Merge pull request #452 from pdziekan/record_aux_const_arrays

add functions to record aux const arrays

Author: pdziekan

libmpdata++/output/hdf5.hpp

@@ -48,11 +48,11 @@ namespace libmpdataxx
       // HDF types of host data
       const H5::FloatType
         flttype_solver =
-	  sizeof(typename solver_t::real_t) == sizeof(long double)
-	    ? H5::PredType::NATIVE_LDOUBLE
-	    : sizeof(typename solver_t::real_t) == sizeof(double)
-	      ? H5::PredType::NATIVE_DOUBLE :
-	      H5::PredType::NATIVE_FLOAT,
+          sizeof(typename solver_t::real_t) == sizeof(long double)
+            ? H5::PredType::NATIVE_LDOUBLE
+            : sizeof(typename solver_t::real_t) == sizeof(double)
+              ? H5::PredType::NATIVE_DOUBLE :
+              H5::PredType::NATIVE_FLOAT,
         flttype_output = H5::PredType::NATIVE_FLOAT; // using floats not to waste disk space
 
       blitz::TinyVector<hsize_t, parent_t::n_dims> cshape, shape, chunk, srfcshape, srfcchunk, offst;
@@ -98,7 +98,7 @@ namespace libmpdataxx
           offst = 0;
 
           for (int d = 0; d < parent_t::n_dims; ++d)
-	    shape[d] = this->mem->distmem.grid_size[d];
+            shape[d] = this->mem->distmem.grid_size[d];
 
           chunk = shape;
 
@@ -114,10 +114,10 @@ namespace libmpdataxx
 #if defined(USE_MPI)
           if (this->mem->distmem.size() > 1)
           {
-	    shape[0] = this->mem->grid_size[0].length();
-	    cshape[0] = this->mem->grid_size[0].length();
+            shape[0] = this->mem->grid_size[0].length();
+            cshape[0] = this->mem->grid_size[0].length();
 
-	    if (this->mem->distmem.rank() == this->mem->distmem.size() - 1) 
+            if (this->mem->distmem.rank() == this->mem->distmem.size() - 1) 
               cshape[0] += 1;
 
             offst[0] = this->mem->grid_size[0].first();
@@ -134,9 +134,9 @@ namespace libmpdataxx
           srfcchunk = chunk;
           *(srfcchunk.end()-1) = 1;
 
-	  params.setChunk(parent_t::n_dims, chunk.data());
+          params.setChunk(parent_t::n_dims, chunk.data());
 #if !defined(USE_MPI)
-	  params.setDeflate(5); // TODO: move such constant to the header
+          params.setDeflate(5); // TODO: move such constant to the header
 #endif
 
           // creating variables
@@ -222,26 +222,26 @@ namespace libmpdataxx
         assert(this->rank == 0);
         //count[1] = 1; TODO
 
-	// creating the timestep file
-	hdfp.reset(new H5::H5File(this->outdir + "/" + hdf_name(), H5F_ACC_TRUNC
+        // creating the timestep file
+        hdfp.reset(new H5::H5File(this->outdir + "/" + hdf_name(), H5F_ACC_TRUNC
 #if defined(USE_MPI)
             , H5P_DEFAULT, fapl_id
 #endif
-	));
+        ));
 
         {
           std::map<int, H5::DataSet> vars;
 
-	  for (const auto &v : this->outvars)
-	  {
-	    // creating the user-requested variables
-	    vars[v.first] = (*hdfp).createDataSet(
-	      v.second.name,
-	      flttype_output,
-	      sspace,
-	      params
-	    );
-	    // TODO: units attribute
+          for (const auto &v : this->outvars)
+          {
+            // creating the user-requested variables
+            vars[v.first] = (*hdfp).createDataSet(
+              v.second.name,
+              flttype_output,
+              sspace,
+              params
+            );
+            // TODO: units attribute
 
             record_dsc_helper(vars[v.first], this->out_data(v.first));
           }
@@ -313,11 +313,11 @@ namespace libmpdataxx
       }
 
       // data is assumed to be contiguous and in the same layout as hdf variable
-      void record_aux(const std::string &name, typename solver_t::real_t *data)
+      void record_aux_hlpr(const std::string &name, typename solver_t::real_t *data, H5::H5File hdf)
       {
         assert(this->rank == 0);
 
-        auto aux = (*hdfp).createDataSet(
+        auto aux = hdf.createDataSet(
           name,
           flttype_output,
           sspace,
@@ -328,16 +328,21 @@ namespace libmpdataxx
         space.selectHyperslab(H5S_SELECT_SET, shape.data(), offst.data());
         aux.write(data, flttype_solver, H5::DataSpace(parent_t::n_dims, shape.data()), space, dxpl_id);
       }
+
+      void record_aux(const std::string &name, typename solver_t::real_t *data)
+      {
+        record_aux_hlpr(name, data, *hdfp);
+      }
 
       // for discontiguous array with halos
-      void record_aux_dsc(const std::string &name, const typename solver_t::arr_t &arr, bool srfc = false)
+      void record_aux_dsc_hlpr(const std::string &name, const typename solver_t::arr_t &arr, H5::H5File hdf, bool srfc = false)
       {
         assert(this->rank == 0);
 
         if(srfc)
-	  params.setChunk(parent_t::n_dims, srfcchunk.data());
+          params.setChunk(parent_t::n_dims, srfcchunk.data());
 
-        auto aux = (*hdfp).createDataSet(
+        auto aux = hdf.createDataSet(
           name,
           flttype_output,
           srfc ? srfcspace : sspace,
@@ -347,13 +352,19 @@ namespace libmpdataxx
         if(srfc)
         {
           // revert to default chunk
-	  params.setChunk(parent_t::n_dims, chunk.data());
+          params.setChunk(parent_t::n_dims, chunk.data());
           record_dsc_srfc_helper(aux, arr);
         }
         else
           record_dsc_helper(aux, arr);
       }
 
+      void record_aux_dsc(const std::string &name, const typename solver_t::arr_t &arr, bool srfc = false)
+      {
+        record_aux_dsc_hlpr(name, arr, *hdfp, srfc);
+      }
+
+
       void record_scalar_hlpr(const std::string &name, const std::string &group_name, typename solver_t::real_t data, H5::H5File hdf)
       {
         assert(this->rank == 0);
@@ -373,6 +384,19 @@ namespace libmpdataxx
       }
 
       // has to be called after const file was created (i.e. after start())
+      void record_aux_const(const std::string &name, typename solver_t::real_t *data)
+      {
+        H5::H5File hdfcp(const_file, H5F_ACC_RDWR); // reopen the const file
+        record_aux_hlpr(name, data, hdfcp);
+      }
+
+      // has to be called after const file was created (i.e. after start())
+      void record_aux_dsc_const(const std::string &name,  const typename solver_t::arr_t &arr)
+      {
+        H5::H5File hdfcp(const_file, H5F_ACC_RDWR); // reopen the const file
+        record_aux_dsc_hlpr(name, arr, hdfcp);
+      }
+
       void record_aux_const(const std::string &name, const std::string &group_name, typename solver_t::real_t data)
       {
         H5::H5File hdfcp(const_file, H5F_ACC_RDWR
@@ -593,8 +617,8 @@ namespace libmpdataxx
 
       // ctor
       hdf5(
-	typename parent_t::ctor_args_t args,
-	const typename parent_t::rt_params_t &p
+        typename parent_t::ctor_args_t args,
+        const typename parent_t::rt_params_t &p
       ) : parent_t(args, p)
       {
 #if defined(USE_MPI)