enh: add interface to view and set hdf5 options (#153)

* add interface to view and set hdf5 chunking and compression options
* add compact storage option

the supported options are:

chunking/enabled = "true" | "false"
  should chunking be used

chunking/threshold = (int)
  a threshold number of bytes in dataset before using chunking

chunking/chunk_size = (int)
  the size of chunks (in bytes) to be used

chunking/compression/method = "none" | "gzip"
  compression method

chunking/compression/level = (int)
  compression level option for gzip

compact_storage/enabled = "true" | "false"
  should compact storage be used

compact_storage/threshold = (int)
  a threshold max number of bytes in dataset to use compact storage

These options appear in relay::about() and can be set using:

io::hdf5_set_options(n);

Which is included in the conduit_relay_hdf5 header.

* add link of hdf5 for using with make example 

to solve issues with static build testing

* hdf5 group creation property tweaks

* add helper to check if hdf5 path exists

* enable compact by default, simplify chunking logic

.travis.yml

@@ -130,8 +130,8 @@ script:
   - ./example
   # using with make example
   - cd ${TRAVIS_BUILD_DIR}/src/examples/using-with-make
-  - env CXX=${CONDUIT_CXX} CONDUIT_DIR=${TRAVIS_BUILD_DIR}/travis-debug-install make
-  - env LD_LIBRARY_PATH=${TRAVIS_BUILD_DIR}/travis-debug-install/lib/ ./example
+  - env CXX=${CONDUIT_CXX} CONDUIT_DIR=${TRAVIS_BUILD_DIR}/travis-debug-install HDF5_DIR=${TRAVIS_HOME}/miniconda/lib make
+  - env LD_LIBRARY_PATH=${TRAVIS_BUILD_DIR}/travis-debug-install/lib/:${TRAVIS_HOME}/miniconda/lib ./example
 
 after_success:
   - test ${ENABLE_COVERAGE} = "ON" && coveralls --gcov /usr/bin/gcov-4.8 --include src/libs/conduit --include src/libs/blueprint --gcov-options '\-lp' --root $TRAVIS_BUILD_DIR --build-root $TRAVIS_BUILD_DIR/travis-debug-build;

src/examples/using-with-make/Makefile

@@ -59,7 +59,7 @@
 
 
 INC_FLAGS=-I$(CONDUIT_DIR)/include/conduit
-LINK_FLAGS=-L$(CONDUIT_DIR)/lib/ -lconduit -lconduit_relay -lconduit_blueprint
+LINK_FLAGS=-L$(CONDUIT_DIR)/lib/ -lconduit -lconduit_relay -lconduit_blueprint -L$(HDF5_DIR) -lhdf5 
 
 main:
 	$(CXX) $(INC_FLAGS) example.cpp $(LINK_FLAGS) -o example

src/libs/relay/conduit_relay.cpp

@@ -50,6 +50,10 @@
 
 #include "conduit_relay.hpp"
 
+#ifdef CONDUIT_RELAY_IO_HDF5_ENABLED
+#include "conduit_relay_hdf5.hpp"
+#endif
+
 //-----------------------------------------------------------------------------
 // standard lib includes
 //-----------------------------------------------------------------------------
@@ -103,6 +107,8 @@ about(Node &n)
 #ifdef CONDUIT_RELAY_IO_HDF5_ENABLED
     // straight hdf5 
     io_protos["hdf5"] = "enabled";
+
+    io::hdf5_options(n["io/options/hdf5"]);
 #else
     // straight hdf5 
     io_protos["hdf5"] = "disabled";