Add thread-safe execution support to netcdf-c

.github/workflows/run_tests_ubuntu.yml

@@ -74,7 +74,7 @@ jobs:
 
       - name: Install System dependencies
         shell: bash -l {0}
-        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev 
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev
 
         ###
         # Installing libhdf5
@@ -135,7 +135,7 @@ jobs:
 
       - name: Install System dependencies
         shell: bash -l {0}
-        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen valgrind
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen
 
         ###
         # Set Environmental Variables
@@ -171,7 +171,7 @@ jobs:
 
       - name: Configure
         shell: bash -l {0}
-        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf5 --enable-dap --disable-dap-remote-tests  --enable-doxygen  --enable-external-server-tests --disable-xml2
+        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf5 --enable-dap --disable-dap-remote-tests  --enable-doxygen  --enable-external-server-tests --disable-xml2 --enable-threadsafe
         if: ${{ success() }}
 
       - name: Look at config.log if error
@@ -230,7 +230,7 @@ jobs:
 
       - name: Install System dependencies
         shell: bash -l {0}
-        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev 
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev
 
         ###
         # Set Environmental Variables
@@ -344,7 +344,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} -DENABLE_DAP=TRUE -DENABLE_HDF5=TRUE -DENABLE_NCZARR=TRUE -DENABLE_DAP_LONG_TESTS=TRUE -DENABLE_XML2=FALSE
+          LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} -DENABLE_DAP=TRUE -DENABLE_HDF5=TRUE -DENABLE_NCZARR=TRUE -DENABLE_DAP_LONG_TESTS=TRUE -DENABLE_XML2=FALSE -DENABLE_THREADSAFE=TRUE
 
       - name: Print Summary
         shell: bash -l {0}
@@ -391,7 +391,7 @@ jobs:
 
       - name: Install System dependencies
         shell: bash -l {0}
-        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen mpich libmpich-dev 
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen mpich libmpich-dev
 
       ###
       # Set Environmental Variables

.github/workflows/run_tests_win_cygwin.yml

@@ -53,8 +53,7 @@ jobs:
           --disable-static --enable-dap --disable-dap-remote-tests
           --enable-plugins ${{ matrix.plugin_dir_option }}
           --disable-nczarr --disable-nczarr-filters
-          --disable-s3 --with-s3-testing=no
-
+          --disable-s3 --with-s3-testing=no --enable-threadsafe
 
       - name: Look at config.log if error
         if: ${{ failure() }}

.github/workflows/run_tests_win_mingw.yml

@@ -41,7 +41,7 @@ jobs:
         run: autoreconf -if
 
       - name: (Autotools) Configure Build
-        run: ./configure --enable-hdf5 --enable-dap --disable-dap-remote-tests --disable-static --disable-byterange --disable-dap-remote-tests --disable-logging --enable-plugins --disable-nczarr-filters --disable-s3
+        run: ./configure --enable-hdf5 --enable-dap --disable-dap-remote-tests --disable-static --disable-byterange --disable-dap-remote-tests --disable-logging --enable-plugins --disable-nczarr-filters --disable-s3 --enable-threadsafe
         if: ${{ success() }}
 
       - name: (Autotools) Look at config.log if error

CMakeLists.txt

@@ -431,6 +431,54 @@ IF(MSVC)
   ENDIF()
 ENDIF()
 
