Merge pull request #1787 from williamfgc/bp4_bug

Modify data file name functions in BP3 and BP4
ornladios · Sep 26, 2019 · 7b754a9 · 7b754a9
2 parents 97bbabc + d329483
commit 7b754a9
Show file tree

Hide file tree

Showing 9 changed files with 50 additions and 44 deletions.
diff --git a/source/adios2/engine/bp3/BP3Reader.tcc b/source/adios2/engine/bp3/BP3Reader.tcc
@@ -86,7 +86,7 @@ void BP3Reader::ReadVariableBlocks(Variable<T> &variable)
                     const std::string subFileName =
                         m_BP3Deserializer.GetBPSubFileName(
                             m_Name, subStreamBoxInfo.SubStreamID,
-                            m_BP3Deserializer.m_Minifooter.HasSubFiles);
+                            m_BP3Deserializer.m_Minifooter.HasSubFiles, true);
 
                     m_SubFileManager.OpenFileID(
                         subFileName, subStreamBoxInfo.SubStreamID, Mode::Read,

diff --git a/source/adios2/engine/bp4/BP4Reader.tcc b/source/adios2/engine/bp4/BP4Reader.tcc
@@ -86,7 +86,7 @@ void BP4Reader::ReadVariableBlocks(Variable<T> &variable)
                     const std::string subFileName =
                         m_BP4Deserializer.GetBPSubFileName(
                             m_Name, subStreamBoxInfo.SubStreamID,
-                            m_BP4Deserializer.m_Minifooter.HasSubFiles);
+                            m_BP4Deserializer.m_Minifooter.HasSubFiles, true);
 
                     m_DataFileManager.OpenFileID(
                         subFileName, subStreamBoxInfo.SubStreamID, Mode::Read,

diff --git a/source/adios2/toolkit/format/bp/BPBase.cpp b/source/adios2/toolkit/format/bp/BPBase.cpp
@@ -170,7 +170,11 @@ void BPBase::Init(const Params &parameters, const std::string hint)
             {
                 subStreams = m_SizeMPI;
             }
-            m_Aggregator.Init(subStreams, m_Comm);
+
+            if (subStreams < m_SizeMPI)
+            {
+                m_Aggregator.Init(subStreams, m_Comm);
+            }
         }
         else if (key == "node-local")
         {

diff --git a/source/adios2/toolkit/format/bp/bp3/BP3Base.cpp b/source/adios2/toolkit/format/bp/bp3/BP3Base.cpp
@@ -76,9 +76,10 @@ BP3Base::GetBPSubStreamNames(const std::vector<std::string> &names) const
 
 std::string BP3Base::GetBPSubFileName(const std::string &name,
                                       const size_t subFileIndex,
-                                      const bool hasSubFiles) const noexcept
+                                      const bool hasSubFiles,
+                                      const bool isReader) const noexcept
 {
-    return GetBPSubStreamName(name, subFileIndex, hasSubFiles);
+    return GetBPSubStreamName(name, subFileIndex, hasSubFiles, isReader);
 }
 
 size_t BP3Base::GetBPIndexSizeInData(const std::string &variableName,
@@ -142,8 +143,8 @@ BP3Base::ReadElementIndexHeader(const std::vector<char> &buffer,
 
 // PRIVATE
 std::string BP3Base::GetBPSubStreamName(const std::string &name,
-                                        const size_t rank,
-                                        const bool hasSubFiles) const noexcept
+                                        const size_t id, const bool hasSubFiles,
+                                        const bool isReader) const noexcept
 {
     if (!hasSubFiles)
     {
@@ -162,7 +163,8 @@ std::string BP3Base::GetBPSubStreamName(const std::string &name,
     }
 
     const size_t index =
-        m_Aggregator.m_IsActive ? m_Aggregator.m_SubStreamIndex : rank;
+        isReader ? id
+                 : m_Aggregator.m_IsActive ? m_Aggregator.m_SubStreamIndex : id;
 
