[WIP] Add MPISeries Class

CMakeLists.txt

@@ -315,6 +315,9 @@ set(CORE_SOURCE
         src/backend/Writable.cpp
         src/benchmark/mpi/OneDimensionalBlockSlicer.cpp
         src/helper/list_series.cpp)
+if(openPMD_HAVE_MPI)
+    set(CORE_SOURCE ${CORE_SOURCE} src/MPISeries.cpp)  # TODO: MPI_SOURCE and own target
+endif()
 set(IO_SOURCE
         src/IO/AbstractIOHandlerHelper.cpp
         src/IO/DummyIOHandler.cpp

NEWS.rst

@@ -3,6 +3,27 @@
 Upgrade Guide
 =============
 
+0.12.0-alpha
+------------
+
+MPI-parallel C++ functionality has its own include ``<openPMD/MPI.hpp>`` and ``MPISeries`` class  now.
+The old ``Series(std::string, AccessType, MPI_Comm)`` constructor has been deprecated and will be removed in a future version.
+New usage for MPI-parallel I/O:
+
+.. code-block:: cpp
+
+   #include <openPMD/MPI.hpp>  // new include
+
+   using namespace io = openPMD;
+
+   // ...
+   auto series = io::MPISeries(  // instead of io::Series
+       "path/to/data_files_%T.h5",
+       io::AccessType::READ_ONLY,
+       MPI_COMM_WORLD
+   );
+
+
 0.11.0-alpha
 ------------
 

docs/source/details/doxygen.rst

@@ -14,7 +14,8 @@ Public Headers
 ===========================  =======================================================
 Include                      Description
 ===========================  =======================================================
-``<openPMD/openPMD.hpp>``    Public facade header (serial and MPI)
+``<openPMD/openPMD.hpp>``    Public facade header (serial)
+``<openPMD/MPI.hpp>``        Public facade header (MPI)
 ``<openPMD/benchmark/...>``  Optional :ref:`benchmark <utilities-benchmark>` helpers
 ===========================  =======================================================
 

include/openPMD/MPI.hpp

@@ -0,0 +1,27 @@
+/* Copyright 2020 Axel Huebl
+ *
+ * This file is part of openPMD-api.
+ *
+ * openPMD-api is free software: you can redistribute it and/or modify
+ * it under the terms of of either the GNU General Public License or
+ * the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * openPMD-api is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License and the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * and the GNU Lesser General Public License along with openPMD-api.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+#pragma once
+
+// IWYU pragma: begin_exports
+#include "openPMD/MPISeries.hpp"
+
+#include "openPMD/openPMD.hpp"
+// IWYU pragma: end_exports

include/openPMD/MPISeries.hpp

@@ -0,0 +1,56 @@
+/* Copyright 2017-2020 Fabian Koller, Axel Huebl
+ *
+ * This file is part of openPMD-api.
+ *
+ * openPMD-api is free software: you can redistribute it and/or modify
+ * it under the terms of of either the GNU General Public License or
+ * the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * openPMD-api is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License and the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * and the GNU Lesser General Public License along with openPMD-api.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+#pragma once
+
+#include "openPMD/config.hpp"
+#include "openPMD/Series.hpp"
+#include "openPMD/IO/AccessType.hpp"
+
+#if openPMD_HAVE_MPI
+#   include <mpi.h>
+#else
+#   error "Including <openPMD/MPI.hpp> requires an MPI-enabled installation"
+#endif
+
+#include <string>
+
+
+namespace openPMD
+{
+    /** @brief  Root level of the openPMD hierarchy for MPI-parallel I/O.
+     *
+     * Entry point and common link between all iterations of particle and mesh data.
+     *
+     * @see Series
+     */
+    class MPISeries : public Series
+    {
+        //friend class Iteration;
+        //friend class Series;
+
+    public:
+        MPISeries(std::string const& filepath,
+                  AccessType at,
+                  MPI_Comm comm);
+
+        ~MPISeries();
+    }; // MPISeries
+} // namespace openPMD

include/openPMD/Series.hpp

@@ -22,6 +22,7 @@
 
 #include "openPMD/config.hpp"
 #include "openPMD/auxiliary/Deprecated.hpp"
+#include "openPMD/auxiliary/ParsedInput.hpp"
 #include "openPMD/backend/Attributable.hpp"
 #include "openPMD/backend/Container.hpp"
 #include "openPMD/IO/AbstractIOHandler.hpp"
@@ -41,6 +42,9 @@
 #ifndef OPENPMD_private
 #   define OPENPMD_private private
 #endif
+#ifndef OPENPMD_protected
+#   define OPENPMD_protected protected
+#endif
 
 
 namespace openPMD
@@ -58,6 +62,7 @@ class Series : public Attributable
 
 public:
 #if openPMD_HAVE_MPI
+    OPENPMDAPI_DEPRECATED("Please include <openPMD/MPI.h> and use the class MPISeries for MPI-parallel I/O.")
     Series(std::string const& filepath,
            AccessType at,
            MPI_Comm comm);
@@ -252,10 +257,19 @@ class Series : public Attributable
 
     Container< Iteration, uint64_t > iterations;
 
