Merge pull request #2134 from DennisHeimbigner/zarrs3part2.dmh

Author: WardF

CMakeLists.txt

@@ -1049,7 +1049,6 @@ IF(!MSVC)
 #FIND_LIBRARY(SZIP PATH NAMES szip sz)
 SET(SZIP_LIBRARY ${SZIP})
 ENDIF()
-message("xxx: ${SZIP_FOUND} ; ${SZIP}")
 # Define a test flag for have szip library
 IF(SZIP_FOUND)
   INCLUDE_DIRECTORIES(${SZIP_INCLUDE_DIRS})
@@ -1133,10 +1132,10 @@ ENDIF()
 # See if aws-s3-sdk is available
 # But only if enabled
 IF(ENABLE_NCZARR_S3)
-find_package(AWSSDK REQUIRED)
-set(SERVICE s3)
-AWSSDK_DETERMINE_LIBS_TO_LINK(SERVICE AWSSDK_LINK_LIBRARIES)
+find_package(AWSSDK REQUIRED COMPONENTS s3;core)
 IF(AWSSDK_FOUND)
+  SET(service s3;core)
+  AWSSDK_DETERMINE_LIBS_TO_LINK(service AWS_LINK_LIBRARIES)
   SET(ENABLE_S3_SDK ON CACHE BOOL "S3 SDK" FORCE)
 ELSE()
   SET(ENABLE_S3_SDK OFF CACHE BOOL "S3 SDK" FORCE)
@@ -1712,7 +1711,17 @@ CHECK_FUNCTION_EXISTS(fileno HAVE_FILENO)
 
 CHECK_FUNCTION_EXISTS(clock_gettime  HAVE_CLOCK_GETTIME)
 CHECK_SYMBOL_EXISTS("struct timespec" "time.h" HAVE_STRUCT_TIMESPEC)
+CHECK_FUNCTION_EXISTS(atexit HAVE_ATEXIT)
 
+# Control invoking nc_finalize at exit
+OPTION(ENABLE_ATEXIT_FINALIZE "Invoke nc_finalize at exit." ON)
+IF(NOT HAVE_ATEXIT)
+IF(ENABLE_ATEXIT_FINALIZE AND NOT HAVE_ATEXIT)
+  SET(ENABLE_ATEXIT_FINALIZE OFF CACHE BOOL "Enable ATEXIT" FORCE)
+  MESSAGE(WARNING "ENABLE_ATEXIT_FINALIZE set but atexit() function not defined")
+ENDIF()
+ENDIF()
+ 
 # Check to see if MAP_ANONYMOUS is defined.
 IF(MSVC)
 MESSAGE(WARNING "mmap not supported under visual studio: disabling MMAP support.")

RELEASE_NOTES.md

@@ -7,6 +7,7 @@ This file contains a high-level description of this package's evolution. Release
 
 ## 4.8.2 - TBD
 
+* [Enhancement] Support byte-range reading of netcdf-3 files stored in private buckets in S3. See [Github #2134](https://github.com/Unidata/netcdf-c/pull/2134)
 * [Enhancement] Support Amazon S3 access for NCZarr. Also support use of the existing Amazon SDK credentials system. See [Github #2114](https://github.com/Unidata/netcdf-c/pull/2114)
 * [Bug Fix] Fix string allocation error in H5FDhttp.c. See [Github #2127](https://github.com/Unidata/netcdf-c/pull/2127).
 * [Bug Fix] Apply patches for ezxml and for selected  oss-fuzz detected errors. See [Github #2125](https://github.com/Unidata/netcdf-c/pull/2125).

config.h.cmake.in

@@ -126,6 +126,9 @@ are set when opening a binary file on Windows. */
 /* set this only when building a DLL under MinGW */
 #cmakedefine DLL_NETCDF 1
 
+/* if true, use atexist */
+#cmakedefine ENABLE_ATEXIT_FINALIZE 1
+
 /* if true, build byte-range Client */
 #cmakedefine ENABLE_BYTERANGE 1
 
@@ -183,10 +186,12 @@ are set when opening a binary file on Windows. */
 /* Define to 1 if you have `alloca', as a function or macro. */
 #cmakedefine HAVE_ALLOCA 1
 
-/* Define to 1 if you have <alloca.h> and it should be used (not on Ultrix).
-   */
+/* Define to 1 if you have <alloca.h> and it should be used (not on Ultrix). */
 #cmakedefine HAVE_ALLOCA_H 1
 
