and timestep % self.__LiveVisualizationFrequency == 0 \
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+ if self.__EnableLiveVisualization and self.NeedToOutput(timestep, self.__LiveVisualizationFrequency) \
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and self.__LiveVisualizationLink:
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if self.__LiveVisualizationLink.Initialize(servermanager.ActiveConnection.Session.GetSessionProxyManager()):
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num_inputs = datadescription.GetNumberOfInputDescriptions()
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@@ -132,13 +136,13 @@
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# hasn't been set up yet). If we don't have live enabled
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# we know that the output frequencies aren't changed and can
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# just use the initial frequencies.
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- if self.__InitialFrequencies or not self.__EnableLiveVisualization:
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+ if self.__ForceOutputAtFirstCall or self.__InitialFrequencies or not self.__EnableLiveVisualization:
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num_inputs = datadescription.GetNumberOfInputDescriptions()
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for cc in range(num_inputs):
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input_name = datadescription.GetInputDescriptionName(cc)
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freqs = self.__InitialFrequencies.get(input_name, [])
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- if self.__EnableLiveVisualization or ( self and IsInModulo(timestep, freqs) ):
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+ if self.__EnableLiveVisualization or ( self and self.IsInModulo(timestep, freqs) ):
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datadescription.GetInputDescription(cc).AllFieldsOn()
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datadescription.GetInputDescription(cc).GenerateMeshOn()
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else:
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@@ -149,15 +153,14 @@
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for writer in self.__WritersList:
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frequency = writer.parameters.GetProperty(
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"WriteFrequency").GetElement(0)
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- if (timestep % frequency) == 0 or \
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- datadescription.GetForceOutput() == True:
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+ if self.NeedToOutput(timestep, frequency) or datadescription.GetForceOutput() == True:
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writerinputs = cpstate.locate_simulation_inputs(writer)
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for writerinput in writerinputs:
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datadescription.GetInputDescriptionByName(writerinput).AllFieldsOn()
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datadescription.GetInputDescriptionByName(writerinput).GenerateMeshOn()
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for view in self.__ViewsList:
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- if (view.cpFrequency and timestep % view.cpFrequency == 0) or \
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+ if (view.cpFrequency and self.NeedToOutput(timestep, view.cpFrequency)) or \
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datadescription.GetForceOutput() == True:
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viewinputs = cpstate.locate_simulation_inputs_for_view(view)
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for viewinput in viewinputs:
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@@ -192,8 +195,7 @@
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for writer in self.__WritersList:
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frequency = writer.parameters.GetProperty(
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"WriteFrequency").GetElement(0)
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- if (timestep % frequency) == 0 or \
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- datadescription.GetForceOutput() == True:
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+ if self.NeedToOutput(timestep, frequency) or datadescription.GetForceOutput() == True:
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fileName = writer.parameters.GetProperty("FileName").GetElement(0)
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paddingamount = writer.parameters.GetProperty("PaddingAmount").GetElement(0)
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|
helperName = writer.GetXMLName()
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@@ -203,6 +205,23 @@
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else:
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ts = str(timestep).rjust(paddingamount, '0')
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|
writer.FileName = fileName.replace("%t", ts)
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|
+ if '/' in writer.FileName and createDirectoriesIfNeeded:
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+ oktowrite = [1.]
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+ import vtk
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|
+ comm = vtk.vtkMultiProcessController.GetGlobalController()
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|
+ if comm.GetLocalProcessId() == 0:
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|
+ import os
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|
+ newDir = writer.FileName[0:writer.FileName.rfind('/')]
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|
+ try:
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|
+ os.makedirs(newDir)
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|
+ except OSError:
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|
+ if not os.path.isdir(newDir):
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|
+ print ("ERROR: Cannot make directory for", writer.FileName, ". No data will be written.")
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|
+ oktowrite[0] = 0.
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|
+ comm.Broadcast(oktowrite, 1, 0)
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|
+ if oktowrite[0] == 0:
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|
+ # we can't make the directory so no reason to update the pipeline
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|
+ 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
|