adios2: add latest release (#36563)
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Vicente Bolea
GitHub
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1fb5707235
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9684b03bff
5 changed files with 242 additions and 0 deletions
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@ -21,6 +21,11 @@ class Adios2(CMakePackage, CudaPackage):
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tags = ["e4s"]
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version("master", branch="master")
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version(
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"2.9.0",
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sha256="69f98ef58c818bb5410133e1891ac192653b0ec96eb9468590140f2552b6e5d1",
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preferred=True,
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)
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version("2.8.3", sha256="4906ab1899721c41dd918dddb039ba2848a1fb0cf84f3a563a1179b9d6ee0d9f")
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version("2.8.2", sha256="9909f6409dc44b2c28c1fda0042dab4b711f25ec3277ef0cb6ffc40f5483910d")
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version("2.8.1", sha256="3f515b442bbd52e3189866b121613fe3b59edb8845692ea86fad83d1eba35d93")
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@ -0,0 +1,31 @@
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From fdb93d3e9d447b9dd6ce5c77aca18396cf9b6aa3 Mon Sep 17 00:00:00 2001
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From: Vicente Bolea <vicente.bolea@kitware.com>
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Date: Mon, 3 Apr 2023 12:58:58 -0400
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Subject: [PATCH] Update /VTK/IO/ADIOS2/vtkADIOS2CoreImageReader.cxx
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---
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VTK/IO/ADIOS2/vtkADIOS2CoreImageReader.cxx | 4 ++--
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1 file changed, 2 insertions(+), 2 deletions(-)
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diff --git a/VTK/IO/ADIOS2/vtkADIOS2CoreImageReader.cxx b/VTK/IO/ADIOS2/vtkADIOS2CoreImageReader.cxx
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index 5d58905a88..3ce039345a 100644
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--- a/VTK/IO/ADIOS2/vtkADIOS2CoreImageReader.cxx
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+++ b/VTK/IO/ADIOS2/vtkADIOS2CoreImageReader.cxx
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@@ -361,12 +361,12 @@ bool vtkADIOS2CoreImageReader::OpenAndReadMetaData()
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vtkMPICommunicator* comm =
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static_cast<vtkMPICommunicator*>(this->Controller->GetCommunicator());
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- this->Impl->Adios.reset(new adios2::ADIOS(*comm->GetMPIComm()->GetHandle(), adios2::DebugON));
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+ this->Impl->Adios.reset(new adios2::ADIOS(*comm->GetMPIComm()->GetHandle()));
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#else
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// Make sure the ADIOS subsystem is initialized before processing any
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// sort of request.
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- this->Impl->Adios.reset(new adios2::ADIOS(adios2::DebugON));
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+ this->Impl->Adios.reset(new adios2::ADIOS());
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// Before processing any request, read the meta data first
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#endif
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}
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--
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2.35.3
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@ -285,6 +285,10 @@ class Paraview(CMakePackage, CudaPackage, ROCmPackage):
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# Fix VTK to work with external freetype using CONFIG mode for find_package
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patch("FindFreetype.cmake.patch", when="@5.10.1:")
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# Fix VTK to remove deprecated ADIOS2 functions
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# https://gitlab.kitware.com/vtk/vtk/-/merge_requests/10113
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patch("adios2-remove-deprecated-functions.patch", when="@5.10: ^adios2@2.9:")
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generator("ninja", "make", default="ninja")
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# https://gitlab.kitware.com/paraview/paraview/-/issues/21223
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conflicts("generator=ninja", when="%xl")
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@ -0,0 +1,200 @@
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From 9a2d334febe1cf62efd7bc857ea6fbd958a3cb11 Mon Sep 17 00:00:00 2001
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From: Vicente Bolea <vicente.bolea@gmail.com>
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Date: Mon, 3 Apr 2023 16:51:58 +0000
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Subject: [PATCH] Removed ADIOS2 deprecated functions invokation
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---
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sensei/ADIOS2AnalysisAdaptor.cxx | 10 ++++++----
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sensei/ADIOS2AnalysisAdaptor.h | 4 ----
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sensei/ADIOS2DataAdaptor.cxx | 8 --------
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sensei/ADIOS2DataAdaptor.h | 3 ---
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sensei/ADIOS2Schema.cxx | 6 +++++-
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sensei/ADIOS2Schema.h | 8 +-------
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sensei/testing/testADIOS2Read.py | 1 -
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sensei/testing/testADIOS2Write.py | 1 -
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8 files changed, 12 insertions(+), 29 deletions(-)
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diff --git a/sensei/ADIOS2AnalysisAdaptor.cxx b/sensei/ADIOS2AnalysisAdaptor.cxx
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index 4358e4d..73cd408 100644
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--- a/sensei/ADIOS2AnalysisAdaptor.cxx
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+++ b/sensei/ADIOS2AnalysisAdaptor.cxx
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@@ -46,7 +46,7 @@ senseiNewMacro(ADIOS2AnalysisAdaptor);
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//----------------------------------------------------------------------------
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ADIOS2AnalysisAdaptor::ADIOS2AnalysisAdaptor() :
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- Schema(nullptr), FileName("sensei.bp"), DebugMode(0),
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+ Schema(nullptr), FileName("sensei.bp"),
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StepsPerFile(0), StepIndex(0), FileIndex(0)