     const std::string bpRankName(bpName + ".dir" + PathSeparator + bpRoot +
                                  "." + std::to_string(index));

diff --git a/source/adios2/toolkit/format/bp/bp3/BP3Base.h b/source/adios2/toolkit/format/bp/bp3/BP3Base.h
@@ -82,7 +82,8 @@ class BP3Base : virtual public BPBase
 
     std::string GetBPSubFileName(const std::string &name,
                                  const size_t subFileIndex,
-                                 const bool hasSubFiles = true) const noexcept;
+                                 const bool hasSubFiles = true,
+                                 const bool isReader = false) const noexcept;
 
     /**
      * Returns the estimated variable index size. Used by ResizeBuffer public
@@ -100,9 +101,9 @@ class BP3Base : virtual public BPBase
         noexcept final;
 
 private:
-    std::string GetBPSubStreamName(const std::string &name, const size_t rank,
-                                   const bool hasSubFiles = true) const
-        noexcept;
+    std::string GetBPSubStreamName(const std::string &name, const size_t id,
+                                   const bool hasSubFiles = true,
+                                   const bool isReader = false) const noexcept;
 };
 
 } // end namespace format

diff --git a/source/adios2/toolkit/format/bp/bp4/BP4Base.cpp b/source/adios2/toolkit/format/bp/bp4/BP4Base.cpp
@@ -113,9 +113,10 @@ BP4Base::GetBPSubStreamNames(const std::vector<std::string> &names) const
 
 std::string BP4Base::GetBPSubFileName(const std::string &name,
                                       const size_t subFileIndex,
-                                      const bool hasSubFiles) const noexcept
+                                      const bool hasSubFiles,
+                                      const bool isReader) const noexcept
 {
-    return GetBPSubStreamName(name, subFileIndex, hasSubFiles);
+    return GetBPSubStreamName(name, subFileIndex, hasSubFiles, isReader);
 }
 
 size_t BP4Base::GetBPIndexSizeInData(const std::string &variableName,
@@ -188,8 +189,8 @@ BP4Base::ReadElementIndexHeader(const std::vector<char> &buffer,
 
 // PRIVATE
 std::string BP4Base::GetBPSubStreamName(const std::string &name,
-                                        const size_t rank,
-                                        const bool hasSubFiles) const noexcept
+                                        const size_t id, const bool hasSubFiles,
+                                        const bool isReader) const noexcept
 {
     if (!hasSubFiles)
     {
@@ -199,7 +200,8 @@ std::string BP4Base::GetBPSubStreamName(const std::string &name,
     const std::string bpName = RemoveTrailingSlash(name);
 
     const size_t index =
-        m_Aggregator.m_IsActive ? m_Aggregator.m_SubStreamIndex : rank;
+        isReader ? id
+                 : m_Aggregator.m_IsActive ? m_Aggregator.m_SubStreamIndex : id;
 
     /* the name of a data file starts with "data." */
     const std::string bpRankName(bpName + PathSeparator + "data." +

diff --git a/source/adios2/toolkit/format/bp/bp4/BP4Base.h b/source/adios2/toolkit/format/bp/bp4/BP4Base.h
@@ -111,7 +111,8 @@ class BP4Base : virtual public BPBase
 
     std::string GetBPSubFileName(const std::string &name,
                                  const size_t subFileIndex,
-                                 const bool hasSubFiles = true) const noexcept;
+                                 const bool hasSubFiles = true,
+                                 const bool isReader = false) const noexcept;
 
     /**
      * Returns the estimated variable index size. Used by ResizeBuffer public
@@ -139,9 +140,9 @@ class BP4Base : virtual public BPBase
         noexcept final;
 
 private:
-    std::string GetBPSubStreamName(const std::string &name, const size_t rank,
-                                   const bool hasSubFiles = true) const
-        noexcept;
+    std::string GetBPSubStreamName(const std::string &name, const size_t id,
+                                   const bool hasSubFiles = true,
+                                   const bool isReader = false) const noexcept;
 };
 