+/* Define to 1 if you have the `atexit function. */
+#cmakedefine HAVE_ATEXIT 1
+
 /* Define to 1 if you have hdf5_coll_metadata_ops */
 #cmakedefine HDF5_HAS_COLL_METADATA_OPS 1
 

configure.ac

@@ -1113,6 +1113,29 @@ if test "x$enable_byterange" = xyes; then
     AC_DEFINE([ENABLE_BYTERANGE], [1], [if true, support byte-range read of remote datasets.])
 fi
 
+# Does the user want to disable atexit?
+AC_MSG_CHECKING([whether nc_finalize should be invoked at exit])
+AC_ARG_ENABLE([atexit-finalize],
+               [AS_HELP_STRING([--disable-atexit-finalize],
+                               [disable invoking nc_finalize at exit])])
+test "x$enable_atexit_finalize" = xno || enable_atexit_finalize=yes
+AC_MSG_RESULT($enable_atexit_finalize)
+ 
+# Check for atexit
+AC_CHECK_FUNCS([atexit])
+
+# If no atexit, then disable atexit finalize
+if test "x$enable_atexit_finalize" = xyes ; then
+  if test "x$ac_cv_func_function" = xno ; then
+    enable_atexit_finalize=no
+    AC_MSG_ERROR([atexit() required for enable-atexit-finalize.])
+  fi
+fi
+
+if test "x$enable_atexit_finalize" = xyes ; then
+  AC_DEFINE([ENABLE_ATEXIT_FINALIZE], [1], [If true, enable nc_finalize via atexit()])
+fi
+
 # Need libdl(d) for plugins
 AC_CHECK_LIB([dl],[dlopen],[have_libdld=yes],[have_libdld=no])
 if test "x$have_libdld" = "xyes" ; then

docs/nczarr.md

@@ -554,24 +554,6 @@ The relevant tests for S3 support are in the _nczarr_test_ directory.
 Currently, by default, testing of S3 with NCZarr is supported only for Unidata members of the NetCDF Development Group.
 This is because it uses a Unidata-specific bucket is inaccessible to the general user.
 
-However, an untested mechanism exists by which others may be able to run the S3 specific tests.
- If someone else wants to attempt these tests, then they need to define the following environment variables:
-* NCZARR_S3_TEST_HOST=\<host\>
-* NCZARR_S3_TEST_BUCKET=\<bucket-name\>
-
-This assumes a Path Style address (see above) where
-* host -- the complete host part of the url
-* bucket -- a bucket in which testing can occur without fear of damaging anything.
-
-_Example:_
-
-````
-NCZARR_S3_TEST_HOST=s3.us-west-1.amazonaws.com
-NCZARR_S3_TEST_BUCKET=testbucket
-````
-If anyone tries to use this mechanism, it would be appreciated
-it any difficulties were reported to Unidata as a Github issue.
-
 # Appendix B. Building aws-sdk-cpp {#nczarr_s3sdk}
 
 In order to use the S3 storage driver, it is necessary to install the Amazon [aws-sdk-cpp library](https://github.com/aws/aws-sdk-cpp.git).
@@ -580,19 +562,22 @@ Building this package from scratch has proven to be a formidable task.
 This appears to be due to dependencies on very specific versions of,
 for example, openssl.
 
-However, the following context does work. Of course your mileage may vary.
+## **nix** Build
+
+For linux, the following context works. Of course your mileage may vary.
 * OS: ubuntu 21
-* aws-sdk-cpp version 1.9.96 or later?
+* aws-sdk-cpp version 1.9.96 (or later?)
 * Required installed libraries: openssl, libcurl, cmake, ninja (ninja-build in apt)
 
-The recipe used:
+### AWS-SDK-CPP Build Recipe
+
 ````
 git clone --recurse-submodules https://www.github.com/aws/aws-sdk-cpp
 pushd aws-sdk-cpp
 mkdir build
 cd build
 PREFIX=/usr/local
-FLAGS="-DCMAKE_INSTALL_PREFIX=${PREFIX}
+FLAGS="-DCMAKE_INSTALL_PREFIX=${PREFIX} \
        -DCMAKE_INSTALL_LIBDIR=lib \
        -DCMAKE_MODULE_PATH=${PREFIX}/lib/cmake \
        -DCMAKE_POLICY_DEFAULT_CMP0075=NEW \
@@ -608,8 +593,84 @@ cd ..
 popd
 ````
 