+# Control thread-safe operation
+OPTION (ENABLE_THREADSAFE "Enable Thread safe operation" OFF)
+
+SET(Threads_FOUND FALSE)
+IF(MSVC)
+  FIND_PACKAGE(PTHREADS4W QUIET)
+  IF(PTHREADS4W_FOUND)
+    GET_TARGET_PROPERTY(PTHREADS4W_LIBS Threads::Threads IMPORTED_IMPLIB_RELEASE)
+    GET_TARGET_PROPERTY(PTHREADS4W_IMPL Threads::Threads IMPORTED_LOCATION_RELEASE)
+    GET_TARGET_PROPERTY(PTHREADS4W_INCLUDE_DIR Threads::Threads INTERFACE_INCLUDE_DIRECTORIES)
+    SET(Threads_FOUND ${PTHREADS4W_FOUND})
+    SET(CMAKE_THREAD_LIBS_INIT ${PTHREADS4W_LIBS})
+    SET(CMAKE_USE_WIN32_THREADS_INIT FALSE)
+    SET(CMAKE_USE_PTHREADS_INIT TRUE)
+    SET(CMAKE_HP_PTHREADS_INIT FALSE)
+    INCLUDE_DIRECTORIES(${PTHREADS4W_INCLUDE_DIR})
+  ENDIF(PTHREADS4W_FOUND)
+ENDIF(MSVC)
+
+IF(NOT Threads_FOUND)
+  # Look for some other pthreads library
+  SET(THREADS_PREFER_PTHREAD_FLAG TRUE)
+  FIND_PACKAGE(Threads)
+  # If the window's threads is found, then do not use it.
+  if(CMAKE_USE_WIN32_THREADS_INIT)
+    message(WARNING "*** Only WinThreads found, so disable Threads_FOUND")
+    SET(Threads_FOUND FALSE)
+  ENDIF()
+#    SET_TARGET_PROPERTIES(Threads::Threads PROPERTIES IMPORTED_GLOBAL TRUE)
+ENDIF(NOT Threads_FOUND)
+
+IF(Threads_FOUND)
+  SET(HAVE_PTHREADS YES CACHE BOOL "Have pthreads library")
+ELSE()
+  SET(HAVE_PTHREADS NO CACHE BOOL "Have pthreads library")
+ENDIF()
+
+IF(ENABLE_THREADSAFE)
+  SET(PTHREAD_T_MAX_SIZE 64 CACHE STRING "|pthread_t|")
+ELSE()
+  SET(PTHREAD_T_MAX_SIZE 0 CACHE STRING "|pthread_t|")
+ENDIF()
+
+# Consistency
+IF(ENABLE_THREADSAFE AND NOT HAVE_PTHREADS)
+  MESSAGE(FATAL_ERROR "ENABLE_THREADSAFE requires HAVE_PTHREADS; Please disable  ENABLE_THREADSAFE")
+ENDIF()
+
 # Option to build netCDF Version 2
 OPTION (ENABLE_V2_API "Build netCDF Version 2." ON)
 SET(BUILD_V2 ${ENABLE_V2_API})
@@ -840,8 +888,6 @@ IF(USE_HDF5)
 
   ENDIF(HDF5_C_LIBRARY AND HDF5_HL_LIBRARY AND HDF5_INCLUDE_DIR)
 
-  FIND_PACKAGE(Threads)
-
   # There is a missing case in the above code so default it
   IF(NOT HDF5_C_LIBRARY_hdf5 OR "${HDF5_C_LIBRARY_hdf5}" STREQUAL "" )
     SET(HDF5_C_LIBRARY_hdf5 "${HDF5_C_LIBRARY}")
@@ -911,17 +957,22 @@ IF(USE_HDF5)
 
   # H5Pset_fapl_mpiposix and H5Pget_fapl_mpiposix have been removed since HDF5 1.8.12.
   # Use H5Pset_fapl_mpio and H5Pget_fapl_mpio, instead.
-  # CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Pget_fapl_mpiposix "" HDF5_IS_PARALLEL_MPIPOSIX)
+  #  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Pget_fapl_mpiposix "" HDF5_IS_PARALLEL_MPIO)
 
+if(Threads_FOUND)
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Pget_fapl_mpio "" HDF5_IS_PARALLEL_MPIO)
+endif()
+
   IF(HDF5_IS_PARALLEL_MPIO)
     SET(HDF5_PARALLEL ON)
   ELSE()
     SET(HDF5_PARALLEL OFF)
   ENDIF()
 
+if(NOT Threads_FOUND)
   #Check to see if HDF5 library has collective metadata APIs, (HDF5 >= 1.10.0)
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Pset_all_coll_metadata_ops "" HDF5_HAS_COLL_METADATA_OPS)
+endif()
 
   IF(HDF5_PARALLEL)
 	SET(HDF5_CC h5pcc)
@@ -1064,7 +1115,9 @@ ELSE()
   SET(ENABLE_DAP2 OFF CACHE BOOL "")
   SET(ENABLE_DAP4 OFF CACHE BOOL "")
 ENDIF()
-
+# Default disable dap4 for now
+#SET(ENABLE_DAP4 OFF CACHE BOOL "")
+
 # Option to support byte-range reading of remote datasets
 OPTION(ENABLE_BYTERANGE "Enable byte-range access to remote datasets.." ON)
 if(NOT ENABLE_REMOTE_FUNCTIONALITY)
@@ -1263,14 +1316,13 @@ IF(ENABLE_EXTRA_TESTS)
   SET(EXTRA_TESTS ON)
 ENDIF()
 