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{
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this->Handles.io = nullptr;
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@@ -270,9 +270,6 @@ int ADIOS2AnalysisAdaptor::Initialize(pugi::xml_node &node)
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if (!bufferMode.empty())
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this->AddParameter("QueueFullPolicy", bufferMode);
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- // turn on/off debug output
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- this->SetDebugMode(node.attribute("debug_mode").as_int(0));
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-
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// enable file series for file based engines
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this->SetStepsPerFile(node.attribute("steps_per_file").as_int(0));
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@@ -329,8 +326,13 @@ int ADIOS2AnalysisAdaptor::InitializeADIOS2()
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}
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// initialize adios2
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+#if ADIOS2_VERSION_MAJOR > 2 || (ADIOS2_VERSION_MAJOR == 2 && ADIOS2_VERSION_MINOR >= 9)
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+ // adios2_init()'s signature changed in version 2.9.0
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+ this->Adios = adios2_init(this->GetCommunicator());
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+#else
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this->Adios = adios2_init(this->GetCommunicator(),
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adios2_debug_mode(this->DebugMode));
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+#endif
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if (this->Adios == nullptr)
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{
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diff --git a/sensei/ADIOS2AnalysisAdaptor.h b/sensei/ADIOS2AnalysisAdaptor.h
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index 4919ddb..c5c6d2c 100644
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--- a/sensei/ADIOS2AnalysisAdaptor.h
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+++ b/sensei/ADIOS2AnalysisAdaptor.h
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@@ -75,9 +75,6 @@ public:
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void SetStepsPerFile(long steps)
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{ this->StepsPerFile = steps; }
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- /// Enable/disable debugging output. The default value is 0.
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- void SetDebugMode(int mode)
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- { this->DebugMode = mode; }
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/** Adds a set of sensei::DataRequirements, typically this will come from an XML
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* configuratiopn file. Data requirements tell the adaptor what to fetch from
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@@ -146,7 +143,6 @@ protected:
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senseiADIOS2::AdiosHandle Handles;
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adios2_adios *Adios;
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std::vector<std::pair<std::string,std::string>> Parameters;
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- int DebugMode;
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long StepsPerFile;
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long StepIndex;
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long FileIndex;
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diff --git a/sensei/ADIOS2DataAdaptor.cxx b/sensei/ADIOS2DataAdaptor.cxx
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index 5c0c036..bbb093e 100644
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--- a/sensei/ADIOS2DataAdaptor.cxx
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+++ b/sensei/ADIOS2DataAdaptor.cxx
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@@ -56,12 +56,6 @@ void ADIOS2DataAdaptor::SetReadEngine(const std::string &engine)
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this->Internals->Stream.SetReadEngine(engine);
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}
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-//----------------------------------------------------------------------------
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-void ADIOS2DataAdaptor::SetDebugMode(int mode)
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-{
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- this->Internals->Stream.SetDebugMode(mode);
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-}
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-
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//----------------------------------------------------------------------------
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void ADIOS2DataAdaptor::AddParameter(const std::string &name,
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const std::string &value)
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@@ -96,8 +90,6 @@ int ADIOS2DataAdaptor::Initialize(pugi::xml_node &node)
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if (node.attribute("timeout"))
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this->AddParameter("OpenTimeoutSecs", node.attribute("timeout").value());
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- this->SetDebugMode(node.attribute("debug_mode").as_int(0));
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-
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pugi::xml_node params = node.child("engine_parameters");
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if (params)
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{
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diff --git a/sensei/ADIOS2DataAdaptor.h b/sensei/ADIOS2DataAdaptor.h
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index b0c2009..58be416 100644
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--- a/sensei/ADIOS2DataAdaptor.h
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+++ b/sensei/ADIOS2DataAdaptor.h
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@@ -30,9 +30,6 @@ public:
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// given to the write side analysis adaptor
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void SetReadEngine(const std::string &readEngine);
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- // enable/disable adios internal debug messages
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- void SetDebugMode(int mode);
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-
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// add name value pairs to pass into ADIOS after the
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// engine has been created
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void AddParameter(const std::string &name, const std::string &value);
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diff --git a/sensei/ADIOS2Schema.cxx b/sensei/ADIOS2Schema.cxx
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index b1263ca..7b66d19 100644
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--- a/sensei/ADIOS2Schema.cxx
