Subfiling VFD misc fixes (#1938)

* Remove generated file h5fuse.sh

* Link pthreads library when Subfiling VFD is built

CMakeLists.txt

@@ -758,6 +758,18 @@ if (HDF5_ENABLE_SUBFILING_VFD)
   if (NOT HDF5_ENABLE_PARALLEL)
     message (FATAL_ERROR "Subfiling VFD requires a parallel HDF5 build")
   endif()
+
+  if (NOT DEFINED Threads_FOUND)
+    set (THREADS_PREFER_PTHREAD_FLAG ON)
+    find_package (Threads REQUIRED)
+  endif ()
+
+  # For now, make sure we're using pthreads. Once Subfiling can be
+  # supported on Windows, we should allow Win32 threads as well
+  if (NOT ${Threads_FOUND} OR NOT ${CMAKE_USE_PTHREADS_INIT})
+    message (FATAL_ERROR "Subfiling requires pthreads for system thread library")
+  endif ()
+
   CHECK_INCLUDE_FILE("stdatomic.h" HAVE_STDATOMIC_H)
   if (NOT HAVE_STDATOMIC_H)
     message (FATAL_ERROR "Subfiling VFD requires atomic operations support. C11 stdatomic.h NOT available.")

src/CMakeLists.txt

@@ -1235,7 +1235,7 @@ if (NOT ONLY_SHARED_LIBS)
   )
   if (NOT WIN32)
     target_link_libraries (${HDF5_LIB_TARGET}
-      PRIVATE $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:Threads::Threads>
+      PRIVATE $<$<OR:$<BOOL:${HDF5_ENABLE_THREADSAFE}>,$<BOOL:${HDF5_ENABLE_SUBFILING_VFD}>>:Threads::Threads>
     )
   endif ()
   set_global_variable (HDF5_LIBRARIES_TO_EXPORT ${HDF5_LIB_TARGET})
@@ -1272,7 +1272,8 @@ if (BUILD_SHARED_LIBS)
   )
   TARGET_C_PROPERTIES (${HDF5_LIBSH_TARGET} SHARED)
   target_link_libraries (${HDF5_LIBSH_TARGET}
-      PRIVATE ${LINK_LIBS} ${LINK_COMP_LIBS} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>" $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:Threads::Threads>
+      PRIVATE ${LINK_LIBS} ${LINK_COMP_LIBS} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>"
+              $<$<OR:$<BOOL:${HDF5_ENABLE_THREADSAFE}>,$<BOOL:${HDF5_ENABLE_SUBFILING_VFD}>>:Threads::Threads>
       PUBLIC $<$<NOT:$<PLATFORM_ID:Windows>>:${CMAKE_DL_LIBS}>
   )
   set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_LIBSH_TARGET}")

utils/subfiling_vfd/h5fuse.sh

@@ -1,89 +0,0 @@
-#!/bin/bash
-#
-# Copyright by The HDF Group.                                              
-# All rights reserved.                                                     
-#                                                                          
-# This file is part of HDF5. The full HDF5 copyright notice, including     
-# terms governing use, modification, and redistribution, is contained in   
-# the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://www.hdfgroup.org/licenses.
-# If you do not have access to either file, you may request a copy from
-# help@hdfgroup.org.
-#
-
-# Purpose: Combine subfiles into a single HDF5 file. Requires the subfiling 
-# configuration file either as a command-line argument, or the script will 
-# search for the *.config file in the current directory. 
-
-GRN='\033[0;32m'
-RED='\033[0;31m'
-PUR='\033[0;35m'
-NC='\033[0m' # No Color
-
-## CONFIG FILE CHECKS ##
-
-if [ $# -eq 0 ]; then
-    nfiles=$(find . -maxdepth 1 -type f -iname "*.config" -printf '.' | wc -m)
-    if [[ "$nfiles" != "1" ]]; then
-       echo -e "$RED More than one .config file found in current directory. $NC"
-       exit 1
-    fi
-    file_config=$(find . -maxdepth 1 -type f -iname "*.config")
-else
-    file_config=$1
-fi
-
-if [ ! -f "$file_config" ]; then
-    echo -e "$RED $file_config does not exist. $NC"
-    exit 1
-fi
-
-stripe_size=$(grep "stripe_size=" $file_config  | cut -d "=" -f2)
-if test -z "$stripe_size"; then
-    echo -e "$RED failed to find stripe_size in $file_config $NC"
-    exit 1
-fi
-
-subfiles=( $( sed -e '1,/hdf5_file=/d' $file_config ) )
-#for i in "${subfiles[@]}"; do
-#      echo "$i"
-#done
-if test -z "$subfiles"; then
-    echo -e "$RED failed to find subfiles list in $file_config $NC"
-    exit 1
-fi
-
-hdf5_file=$(grep "hdf5_file=" $file_config  | cut -d "=" -f2)
-if test -z "$hdf5_file"; then
-    echo -e "$RED failed to find hdf5 output file in $file_config $NC"
-    exit 1
-fi
-
-rm -f $hdf5_file
-
-## COMBINE SUBFILES INTO AN HDF5 FILE ##
-
-skip=0
-status=$nfiles
-START="$(date +%s%N)"
-while [ $status -gt 0 ]; do
-  icnt=0
-  for i in "${subfiles[@]}"; do
-      fsize=$(wc -c $i | awk '{print $1}')
-      if [ $(($skip*$stripe_size)) -le $fsize ]; then
-          EXEC="dd count=1 bs=$stripe_size if=$i of=$hdf5_file skip=$skip oflag=append conv=notrunc"
-          echo -e "$GRN $EXEC $NC"
-          err="$( $EXEC 2>&1 > /dev/null &)"
-          icnt=$(($icnt+1)) 
-      else
-          subfiles=("${subfiles[@]:0:$icnt}" "${subfiles[@]:$(($icnt+1))}")
-          status=${#subfiles[@]}
-      fi
-  done; wait
-  skip=$(($skip+1))
-done
-END=$[ $(date +%s%N) - ${START} ]
-DURATION_SEC=$(awk -vp=$END -vq=0.000000001 'BEGIN{printf "%.4f" ,p * q}')
-echo -e "$PUR COMPLETION TIME = $DURATION_SEC s $NC"
-
-