-# Option to use bundled XGetopt in place of getopt(). This is mostly useful
-# for MSVC builds. If not building utilities or some tests,
+# Check if getopt is available else use bundled XGetopt.
+# This is mostly useful for MSVC builds. If not building utilities or some tests,
 # getopt() isn't required at all.
 IF(MSVC)
-  OPTION(ENABLE_XGETOPT "Enable bundled XGetOpt instead of external getopt()." ON)
-  IF(ENABLE_XGETOPT)
-    SET(USE_X_GETOPT ON CACHE BOOL "")
-  ENDIF()
+  SET(USE_X_GETOPT ON CACHE BOOL "")
+ELSE()
+  SET(USE_X_GETOPT OFF CACHE BOOL "")
 ENDIF()
 
 SET(MATH "")
@@ -1677,7 +1729,7 @@ OPTION(ENABLE_NCZARR_FILTERS_TESTING "Enable NCZarr filter testing." ON)
 
 # Constraints
 IF (NOT ENABLE_PLUGINS)
-  MESSAGE(WARNING "ENABLE_FILTER_TESTING requires shared libraries. Disabling.")
+  MESSAGE(WARNING "ENABLE_NCZARR_FILTERS requires ENABLE_PLUGINS. Disabling.")
   SET(ENABLE_NCZARR_FILTERS OFF CACHE BOOL "Enable NCZarr Filters." FORCE)
 ENDIF()
 
@@ -1795,7 +1847,7 @@ IF(NOT HAVE_UNISTD_H)
 ENDIF()
 
 CHECK_INCLUDE_FILE("alloca.h"  HAVE_ALLOCA_H)
-CHECK_INCLUDE_FILE("malloc.h"    HAVE_MALLOC_H)
+CHECK_INCLUDE_FILE("malloc.h"  HAVE_MALLOC_H)
 CHECK_INCLUDE_FILE("fcntl.h"   HAVE_FCNTL_H)
 CHECK_INCLUDE_FILE("getopt.h"  HAVE_GETOPT_H)
 CHECK_INCLUDE_FILE("locale.h"  HAVE_LOCALE_H)
@@ -2143,7 +2195,7 @@ ENDMACRO()
 
 # Binary tests which are used by a script looking for a specific name.
 MACRO(build_bin_test_no_prefix F)
-  build_bin_test(${F})
+  build_bin_test(${F} ${ARGN})
   IF(MSVC)
     #SET_PROPERTY(TEST ${F} PROPERTY FOLDER "tests/")
     SET_TARGET_PROPERTIES(${F} PROPERTIES RUNTIME_OUTPUT_DIRECTORY
@@ -2609,6 +2661,7 @@ is_enabled(HAVE_ZSTD HAS_ZSTD)
 is_enabled(HAVE_BLOSC HAS_BLOSC)
 is_enabled(HAVE_BZ2 HAS_BZ2)
 is_enabled(ENABLE_REMOTE_FUNCTIONALITY DO_REMOTE_FUNCTIONALITY)
+is_enabled(ENABLE_THREADSAFE IS_THREADSAFE)
 
 if(ENABLE_S3_INTERNAL)
   SET(WHICH_S3_SDK "internal")

config.h.cmake.in

@@ -166,6 +166,9 @@ are set when opening a binary file on Windows. */
 /* if true, Force use of S3 internal library */
 #cmakedefine ENABLE_S3_INTERNAL 1
 
+/* if true, Support serialized thread safe operation */
+#cmakedefine ENABLE_THREADSAFE 1
+
 /* if true, enable S3 testing*/
 #cmakedefine WITH_S3_TESTING "PUBLIC"
 
@@ -346,6 +349,9 @@ are set when opening a binary file on Windows. */
 /* Define to 1 if you have the `random' function. */
 #cmakedefine HAVE_RANDOM 1
 