+OPENPMD_protected:
+    /** This constructor is only for derived Series-types
+     *
+     * calling this will skip the creation of an ioHandler
+     */
+    Series();
+
+    std::unique_ptr< auxiliary::ParsedInput > parseInput(std::string);
+    void init(std::shared_ptr< AbstractIOHandler >, std::unique_ptr< auxiliary::ParsedInput >);
+
+    std::shared_ptr< IterationEncoding > m_iterationEncoding;
+
 OPENPMD_private:
-    struct ParsedInput;
-    std::unique_ptr< ParsedInput > parseInput(std::string);
-    void init(std::shared_ptr< AbstractIOHandler >, std::unique_ptr< ParsedInput >);
     void initDefaults();
     void flushFileBased();
     void flushGroupBased();
@@ -268,7 +282,6 @@ class Series : public Attributable
 
     static constexpr char const * const BASEPATH = "/data/%T/";
 
-    std::shared_ptr< IterationEncoding > m_iterationEncoding;
     std::shared_ptr< std::string > m_name;
     std::shared_ptr< Format > m_format;
 

include/openPMD/auxiliary/ParsedInput.hpp

@@ -0,0 +1,44 @@
+/* Copyright 2020 Axel Huebl, Fabian Koller
+ *
+ * This file is part of openPMD-api.
+ *
+ * openPMD-api is free software: you can redistribute it and/or modify
+ * it under the terms of of either the GNU General Public License or
+ * the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * openPMD-api is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License and the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * and the GNU Lesser General Public License along with openPMD-api.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+#pragma once
+
+#include "openPMD/IterationEncoding.hpp"
+#include "openPMD/IO/Format.hpp"
+
+#include <string>
+
+
+namespace openPMD
+{
+namespace auxiliary
+{
+    struct ParsedInput
+    {
+        std::string path;
+        std::string name;
+        Format format;
+        IterationEncoding iterationEncoding;
+        std::string filenamePrefix;
+        std::string filenamePostfix;
+        int filenamePadding;
+    }; // ParsedInput
+} // namespace backend
+} // namespace openPMD

include/openPMD/backend/Container.hpp

@@ -75,6 +75,7 @@ class Container : public Attributable
     friend class Iteration;
     friend class ParticleSpecies;
     friend class Series;
+    friend class MPISeries;
 
 public:
     using key_type = typename InternalContainer::key_type;

src/MPISeries.cpp

@@ -0,0 +1,66 @@
+/* Copyright 2017-2020 Fabian Koller, Axel Huebl
+ *
+ * This file is part of openPMD-api.
+ *
+ * openPMD-api is free software: you can redistribute it and/or modify
+ * it under the terms of of either the GNU General Public License or
+ * the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * openPMD-api is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License and the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * and the GNU Lesser General Public License along with openPMD-api.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+#include "openPMD/MPISeries.hpp"
+#include "openPMD/Iteration.hpp"
+#include "openPMD/IterationEncoding.hpp"
+#include "openPMD/backend/Container.hpp"
+#include "openPMD/IO/AbstractIOHandler.hpp"
+#include "openPMD/IO/AbstractIOHandlerHelper.hpp"
+
+#include <iostream>
+#include <memory>
+#include <stdexcept>
+#include <string>
+
+
+namespace openPMD
+{
+    MPISeries::MPISeries(
+        std::string const& filepath,
+        AccessType at,
+        MPI_Comm comm
+    )
+    {
+        iterations = Container< Iteration, uint64_t >();
+        m_iterationEncoding = std::make_shared< IterationEncoding >();
+
+        auto input = parseInput(filepath);
+        auto handler = createIOHandler(input->path, at, input->format, comm);
+        init(handler, std::move(input));
+    }
+
+    MPISeries::~MPISeries()
+    {
+        // we must not throw in a destructor
+        try
+        {
+            flush();
+        }
+        catch( std::exception const & ex )
+        {
+            std::cerr << "[~MPISeries] An error occurred: " << ex.what() << std::endl;
+        }
+        catch( ... )
+        {
+            std::cerr << "[~MPISeries] An error occurred." << std::endl;
+        }
+    }
+} // namespace openPMD

src/Series.cpp

@@ -68,17 +68,6 @@ std::string cleanFilename(std::string const& filename, Format f);
 std::function< std::tuple< bool, int >(std::string const&) >
 matcher(std::string const& prefix, int padding, std::string const& postfix, Format f);
 
-struct Series::ParsedInput
-{
-    std::string path;
-    std::string name;
-    Format format;
-    IterationEncoding iterationEncoding;
-    std::string filenamePrefix;
-    std::string filenamePostfix;
-    int filenamePadding;
-};  //ParsedInput
-
 #if openPMD_HAVE_MPI
 Series::Series(std::string const& filepath,
                AccessType at,
@@ -102,6 +91,10 @@ Series::Series(std::string const& filepath,
     init(handler, std::move(input));
 }
 
+Series::Series()
+{
+}
+
 Series::~Series()
 {
     flush();
@@ -361,10 +354,10 @@ Series::flush()
     IOHandler->flush();
 }
 
-std::unique_ptr< Series::ParsedInput >
+std::unique_ptr< auxiliary::ParsedInput >
 Series::parseInput(std::string filepath)
 {
-    std::unique_ptr< Series::ParsedInput > input{new Series::ParsedInput};
+    std::unique_ptr< auxiliary::ParsedInput > input{new auxiliary::ParsedInput};
 
 #ifdef _WIN32
     if( auxiliary::contains(filepath, '/') )
@@ -462,7 +455,7 @@ Series::parseInput(std::string filepath)
 
 void
 Series::init(std::shared_ptr< AbstractIOHandler > ioHandler,
-             std::unique_ptr< Series::ParsedInput > input)
+             std::unique_ptr< auxiliary::ParsedInput > input)
 {
     m_writable->IOHandler = ioHandler;
     IOHandler = m_writable->IOHandler.get();