Allow setting and retrieving meta info on Series

Author: franzpoeschel

include/openPMD/Series.hpp

@@ -116,6 +116,33 @@ class Series : public Attributable
      */
     Series& setMeshesPath(std::string const& meshesPath);
 
+    /**
+     * @throw   no_such_attribute_error If optional attribute is not present.
+     * @return  Vector with a String per (writing) MPI rank, indicating user-
+     *          defined meta information per rank. Example: host name.
+     */
+    chunk_assignment::RankMeta
+    mpiRanksMetaInfo() const;
+
+    /**
+     * @brief Set the Mpi Ranks Meta Info attribute, i.e. a Vector with
+     *        a String per (writing) MPI rank, indicating user-
+     *        defined meta information per rank. Example: host name.
+     *
+     * @return Reference to modified series.
+     */
+    Series & setMpiRanksMetaInfo( chunk_assignment::RankMeta );
+
+    /**
+     * @brief Set the Mpi Ranks Meta Info attribute, i.e. a Vector with
+     *        a String per (writing) MPI rank, indicating user-
+     *        defined meta information per rank. Example: host name.
+     *
+     * @return Reference to modified series.
+     */
+    Series &
+    setMpiRanksMetaInfo( std::string const & myRankInfo );
+
     /**
      * @throw   no_such_attribute_error If optional attribute is not present.
      * @return  String representing the path to particle species, relative(!) to <CODE>basePath</CODE>.
@@ -282,5 +309,8 @@ class Series : public Attributable
     std::shared_ptr< std::string > m_filenamePrefix;
     std::shared_ptr< std::string > m_filenamePostfix;
     std::shared_ptr< int > m_filenamePadding;
+#if openPMD_HAVE_MPI
+    MPI_Comm m_communicator;
+#endif
 }; // Series
 } // namespace openPMD

include/openPMD/auxiliary/Filesystem.hpp

@@ -87,5 +87,19 @@ remove_directory(std::string const& path);
  */
 bool
 remove_file(std::string const& path);
+struct no_such_file_error
+{
+};
+
+/**
+ * @brief Read a file line by line.
+ *
+ * @param path Path to the file.
+ * @return Lines of the read file, excluding newline characters.
+ *
+ * @throws no_such_file_error
+ */
+std::vector< std::string >
+read_file_by_lines( std::string const & path );
 } // auxiliary
 } // openPMD

include/openPMD/auxiliary/MPI.hpp

@@ -1,5 +1,7 @@
 #pragma once
 
+#include "openPMD/config.hpp"
+
 #if openPMD_HAVE_MPI
 
 #    include <mpi.h>

src/Series.cpp

@@ -20,6 +20,7 @@
  */
 #include "openPMD/auxiliary/Date.hpp"
 #include "openPMD/auxiliary/Filesystem.hpp"
+#include "openPMD/auxiliary/MPI.hpp"
 #include "openPMD/auxiliary/StringManip.hpp"
 #include "openPMD/IO/AbstractIOHandler.hpp"
 #include "openPMD/IO/AbstractIOHandlerHelper.hpp"
@@ -92,6 +93,7 @@ Series::Series(
     std::string const & options )
     : iterations{ Container< Iteration, uint64_t >() }
     , m_iterationEncoding{ std::make_shared< IterationEncoding >() }
+    , m_communicator{ comm }
 {
     auto input = parseInput( filepath );
     auto handler =
@@ -193,6 +195,90 @@ Series::setMeshesPath(std::string const& mp)
     return *this;
 }
 
+chunk_assignment::RankMeta
+Series::mpiRanksMetaInfo() const
+{
+    std::vector< std::string > asContiguousVector;
+    try
+    {
+        asContiguousVector =
+            getAttribute( "rankMetaInfo" ).get< std::vector< std::string > >();
+    }
+    catch( std::runtime_error const & )
+    {
+        // workaround: if vector has length 1, some backends may report a
+        // single value instead of a vector
+        asContiguousVector = {
+            getAttribute( "rankMetaInfo" ).get< std::string >()
+        };
+    }
+    chunk_assignment::RankMeta res;
+    for( size_t i = 0; i < asContiguousVector.size(); ++i )
+    {
+        res[ i ] = std::move( asContiguousVector[ i ] );
+    }
+    return res;
+}
+
+Series &
+Series::setMpiRanksMetaInfo( chunk_assignment::RankMeta rankMeta )
+{
+    std::vector< std::string > asContiguousVector;
+    asContiguousVector.reserve( rankMeta.size() );
+    try
+    {
+        for( size_t i = 0; i < rankMeta.size(); ++i )
+        {
+            asContiguousVector.emplace_back( std::move( rankMeta.at( i ) ) );
+        }
+    }
+    catch( std::out_of_range )
+    {
+        throw std::runtime_error( "[setMpiRanksMetaInfo] Can only set meta "
+                                  "info for contiguous ranks 0 to n." );
+    }
+
+    setAttribute( "rankMetaInfo", std::move( asContiguousVector ) );
+    return *this;
+}
+
+Series &
+Series::setMpiRanksMetaInfo( std::string const & myRankInfo )
+{
+    if( auxiliary::starts_with( myRankInfo, '@' ) )
+    {
+        // read from file
+        std::string fileName = auxiliary::replace_first( myRankInfo, "@", "" );
+        std::vector< std::string > rankMeta;
+        try
+        {
+            rankMeta = auxiliary::read_file_by_lines( fileName );
+        }
+        catch( auxiliary::no_such_file_error const & )
+        {
+            std::cerr << "Not setting rank meta information, because file has "
+                         "not been found: "
+                      << fileName << std::endl;
+            return *this;
+        }
+        setAttribute( "rankMetaInfo", rankMeta );
+        return *this;
+    }
+#if openPMD_HAVE_MPI
+    int rank;
+    MPI_Comm_rank( m_communicator, &rank );
+    std::vector< std::string > rankMeta =
+        auxiliary::collectStringsTo( m_communicator, 0, myRankInfo );
+    if( rank == 0 )
+    {
+        setAttribute( "rankMetaInfo", std::move( rankMeta ) );
+    }
+    return *this;
+#else
+    setAttribute( "rankMetaInfo", std::vector< std::string >{ myRankInfo } );
+#endif
+}
+
 std::string
 Series::particlesPath() const
 {

src/auxiliary/Filesystem.cpp

@@ -32,6 +32,8 @@
 
 #include <stdexcept>
 #include <system_error>
+#include <fstream>
+#include <sstream>
 
 
 namespace openPMD
@@ -168,5 +170,22 @@ remove_file( std::string const& path )
 #endif
 }
 
+std::vector< std::string >
+read_file_by_lines( std::string const & path )
+{
+    std::vector< std::string > res;
+    std::ifstream file( path, std::ios_base::in );
+    if ( file.fail( ) )
+    {
+        throw no_such_file_error( );
+    }
+    std::string line;
+    while( std::getline( file, line ) )
+    {
+        res.push_back( std::move( line ) );
+        line = std::string( );
+    }
+    return res;
+}
 } // auxiliary
 } // openPMD