Merge pull request #989 from keichi/reorganize-params

Allow specifying read/write method parameters in adios_reorganize

source/utils/adios_reorganize/Reorganize.cpp

@@ -30,6 +30,7 @@
 #include "adios2/core/Engine.h"
 #include "adios2/core/IO.h"
 #include "adios2/helper/adiosFunctions.h"
+#include "adios2/helper/adiosString.h"
 
 // C headers
 #include <cerrno>
@@ -56,9 +57,9 @@ Reorganize::Reorganize(int argc, char *argv[])
     infilename = std::string(argv[1]);
     outfilename = std::string(argv[2]);
     rmethodname = std::string(argv[3]);
-    rmethodparams = std::string(argv[4]);
+    rmethodparam_str = std::string(argv[4]);
     wmethodname = std::string(argv[5]);
-    wmethodparams = std::string(argv[6]);
+    wmethodparam_str = std::string(argv[6]);
 
     int nd = 0;
     int j = 7;
@@ -113,9 +114,9 @@ void Reorganize::Run()
     print0("Input stream            = ", infilename);
     print0("Output stream           = ", outfilename);
     print0("Read method             = ", rmethodname);
-    print0("Read method parameters  = ", rmethodparams);
+    print0("Read method parameters  = ", rmethodparam_str);
     print0("Write method            = ", wmethodname);
-    print0("Write method parameters = ", wmethodparams);
+    print0("Write method parameters = ", wmethodparam_str);
 
 #ifdef ADIOS2_HAVE_MPI
     core::ADIOS adios(comm, true, "C++");
@@ -127,11 +128,12 @@ void Reorganize::Run()
     print0("Waiting to open stream ", infilename, "...");
 
     io.SetEngine(rmethodname);
-    io.SetParameter("verbose", "5");
+    io.SetParameters(rmethodparams);
     core::Engine &rStream = io.Open(infilename, adios2::Mode::Read);
     // rStream.FixedSchedule();
 
     io.SetEngine(wmethodname);
+    io.SetParameters(wmethodparams);
     core::Engine &wStream = io.Open(outfilename, adios2::Mode::Write);
 
     int steps = 0;
@@ -205,7 +207,25 @@ void Reorganize::print0(Arg &&arg, Args &&... args)
     }
 }
 
-void Reorganize::ParseArguments() {}
+Params Reorganize::parseParams(const std::string &param_str)
+{
+    std::istringstream ss(param_str);
+    std::vector<std::string> kvs;
+    std::string kv;
+
+    while (std::getline(ss, kv, ','))
+    {
+        kvs.push_back(kv);
+    }
+
+    return helper::BuildParametersMap(kvs, true);
+}
+
+void Reorganize::ParseArguments()
+{
+    rmethodparams = parseParams(rmethodparam_str);
+    wmethodparams = parseParams(wmethodparam_str);
+}
 
 void Reorganize::ProcessParameters() const {}
 

source/utils/adios_reorganize/Reorganize.h

@@ -66,14 +66,15 @@ class Reorganize : public Utils
                         const core::DataMap &attributes, int step);
     int ReadWrite(core::Engine &rStream, core::Engine &wStream, core::IO &io,
                   const core::DataMap &variables, int step);
+    Params parseParams(const std::string &param_str);
 
     // Input arguments
-    std::string infilename;    // File/stream to read
-    std::string outfilename;   // File to write
-    std::string wmethodname;   // ADIOS write method
-    std::string wmethodparams; // ADIOS write method
-    std::string rmethodname;   // ADIOS read method
-    std::string rmethodparams; // ADIOS read method
+    std::string infilename;       // File/stream to read
+    std::string outfilename;      // File to write
+    std::string wmethodname;      // ADIOS write method
+    std::string wmethodparam_str; // ADIOS write method parameter string
+    std::string rmethodname;      // ADIOS read method
+    std::string rmethodparam_str; // ADIOS read method parameter string
 
     static const int max_read_buffer_size = 1024 * 1024 * 1024;
     static const int max_write_buffer_size = 1024 * 1024 * 1024;
@@ -86,6 +87,10 @@ class Reorganize : public Utils
     int numproc = 1;
     MPI_Comm comm;
 
+    // Read/write method parameters
+    Params rmethodparams;
+    Params wmethodparams;
+
     uint64_t write_total = 0;   // data size read/written by one processor
     uint64_t largest_block = 0; // the largest variable block one process reads