Primary changes:
* Add an improved cache system to speed up performance.
* Fix NCZarr to properly handle scalar variables.
Misc. Related Changes:
* Added unit tests for extendible hash and for the generic cache.
* Add config parameter to set size of the NCZarr cache.
* Add initial performance tests but leave them unused.
* Add CRC64 support.
* Move location of ncdumpchunks utility from /ncgen to /ncdump.
* Refactor auth support.
Misc. Unrelated Changes:
* More cleanup of the S3 support
* Add support for S3 authentication in .rc files: HTTP.S3.ACCESSID and HTTP.S3.SECRETKEY.
* Remove the hashkey from the struct OBJHDR since it is never used.
disengagement of enable-netcdf4 from enable-hdf5.
That is, with the advent of nczarr, it is possible
to turn off hdf5 but still need netcdf-4 enabled
because nczarr uses libsrc4, but not libhdf5.
This change involves a bunch of things:
1. Modify configure.ac and CMakelist to make enable_hdf5
control if hdf5 support is provided. For back compatibility,
disable-netcdf4 is treated as disable-hdf5. But internally,
netcdf4 support is controlled only by the enabling of formats
that require it.
2. In support of #1, modify .travis.yml to use enable/disable-hdf5
instead of enable/disable-netcdf4.
3. test_common.in is modified to track selected features,
including enable-hdf5 and enable-s3-tests. This is used in
selected tests that mix netcdf-3 and netcdf4 tests.
4. The conflation of USE_HDF5 and USE_NETCDF4 is common in
code, tests, and build files, so all of those had to be weeded out.
5. It turns out that some of the NC4_dim functions really are HDF5 specific,
but are not treated as such. So they are moved from nc4dim.c to
hdf5dim.c or hdf5dispatch.c
6. Some generic functions in libhdf5 can be (and were) moved to libsrc4.
The current library seems to have some behavior which is N^2 in the number of vars in a file.
The `NC4_inq_dim` routine calls down to `nc4_find_dim_len` which iterates through each `var` in the file/group and calls `find_var_dim_max_length` on each var and finds the largest length of the dim on each of those vars. This is done only for unlimited vars.
I have a file with 129 dim and 1630 vars. The unlimited dimension is of length 41. In my test program, I am reading data from 4 files which have the same dim and var count and reading every 4th time step (unlimited dimension). If I run a profile, I see that 98.2% of the program time is in the `nc_get_vara_float` call tree and most of that is in `find_var_dim_max_length` (94.8%).
There are 66,142 calls to `nc_get_vara_float` resulting in 107,307,290 calls to `find_var_dim_max_length` with twice that number of calls to `malloc/free` and calls to 5 HDF5 routines. All of this, at least in my case, to return the same `41` each time.
The proof of concept patch here will check whether the file is read-only (or no_write) and if so, it will cache the value of the dim length the first time it is calculated. With this change, my example run is sped up by a factor of 60. The time for `NC4_inq_dim` and below drops from 97.2% down to 2.7%.
I'm not sure whether this is the correct fix, or if there is some behavior that I am overlooking, but my users would definitely like a 10 second run compared to a 10 minute run...
This is on current Netcdf master branch.
I will try to attach some valgrind/callgrind profiles.
