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netcdf-c/nczarr_test/CMakeLists.txt
Dennis Heimbigner df3636b959 Mitigate S3 test interference + Unlimited Dimensions in NCZarr 
This PR started as an attempt to add unlimited dimensions to NCZarr.
It did that, but this exposed significant problems with test interference.
So this PR is mostly about fixing -- well mitigating anyway -- test
interference.

The problem of test interference is now documented in the document docs/internal.md.
The solutions implemented here are also describe in that document.
The solution is somewhat fragile but multiple cleanup mechanisms
are provided. Note that this feature requires that the
AWS command line utility must be installed.

## Unlimited Dimensions.
The existing NCZarr extensions to Zarr are modified to support unlimited dimensions.
NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group".
Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms
Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2.
* Form 1: An integer representing the size of the dimension, which is used for simple named dimensions.
* Form 2: A dictionary with the following keys and values"
   - "size" with an integer value representing the (current) size of the dimension.
   - "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension.

For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases.
That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension.
This is the standard semantics for unlimited dimensions.

Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following.
* Did a partial refactor of the slice handling code in zwalk.c to clean it up.
* Added a number of tests for unlimited dimensions derived from the same test in nc_test4.
* Added several NCZarr specific unlimited tests; more are needed.
* Add test of endianness.

## Misc. Other Changes
* Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the
   AWS Transfer Utility mechanism. This is controlled by the
   ```#define TRANSFER```` command in that file. It defaults to being disabled.
* Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE).
* Fixed an obscure memory leak in ncdump.
* Removed some obsolete unit testing code and test cases.
* Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c.
* Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4.
* Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects.
* Modify the semantics of zodom to properly handle stride > 1.
* Add a truncate operation to the libnczarr zmap code.
2023-09-26 16:56:48 -06:00

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CMake
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# Copyright 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014,
# 2015, 2016, 2017, 2018
# University Corporation for Atmospheric Research/Unidata.
# See netcdf-c/COPYRIGHT file for more info.
SET(abs_top_srcdir ${CMAKE_CURRENT_SOURCE_DIR})
remove_definitions(-DDLL_EXPORT)
# Create nczarr tests from nc_test4 tests
macro(NCZARR_SH_TEST basename src)
FILE(READ ${CMAKE_CURRENT_SOURCE_DIR}/../${src}/tst_${basename}.sh SHSOURCE)
# Make sure the order of prepended lines is correct
STRING(PREPEND SHSOURCE "TESTNCZARR=1\n")
STRING(PREPEND SHSOURCE "#!/bin/bash\n")
# Replace with FILE(CONFIGURE) when cmake 3.18 is in common use
FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/run_${basename}.1 "${SHSOURCE}")
CONFIGURE_FILE(${CMAKE_CURRENT_BINARY_DIR}/run_${basename}.1 ${CMAKE_CURRENT_BINARY_DIR}/run_${basename}.sh FILE_PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE @ONLY NEWLINE_STYLE LF)
FILE(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/run_${basename}.1)
endmacro(NCZARR_SH_TEST)
macro(NCZARR_C_TEST basename newname src)
FILE(READ ${CMAKE_CURRENT_SOURCE_DIR}/../${src}/${basename}.c CSOURCE)
STRING(PREPEND CSOURCE "#define TESTNCZARR\n")
FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/${newname}.c "${CSOURCE}")
endmacro(NCZARR_C_TEST)
NCZARR_C_TEST(tst_quantize test_quantize nc_test4)
NCZARR_C_TEST(tst_filter_vlen test_filter_vlen nc_test4)
NCZARR_C_TEST(tst_unlim_vars test_unlim_vars nc_test4)
NCZARR_C_TEST(tst_h5_endians test_endians nc_test4)
NCZARR_C_TEST(tst_put_vars_two_unlim_dim test_put_vars_two_unlim_dim nc_test4)
NCZARR_C_TEST(tst_chunking test_chunking ncdump)
NCZARR_SH_TEST(specific_filters nc_test4)
NCZARR_SH_TEST(unknown nc_test4)
NCZARR_SH_TEST(filter_vlen nc_test4)
# Unlimited tests
NCZARR_SH_TEST(mud ncdump)
NCZARR_SH_TEST(nccopy5 ncdump)
FILE(GLOB COPY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/*.sh