-For Windows we do not yet have solution. If you successfully install
-on Windows, please let us know how you did it.
+### NetCDF Build
+
+In order to build netcdf-c with S3 sdk support,
+the following options must be specified for ./configure.
+````
+--enable-nczarr-s3
+````
+If you have access to the Unidata bucket on Amazon, then you can
+also test S3 support with this option.
+````
+--enable-nczarr-s3-tests
+````
+
+## Windows build
+It is possible to build and install aws-sdk-cpp. It is also possible
+to build netcdf-c using cmake. Unfortunately, testing currently fails.
+
+For Windows, the following context work. Of course your mileage may vary.
+* OS: Windows 10 64-bit with Visual Studio community edition 2019.
+* aws-sdk-cpp version 1.9.96 (or later?)
+* Required installed libraries: openssl, libcurl, cmake
+
+### AWS-SDK-CPP Build Recipe
+
+This command-line build assumes one is using Cygwin or Mingw to provide
+tools such as bash.
+
+````
+git clone --recurse-submodules https://www.github.com/aws/aws-sdk-cpp
+pushd aws-sdk-cpp
+mkdir build
+cd build
+CFG="Release"
+PREFIX="c:/tools/aws-sdk-cpp"
+
+FLAGS="-DCMAKE_INSTALL_PREFIX=${PREFIX} \
+       -DCMAKE_INSTALL_LIBDIR=lib" \
+       -DCMAKE_MODULE_PATH=${PREFIX}/cmake \
+       -DCMAKE_POLICY_DEFAULT_CMP0075=NEW \
+       -DBUILD_ONLY=s3 \
+       -DENABLE_UNITY_BUILD=ON \
+       -DCMAKE_BUILD_TYPE=$CFG \
+       -DSIMPLE_INSTALL=ON"
+
+rm -fr build
+mkdir -p build
+cd build
+cmake -DCMAKE_BUILD_TYPE=${CFG} $FLAGS ..
+cmake --build . --config ${CFG}
+cmake --install . --config ${CFG}
+cd ..
+popd
+````
+Notice that the sdk is being installed in the directory "c:\tools\aws-sdk-cpp"
+rather than the default location "c:\Program Files (x86)/aws-sdk-cpp-all"
+This is because when using a command line, an install path that contains
+blanks may not work.
+
+### NetCDF CMake Build
+
+Enabling S3 support is controlled by these two cmake options:
+````
+-DENABLE_NCZARR_S3=ON
+-DENABLE_NCZARR_S3_TESTS=OFF
+````
+
+However, to find the aws sdk libraries,
+the following environment variables must be set:
+````
+AWSSDK_ROOT_DIR="c:/tools/aws-sdk-cpp"
+AWSSDKBIN="/cygdrive/c/tools/aws-sdk-cpp/bin"
+PATH="$PATH:${AWSSDKBIN}"
+````
+Then the following options must be specified for cmake.
+````
+-DAWSSDK_ROOT_DIR=${AWSSDK_ROOT_DIR}
+-DAWSSDK_DIR=${AWSSDK_ROOT_DIR}/lib/cmake/AWSSDK"
+````
 
 # Appendix C. Amazon S3 Imposed Limits {#nczarr_s3limits}
 

include/CMakeLists.txt

@@ -41,6 +41,10 @@ IF(ENABLE_PNETCDF OR ENABLE_PARALLEL4)
     COMPONENT headers)
 ENDIF()
 
+#INSTALL(FILES ${netCDF_BINARY_DIR}/include/netcdf_json.h
+#    DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+#    COMPONENT headers)
+
 FILE(GLOB CUR_EXTRA_DIST RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/*.h)
 SET(CUR_EXTRA_DIST ${CUR_EXTRA_DIST} Makefile.am CMakeLists.txt)
 ADD_EXTRA_DIST("${CUR_EXTRA_DIST}")

include/Makefile.am

@@ -20,7 +20,7 @@ nc4internal.h nctime.h nc3internal.h onstack.h ncrc.h ncauth.h		\
 ncoffsets.h nctestserver.h nc4dispatch.h nc3dispatch.h ncexternl.h	\
 ncpathmgr.h ncindex.h hdf4dispatch.h hdf5internal.h nc_provenance.h	\
 hdf5dispatch.h ncmodel.h isnan.h nccrc.h ncexhash.h ncxcache.h          \
-ncfilter.h ncjson.h ezxml.h
+ncfilter.h ncjson.h ezxml.h ncs3sdk.h
 