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+++ b/sensei/ADIOS2Schema.cxx
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@@ -422,7 +422,12 @@ int InputStream::Initialize(MPI_Comm comm)
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sensei::TimeEvent<128> mark("senseiADIOS2::InputStream::Initialize");
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// initialize adios2
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+#if ADIOS2_VERSION_MAJOR > 2 || (ADIOS2_VERSION_MAJOR == 2 && ADIOS2_VERSION_MINOR >= 9)
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+ // adios2_init()'s signature changed in version 2.9.0
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+ this->Adios = adios2_init(comm);
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+#else
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this->Adios = adios2_init(comm, adios2_debug_mode(this->DebugMode));
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+#endif
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if (this->Adios == nullptr)
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{
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SENSEI_ERROR("adios2_init failed")
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@@ -651,7 +656,6 @@ int InputStream::Finalize()
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this->Handles.engine = nullptr;
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this->Handles.io = nullptr;
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this->ReadEngine = "";
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- this->DebugMode = 0;
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return 0;
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}
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diff --git a/sensei/ADIOS2Schema.h b/sensei/ADIOS2Schema.h
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index b8e5bfb..bc4f3bc 100644
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--- a/sensei/ADIOS2Schema.h
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+++ b/sensei/ADIOS2Schema.h
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@@ -109,8 +109,7 @@ struct InputStream
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{
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InputStream() : Handles(), Adios(nullptr),
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ReadEngine(""), FileName(""), FileSeries(0),
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- StepsPerFile(0), FileIndex(0), StepIndex(0),
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- DebugMode(0) {}
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+ StepsPerFile(0), FileIndex(0), StepIndex(0) {}
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// pass engine parameters to ADIOS2 in key value pairs
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void AddParameter(const std::string &key, const std::string &value);
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@@ -120,10 +119,6 @@ struct InputStream
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void SetReadEngine(const std::string &engine)
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{ this->ReadEngine = engine; }
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- // set debug mode 0 off, 1 on
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- void SetDebugMode(int mode)
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- { this->DebugMode = mode; }
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-
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/// @brief Set the filename.
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/// Default value is "sensei.bp" which is suitable for use with streams or
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/// transport engines such as SST. When writing files to disk using the BP4
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@@ -165,7 +160,6 @@ struct InputStream
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int FileIndex;
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int StepIndex;
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std::vector<std::pair<std::string,std::string>> Parameters;
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- int DebugMode;
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};
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}
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diff --git a/sensei/testing/testADIOS2Read.py b/sensei/testing/testADIOS2Read.py
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index b2fd8d2..916c28f 100644
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--- a/sensei/testing/testADIOS2Read.py
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+++ b/sensei/testing/testADIOS2Read.py
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@@ -39,7 +39,6 @@ def read_data(engine, fileName, verbose):
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da = ADIOS2DataAdaptor.New()
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da.SetReadEngine(engine)
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da.SetFileName(fileName)
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- da.SetDebugMode(1)
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da.SetPartitioner(BlockPartitioner.New())
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da.OpenStream()
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# process all time steps
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diff --git a/sensei/testing/testADIOS2Write.py b/sensei/testing/testADIOS2Write.py
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index d6f2f67..28a6631 100644
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--- a/sensei/testing/testADIOS2Write.py
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+++ b/sensei/testing/testADIOS2Write.py
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@@ -155,7 +155,6 @@ def write_data(engine, file_name, steps_per_file, n_its):
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aw.SetEngineName(engine)
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aw.SetFileName(file_name)
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aw.SetStepsPerFile(steps_per_file)
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- aw.SetDebugMode(1)
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# create the datasets
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# the first mesh is an image
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--
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2.35.3
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@ -98,6 +98,8 @@ class Sensei(CMakePackage):
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conflicts("+ascent", when="+libsim")
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# Patches
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# https://github.com/SENSEI-insitu/SENSEI/pull/114
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patch("adios2-remove-deprecated-functions.patch", when="@4:4.1 ^adios2@2.9:")
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patch("libsim-add-missing-symbol-visibility-pr67.patch", when="@4.0.0")
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patch("sensei-find-mpi-component-cxx-pr68.patch", when="@4.0.0")
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patch("sensei-install-external-pugixml-pr69.patch", when="@4.0.0")
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