${CMAKE_CURRENT_SOURCE_DIR}/ref*.cdl
${CMAKE_CURRENT_SOURCE_DIR}/ref*.txt
${CMAKE_CURRENT_SOURCE_DIR}/ref*.zmap)
FILE(COPY ${COPY_FILES} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ FILE_PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE)
IF(USE_X_GETOPT)
SET(XGETOPTSRC "${CMAKE_CURRENT_SOURCE_DIR}/../libdispatch/XGetopt.c")
ENDIF()
IF(ENABLE_TESTS)
SET(COMMONSRC ut_util.c ut_test.c ${XGETOPTSRC})
SET(TSTCOMMONSRC test_utils.c test_utils.h ${XGETOPTSRC})
INCLUDE_DIRECTORIES(../libnczarr ../plugins ${CMAKE_SOURCE_DIR}/nczarr_test)
# Base tests
# The tests are set up as a combination of shell scripts and executables that
# must be run in a particular order. It is painful but will use macros to help
# keep it from being too bad.
BUILD_BIN_TEST(ut_map ${COMMONSRC})
BUILD_BIN_TEST(ut_mapapi ${COMMONSRC})
BUILD_BIN_TEST(ut_json ${COMMONSRC})
BUILD_BIN_TEST(test_fillonlyz ${TSTCOMMONSRC})
BUILD_BIN_TEST(test_quantize ${TSTCOMMONSRC})
BUILD_BIN_TEST(test_notzarr ${TSTCOMMONSRC})
# ADD_BIN_TEST(nczarr_test test_endians ${TSTCOMMONSRC})
# Unlimited Tests
IF(USE_HDF5)
ADD_BIN_TEST(nczarr_test test_unlim_vars ${TSTCOMMONSRC})
ADD_BIN_TEST(nczarr_test test_put_vars_two_unlim_dim ${TSTCOMMONSRC})
BUILD_BIN_TEST(test_zchunks ${COMMONSRC})
BUILD_BIN_TEST(test_zchunks2 ${COMMONSRC})
BUILD_BIN_TEST(test_zchunks3 ${COMMONSRC})
BUILD_BIN_TEST(test_unlim_io ${TSTCOMMONSRC})
BUILD_BIN_TEST(test_chunking ${TSTCOMMONSRC})
ADD_SH_TEST(nczarr_test run_nccopyz)
ADD_SH_TEST(nczarr_test run_unlim_io)
ADD_SH_TEST(nczarr_test run_nccopy5)
ADD_SH_TEST(nczarr_test run_mud)
ENDIF()
IF(FALSE) # Obsolete tests
BUILD_BIN_TEST(ut_projections ${COMMONSRC})
BUILD_BIN_TEST(ut_chunking ${COMMONSRC})
BUILD_BIN_TEST(ut_walk ${COMMONSRC})
ENDIF()
# Helper programs for testing
BUILD_BIN_TEST(zhex)
BUILD_BIN_TEST(zisjson ${COMMONSRC})
TARGET_INCLUDE_DIRECTORIES(zisjson PUBLIC ../libnczarr)
BUILD_BIN_TEST(zs3parse ${COMMONSRC})
TARGET_INCLUDE_DIRECTORIES(zs3parse PUBLIC ../libnczarr)
BUILD_BIN_TEST(zmapio ${COMMONSRC})
IF(ENABLE_S3 AND NOT WITH_S3_TESTING STREQUAL "NO")
# Helper programs for testing
BUILD_BIN_TEST(s3util ${COMMONSRC})
endif()
SET(ncdumpchunks_SOURCE ncdumpchunks.c)
SET(ncdumpchunks_SOURCE ${ncdumpchunks_SOURCE} ${XGETOPTSRC})
BUILD_BIN_TEST(ncdumpchunks ${ncdumpchunks_SOURCE})
IF(BUILD_UTILITIES)
add_sh_test(nczarr_test run_ut_map)
add_sh_test(nczarr_test run_ut_mapapi)
add_sh_test(nczarr_test run_ut_misc)
add_sh_test(nczarr_test run_ncgen4)
if(LARGE_FILE_TESTS)
BUILD_BIN_TEST(test_readcaching})
BUILD_BIN_TEST(test_writecaching})
BUILD_BIN_TEST(test_chunkcases ${TSTCOMMONSRC})
add_sh_test(nczarr_test run_cachetest)
add_sh_test(nczarr_test run_chunkcases)
ENDIF()
add_sh_test(nczarr_test run_purezarr)
add_sh_test(nczarr_test run_misc)
add_sh_test(nczarr_test run_nczarr_fill)
add_sh_test(nczarr_test run_jsonconvention)
add_sh_test(nczarr_test run_strings)
add_sh_test(nczarr_test run_scalar)
add_sh_test(nczarr_test run_nulls)
add_sh_test(nczarr_test run_external)
add_sh_test(nczarr_test run_quantize)
add_sh_test(nczarr_test run_notzarr)
# This has timeout under CMake
# if(NOT ISCMAKE)
add_sh_test(nczarr_test run_interop)
# ENDIF()
IF(USE_HDF5)
add_sh_test(nczarr_test run_fillonlyz)
ENDIF()
IF(ENABLE_NCZARR_FILTERS)
IF(ENABLE_FILTER_TESTING)
build_bin_test(test_nczfilter)
build_bin_test(test_filter_vlen)
build_bin_test(testfilter)
build_bin_test(testfilter_misc)
build_bin_test(testfilter_multi)
build_bin_test(testfilter_order)
build_bin_test(testfilter_repeat)
ADD_SH_TEST(nczarr_test run_nczfilter)
ADD_SH_TEST(nczarr_test run_filter)
ADD_SH_TEST(nczarr_test run_specific_filters)
ADD_SH_TEST(nczarr_test run_filter_vlen)
IF(FALSE)
# This test is too dangerous to run in a parallel make environment.
# It causes race conditions. So suppress and only test by hand.
ADD_SH_TEST(nczarr_test run_unknown)
ENDIF(FALSE)
ENDIF(ENABLE_FILTER_TESTING)
ENDIF(ENABLE_NCZARR_FILTERS)
if(ENABLE_NCZARR_ZIP)
add_sh_test(nczarr_test run_newformat)
endif()
IF(FALSE) # Obsolete tests
add_sh_test(nczarr_test run_ut_chunk)
ENDIF()
ENDIF(BUILD_UTILITIES)
ENDIF(ENABLE_TESTS)
## Specify files to be distributed by 'make dist'
FILE(GLOB CUR_EXTRA_DIST RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/*.c ${CMAKE_CURRENT_SOURCE_DIR}/*.h ${CMAKE_CURRENT_SOURCE_DIR}/*.sh ${CMAKE_CURRENT_SOURCE_DIR}/*.cdl)
SET(CUR_EXTRA_DIST ${CUR_EXTRA_DIST} CMakeLists.txt Makefile.am zmapio.c zhex.c ncdumpchunks.c)
ADD_EXTRA_DIST("${CUR_EXTRA_DIST}")
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