 } // end namespace format

diff --git a/source/adios2/toolkit/format/bp/bp4/BP4Serializer.tcc b/source/adios2/toolkit/format/bp/bp4/BP4Serializer.tcc
@@ -436,23 +436,22 @@ size_t BP4Serializer::PutVariableMetadataInData(
                                      position);
 
     // here align pointer for span
-    if (span != nullptr)
-    {
-        const size_t padLengthPosition = position;
-        uint8_t zero = 0;
-        // skip 1 for paddingLength and 4 for VMD] ending
-        helper::CopyToBuffer(buffer, position, &zero, 5);
-        // here check for the next aligned pointer
-        const size_t extraBytes = m_Data.Align<T>();
-        const std::string pad = std::string(extraBytes, '\0') + "VMD]";
-
-        size_t backPosition = padLengthPosition;
-        const uint8_t padLength = static_cast<uint8_t>(pad.size());
-        helper::CopyToBuffer(buffer, backPosition, &padLength);
-        helper::CopyToBuffer(buffer, backPosition, pad.c_str(), pad.size());
-
-        position += extraBytes;
-    }
+
+    const size_t padLengthPosition = position;
+    uint8_t zero = 0;
+    // skip 1 for paddingLength and 4 for VMD] ending
+    helper::CopyToBuffer(buffer, position, &zero, 5);
+    // here check for the next aligned pointer
+    const size_t extraBytes = m_Data.Align<T>();
+    const std::string pad =
+        span == nullptr ? "VMD]" : std::string(extraBytes, '\0') + "VMD]";
+
+    size_t backPosition = padLengthPosition;
+    const uint8_t padLength = static_cast<uint8_t>(pad.size());
+    helper::CopyToBuffer(buffer, backPosition, &padLength);
+    helper::CopyToBuffer(buffer, backPosition, pad.c_str(), pad.size());
+
+    position += extraBytes;
 
     absolutePosition += position - mdBeginPosition;
     return varLengthPosition;

diff --git a/testing/adios2/engine/bp/TestBPWriteAggregateRead.cpp b/testing/adios2/engine/bp/TestBPWriteAggregateRead.cpp
@@ -21,8 +21,7 @@ void WriteAggRead1D8(const std::string substreams)
 {
     // Each process would write a 1x8 array and all processes would
     // form a mpiSize * Nx 1D array
-    const std::string fname("ADIOS2BPWriteAggregateRead1D8_" + substreams +
-                            ".bp");
+    const std::string fname("BPWriteAggregateRead1D8_" + substreams + ".bp");
 
     int mpiRank = 0, mpiSize = 1;
     // Number of rows
@@ -322,8 +321,7 @@ void WriteAggRead2D4x2(const std::string substreams)
 {
     // Each process would write a 2x4 array and all processes would
     // form a 2D 2 * (numberOfProcess*Nx) matrix where Nx is 4 here
-    const std::string fname("ADIOS2BPWriteAggregateRead2D2x4_" + substreams +
-                            ".bp");
+    const std::string fname("BPWriteAggregateRead2D2x4_" + substreams + ".bp");
 
     int mpiRank = 0, mpiSize = 1;
     // Number of rows
@@ -634,8 +632,7 @@ void WriteAggRead2D2x4(const std::string substreams)
 {
     // Each process would write a 4x2 array and all processes would
     // form a 2D 4 * (NumberOfProcess * Nx) matrix where Nx is 2 here
-    const std::string fname("ADIOS2BPWriteAggregateRead2D4x2_" + substreams +
-                            ".bp");
+    const std::string fname("BPWriteAggregateRead2D4x2_" + substreams + ".bp");
 
     int mpiRank = 0, mpiSize = 1;
     // Number of rows