+/* Define to 1 if you have the pthreads library */
+#cmakedefine HAVE_PTHREADS 1
+
 /* Define to 1 if you have the `snprintf' function. */
 #cmakedefine HAVE_SNPRINTF 1
 
@@ -534,6 +540,9 @@ with zip */
 /* define the possible sources for remote test servers */
 #cmakedefine REMOTETESTSERVERS	"${REMOTETESTSERVERS}"
 
+/* Max size for pthread_t instance */
+#cmakedefine PTHREAD_T_MAX_SIZE @PTHREAD_T_MAX_SIZE@
+
 /* The size of `ulonglong` as computed by sizeof. */
 #cmakedefine SIZEOF_ULONGLONG @SIZEOF_ULONGLONG@
 

configure.ac

@@ -117,8 +117,35 @@ ISMINGW=yes
 ISMSYS=yes
 fi
 
+# See if we have libpthreads
+AC_SEARCH_LIBS([pthread_mutex_init],[pthreads pthreads.dll cygpthreads.dll], [have_pthreads=yes], [have_pthreads=no])
+if test "x$have_pthreads" = "xyes" ; then
+  AC_CHECK_LIB([pthread],[pthread_mutex_init],[],[]) # Make sure it gets included in the lib list
+  AC_DEFINE([HAVE_PTHREADS], [1], [if true, pthreads is available])
+fi
+
+AC_MSG_CHECKING([whether we should enable thread safety])
+AC_ARG_ENABLE([threadsafe], [AS_HELP_STRING([--enable-threadsafe],
+              [enable thread-safe operation (default=no)])])
+test "x$enable_threadsafe" = xyes || enable_threadsafe=no
+AC_MSG_RESULT([$enable_threadsafe])
+if test "x$enable_threadsafe" = xyes && test "x$have_pthreads" = xno ; then
+  AC_MSG_NOTICE([!pthreads => !threadsafe])
+  enable_threadsafe=no
+fi
+
+if test "x$enable_threadsafe" = xyes ; then
+AC_DEFINE([ENABLE_THREADSAFE], [1], [if true, include experimental thread safe code])
+AC_DEFINE_UNQUOTED([PTHREAD_T_MAX_SIZE], [64], [|pthread_t|])
+else
+AC_DEFINE_UNQUOTED([PTHREAD_T_MAX_SIZE], [0], [|pthread_t|])
+fi
+AM_CONDITIONAL(ENABLE_THREADSAFE, [test "x$enable_threadsafe" = xyes])
+
+# Setup the config.h
+
 # Get windows version info
-if test "x$ISMSVC" = xyes ; then
+if test "x$ISMINGW" = xyes || test "x$ISMSVC" = xyes ; then
 WINVER=`systeminfo | sed -e '/^OS Version:/p' -ed | sed -e 's|[^0-9]*\([0-9.]*\).*|\1|'`
 else
 WINVER="0.0.0"
@@ -621,7 +648,6 @@ fi
 AM_CONDITIONAL(ENABLE_QUANTIZE, [test x$enable_quantize = xyes])
 
 # --enable-dap => enable-dap4
-enable_dap4=$enable_dap
 AC_MSG_CHECKING([whether dap use of remotetest server should be enabled])
 AC_ARG_ENABLE([dap-remote-tests],
               [AS_HELP_STRING([--disable-dap-remote-tests],
@@ -1303,6 +1329,11 @@ AC_CHECK_HEADERS([libgen.h])
 AC_HEADER_STDC
 AC_CHECK_HEADERS([locale.h stdio.h stdarg.h fcntl.h malloc.h stdlib.h string.h strings.h unistd.h sys/stat.h getopt.h sys/time.h sys/types.h time.h dirent.h stdint.h ctype.h])
 
+# Do getopt.h separately so we can AM_CONDITIONAL it.
+# This should still do the implicit AC_DEFINE.
+AC_CHECK_HEADERS([getopt.h],[havegetopth=yes],[havegetopth=no])
+AM_CONDITIONAL(HAVE_GETOPT_H, [test "x$havegetopth" = xyes])
+
 # Do sys/resource.h separately
 #AC_CHECK_HEADERS([sys/resource.h],[havesysresource=1],[havesysresource=0])
 #if test "x$enable_dll" != xyes ; then
@@ -2057,6 +2088,7 @@ AC_SUBST(HAS_SZLIB_WRITE, [$have_sz])
 AC_SUBST(HAS_ZSTD,[$have_zstd])
 AC_SUBST(DO_LARGE_TESTS,[$enable_large_file_tests])
 AC_SUBST(DO_REMOTE_FUNCTIONALITY,[$enable_remote_functionality])
+AC_SUBST(IS_THREADSAFE,[$enable_threadsafe])
 
