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Add support for HDF5 array outputs #33

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merged 8 commits into from
Jun 20, 2017
Merged

Add support for HDF5 array outputs #33

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0471da7
Add new h5 format with array layout similar to netcdf
Jun 10, 2017
09ce355
Add a third dimension for the outputs
Jun 20, 2017
8552680
Fix the output file extensions
Jun 20, 2017
40320c0
Update the documentation
Jun 20, 2017
21a72cd
Cleanup
Jun 20, 2017
f4b71e4
Try to use a newer distro on Travis
Jun 20, 2017
7d91a63
Revert to default Travis distro
Jun 20, 2017
773e607
Define HDF5 compatiblity macros
Jun 20, 2017
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5 changes: 3 additions & 2 deletions docs/input_output.rst
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Expand Up @@ -75,7 +75,7 @@ Here is a typical global file taken from the examples folder:
0

%Where to put write hydrographs
%(0 = no output, 1 = .dat file, 2 = .csv file, 3 = database, 5 = .h5)
%(0 = no output, 1 = .dat file, 2 = .csv file, 3 = database, 5 = .h5 packet, 6 = .h5 array)
5 5.0 outputs.h5

%Where to put peakflow data
Expand Down Expand Up @@ -388,7 +388,8 @@ where :math:`A` is the upstream of the link, measured in km2.
A time series flag of ``1`` indicates the results of the simulation will be saved as a .dat file. The filename complete with a path must be specified. If a file with the name and path given already exists, it is overwritten.
A time series flag of ``2`` indicates the results will be stored as a .csv file.
A time series flag of ``3`` indicates the results will be uploaded into the database described by the given .dbc file. In this case, a table name accessible by the queries in the .dbc file must be specified.
A time series flag of ``5`` indicates indicates the results will be stored as a .h5 HDF5 file.
A time series flag of ``5`` indicates the results will be stored as a .h5 HDF5 file with a packet layout compatible with PyTable.
A time series flag of ``6`` indicates the results will be stored as a .h5 HDF5 file with an 3D array layout. Time, link id and output indexes are given as additional 1D "dimension" arrays. Selected outputs in :ref:`Solver Outputs` must have the same type (ASYNCH_FLOAT).

This section is independent of the section for Link IDs to Save described below (see :ref:`Global Parameters`) For example, if link ids are specified in the Link IDs to Save section and the time series flag in the Time Series Locations set to ``0``, no output is generated. Similarly, if *the time series id flag* is set to ``0`` in the Link IDs to Save section and the time series flag is set to ``1``, a .dat file with ``0`` time series is produced.

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8 changes: 3 additions & 5 deletions examples/clearcreek.gbl
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Expand Up @@ -8,9 +8,7 @@
0 %Parameters to filenames

%Components to print
4
Time
LinkID
2
State0
State6

Expand Down Expand Up @@ -55,8 +53,8 @@ Classic
0

%Where to put write hydrographs
%(0 = no output, 1 = .dat file, 2 = .csv file, 3 = database)
1 5.0 clearcreek.dat
%(0 = no output, 1 = .dat file, 2 = .csv file, 3 = database, 5 = .h5 packet, 6 = .h5 array)
6 5.0 clearcreek.h5

%Where to put peakflow data
%(0 = no output, 1 = .pea file, 2 = database)
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4 changes: 0 additions & 4 deletions ide/msvc/asynch/asynch.vcxproj
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Expand Up @@ -109,10 +109,6 @@
</ClCompile>
<ClCompile Include="..\..\..\src\optparse.c" />
</ItemGroup>
<ItemGroup>
<None Include="$(RootDir)\src\LICENSE" />
<None Include="$(RootDir)\src\makefile" />
</ItemGroup>
<ItemGroup>
<ProjectReference Include="..\asynchlib\asynchlib.vcxproj">
<Project>{b7c669bc-cb73-4fd5-b095-65aa2c1d6d1b}</Project>
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4 changes: 0 additions & 4 deletions ide/msvc/asynch/asynch.vcxproj.filters
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Expand Up @@ -36,8 +36,4 @@
<Filter>Source Files</Filter>
</ClCompile>
</ItemGroup>
<ItemGroup>
<None Include="$(RootDir)\src\LICENSE" />
<None Include="$(RootDir)\src\makefile" />
</ItemGroup>
</Project>
1 change: 0 additions & 1 deletion ide/msvc/asynchlib/asynchlib.vcxproj
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Expand Up @@ -175,7 +175,6 @@
</ItemGroup>
<ItemGroup>
<None Include="$(RootDir)\LICENSE" />
<None Include="$(RootDir)\makefile" />
</ItemGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
<ImportGroup Label="ExtensionTargets">
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1 change: 0 additions & 1 deletion ide/msvc/asynchlib/asynchlib.vcxproj.filters
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Expand Up @@ -239,6 +239,5 @@
</ItemGroup>
<ItemGroup>
<None Include="$(RootDir)\LICENSE" />
<None Include="$(RootDir)\makefile" />
</ItemGroup>
</Project>
3 changes: 3 additions & 0 deletions src/asynch_interface.c
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Expand Up @@ -1058,6 +1058,9 @@ int Asynch_Check_Peakflow_Output(AsynchSolver* asynch, char* name)

int Asynch_Delete_Temporary_Files(AsynchSolver* asynch)
{
if (asynch->outputfile)
fclose(asynch->outputfile);

int ret_val = RemoveTemporaryFiles(asynch->globals, asynch->my_save_size, NULL);
//if(ret_val == 1) printf("[%i]: Error deleting temp file. File does not exist.\n");
if (ret_val != 0) printf("[%i]: Error [%i] while deleting temp file.\n", my_rank, ret_val);
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4 changes: 3 additions & 1 deletion src/config_gbl.c
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Expand Up @@ -439,7 +439,7 @@ GlobalVars* Read_Global_Data(
globals->hydros_loc_filename = NULL;
globals->hydro_table = NULL;

if (globals->hydros_loc_flag == 1 || globals->hydros_loc_flag == 2 || globals->hydros_loc_flag == 4 || globals->hydros_loc_flag == 5)
if (globals->hydros_loc_flag == 1 || globals->hydros_loc_flag == 2 || globals->hydros_loc_flag == 4 || globals->hydros_loc_flag == 5 || globals->hydros_loc_flag == 6)
{
globals->hydros_loc_filename = (char*)malloc(ASYNCH_MAX_PATH_LENGTH * sizeof(char));
valsread = sscanf(line_buffer, "%*u %lf %s", &(globals->print_time), globals->hydros_loc_filename);
Expand All @@ -448,12 +448,14 @@ GlobalVars* Read_Global_Data(
if (globals->hydros_loc_flag == 2 && !CheckFilenameExtension(globals->hydros_loc_filename, ".csv")) return NULL;
if (globals->hydros_loc_flag == 4 && !CheckFilenameExtension(globals->hydros_loc_filename, ".rad")) return NULL;
if (globals->hydros_loc_flag == 5 && !CheckFilenameExtension(globals->hydros_loc_filename, ".h5")) return NULL;
if (globals->hydros_loc_flag == 6 && !CheckFilenameExtension(globals->hydros_loc_filename, ".h5")) return NULL;
//globals->output_flag = (globals->hydros_loc_flag == 1) ? 0 : 1;

if (globals->hydros_loc_flag == 1) RemoveSuffix(globals->hydros_loc_filename, ".dat");
else if (globals->hydros_loc_flag == 2) RemoveSuffix(globals->hydros_loc_filename, ".csv");
else if (globals->hydros_loc_flag == 4) RemoveSuffix(globals->hydros_loc_filename, ".rad");
else if (globals->hydros_loc_flag == 5) RemoveSuffix(globals->hydros_loc_filename, ".h5");
else if (globals->hydros_loc_flag == 6) RemoveSuffix(globals->hydros_loc_filename, ".h5");
}
else if (globals->hydros_loc_flag == 3)
{
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2 changes: 1 addition & 1 deletion src/io.c
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Expand Up @@ -45,7 +45,7 @@ void OutputFunc_Init(
output_func->PreparePeakflowOutput = NULL;

//Create Final Time Series Output
if (hydros_loc_flag == 1 || hydros_loc_flag == 2 || hydros_loc_flag == 4 || hydros_loc_flag == 5)
if (hydros_loc_flag == 1 || hydros_loc_flag == 2 || hydros_loc_flag == 4 || hydros_loc_flag == 5 || hydros_loc_flag == 6)
output_func->CreateOutput = &DumpTimeSerieFile;
else if (hydros_loc_flag == 3)
{
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