 if USE_DAP
 noinst_HEADERS += ncdap.h
@@ -32,10 +32,10 @@ endif
 
 EXTRA_DIST = CMakeLists.txt XGetopt.h netcdf_meta.h.in netcdf_dispatch.h.in
 
-DISTCLEANFILES = netcdf_json.h
-
-BUILT_SOURCES = netcdf_json.h 
-netcdf_json.h: Makefile ${srcdir}/ncjson.h ${srcdir}/../libdispatch/ncjson.c
+# netcdf_json.h is part of the distribution.
+# If either of the files ncjson.h ../libdispatch/ncjson.c is changed
+# then netcdf_json.h should be reconstructed using this recipe.
+build_netcdf_json.h::
 	sed -e 's/NCJSON_H/NETCDF_JSON_H/' -e '/ncjson.h/d' <${srcdir}/ncjson.h > $@
 	sed -e '/ncjson.h/d' < ${srcdir}/../libdispatch/ncjson.c >> $@
 

include/hdf5internal.h

@@ -60,12 +60,12 @@ struct NCauth;
 /** Struct to hold HDF5-specific info for the file. */
 typedef struct NC_HDF5_FILE_INFO {
    hid_t hdfid;
-#if defined(ENABLE_BYTERANGE) || defined(ENABLE_HDF5_ROS3) || defined(ENABLE_S3_SDK)
-   struct HTTP {
-	NCURI* uri; /* Parse of the incoming path, if url */
-	int iosp; /* We are using the S3 rawvirtual file driver */
-        struct NCauth* auth;
-   } http;
+#if defined(ENABLE_BYTERANGE)
+   int byterange;
+   NCURI* uri; /* Parse of the incoming path, if url */
+#if defined(ENABLE_HDF5_ROS3) || defined(ENABLE_S3_SDK)
+   struct NCauth* auth;
+#endif
 #endif
 } NC_HDF5_FILE_INFO_T;
 

include/nchttp.h

@@ -34,7 +34,7 @@ typedef struct NC_HTTP_STATE {
 
 extern int nc_http_init(NC_HTTP_STATE** state);
 extern int nc_http_init_verbose(NC_HTTP_STATE** state, int verbose);
-extern int nc_http_size(NC_HTTP_STATE* state, const char* url, long long* sizep);
+extern int nc_http_size(NC_HTTP_STATE* state, const char* url, long long unsigned* sizep);
 extern int nc_http_read(NC_HTTP_STATE* state, const char* url, size64_t start, size64_t count, NCbytes* buf);
 extern int nc_http_write(NC_HTTP_STATE* state, const char* url, NCbytes* payload);
 extern int nc_http_close(NC_HTTP_STATE* state);

include/ncrc.h

@@ -65,6 +65,14 @@ struct AWSentry {
     char* value;
 };
 
+typedef struct NCS3INFO {
+    char* host; /* non-null if other*/
+    char* region; /* region */
+    char* bucket; /* bucket name */
+    char* rootkey;
+    char* profile;
+} NCS3INFO;
+
 #if defined(__cplusplus)
 extern "C" {
 #endif
@@ -95,15 +103,22 @@ EXTERNL char* NC_entityescape(const char* s);
 EXTERNL int NC_readfile(const char* filename, NCbytes* content);
 EXTERNL int NC_writefile(const char* filename, size_t size, void* content);
 EXTERNL char* NC_mktmp(const char* base);
-EXTERNL int NC_getmodelist(const char* url, NClist** modelistp);
-EXTERNL int NC_testmode(const char* path, const char* tag);
+EXTERNL int NC_getmodelist(const char* modestr, NClist** modelistp);
+EXTERNL int NC_testmode(NCURI* uri, const char* tag);
+EXTERNL int NC_testpathmode(const char* path, const char* tag);
 EXTERNL int NC_split_delim(const char* path, char delim, NClist* segments);
+EXTERNL int NC_join(struct NClist* segments, char** pathp);
+
+/* From ds3util.c */
+/* S3 profiles */
 EXTERNL int NC_s3urlrebuild(NCURI* url, NCURI** newurlp, char** bucketp, char** regionp);
 EXTERNL int NC_getactives3profile(NCURI* uri, const char** profilep);
 EXTERNL int NC_getdefaults3region(NCURI* uri, const char** regionp);
-/* S3 profiles */
 EXTERNL int NC_authgets3profile(const char* profile, struct AWSprofile** profilep);
 EXTERNL int NC_s3profilelookup(const char* profile, const char* key, const char** valuep);
+EXTERNL int NC_s3urlprocess(NCURI* url, NCS3INFO* s3);
+EXTERNL int NC_s3clear(NCS3INFO* s3);
+EXTERNL int NC_iss3(NCURI* uri);
 
 #if defined(__cplusplus)
 }