 if test "x$enable_s3_aws" = xyes ; then
 AC_SUBST(WHICH_S3_SDK,[aws-sdk-cpp])
@@ -2217,6 +2249,7 @@ AX_SET_META([NC_HAS_SZIP],[$enable_hdf5_szip],[yes])
 AX_SET_META([NC_HAS_ZSTD],[$have_zstd],[yes])
 AX_SET_META([NC_HAS_BLOSC],[$have_blosc],[yes])
 AX_SET_META([NC_HAS_BZ2],[$have_bz2],[yes])
+AX_SET_META([NC_IS_THREADSAFE],[$enable_threadsafe],[yes])
 
 # This is the version of the dispatch table. If the dispatch table is
 # changed, this should be incremented, so that user-defined format

dap4_test/CMakeLists.txt

@@ -21,6 +21,8 @@ FILE(GLOB COPY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/*.sh)
 
 FILE(COPY ${COPY_FILES} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ FILE_PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE)
 
+INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/libdap4)
+
 IF(ENABLE_DAP_REMOTE_TESTS)
     # Change name (add '4') to avoid cmake
     # complaint about duplicate targets.
@@ -36,7 +38,6 @@ IF(ENABLE_TESTS)
   # keep it from being too bad.
 
   IF(BUILD_UTILITIES)
-      INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/libdap4)
       build_bin_test(test_parse)
       build_bin_test(test_meta)
 IF(USE_X_GETOPT)

docs/CMakeLists.txt

@@ -96,6 +96,6 @@ inmemory.md DAP2.dox FAQ.md
 known_problems.md
 COPYRIGHT.dox user_defined_formats.md DAP4.md DAP4.dox
 testserver.dox byterange.md filters.md nczarr.md auth.md quantize.md
-quickstart_paths.md cloud.md)
+quickstart_paths.md cloud.md threadsafe.md)
 
 ADD_EXTRA_DIST("${CUR_EXTRA_DIST}")

docs/Doxyfile.in

@@ -825,6 +825,7 @@ INPUT                  = @abs_top_srcdir@/docs/mainpage.dox \
                          @abs_top_srcdir@/docs/indexing.dox \
                          @abs_top_srcdir@/docs/testserver.dox \
                          @abs_top_srcdir@/docs/quantize.md \
+                         @abs_top_srcdir@/docs/threadsafe.md \
                          @abs_top_srcdir@/docs/attribute_conventions.md \
                          @abs_top_srcdir@/docs/file_format_specifications.md \
                          @abs_top_srcdir@/docs/all-error-codes.md \

docs/Makefile.am

@@ -14,7 +14,7 @@ notes.md install-fortran.md credits.md auth.md filters.md		\
 obsolete/fan_utils.html indexing.dox inmemory.md FAQ.md			\
 known_problems.md COPYRIGHT.md inmeminternal.dox testserver.dox		\
 byterange.md nczarr.md quantize.md all-error-codes.md                   \
-quickstart_paths.md cloud.md
+quickstart_paths.md cloud.md threadsafe.md
 
 # Turn off parallel builds in this directory.
 .NOTPARALLEL:

docs/nczarr.md

@@ -611,12 +611,12 @@ There are mutiple cases to consider.
 3. The netcdf attribute **is** of type NC_CHAR and its value – taken as a single sequence of characters –
 **is** parseable as a legal JSON expression.
     * Parse to produce a JSON expression and write that expression.
-    * Use "|U1" as the dtype and store in the NCZarr metadata.
+    * Use ">S1" as the dtype and store in the NCZarr metadata.
 
 4. The netcdf attribute **is** of type NC_CHAR and its value – taken as a single sequence of characters –
 **is not** parseable as a legal JSON expression.
     * Convert to a JSON string and write that expression
-    * Use "|U1" as the dtype and store in the NCZarr metadata.
+    * Use ">S1" as the dtype and store in the NCZarr metadata.
 
 ## Reading an attribute: