diff options
| -rw-r--r-- | CMakeLists.txt | 12 | ||||
| -rw-r--r-- | src/CMakeLists.txt | 5 | ||||
| -rwxr-xr-x | utils/subfiling_vfd/h5fuse.sh | 89 |
3 files changed, 15 insertions, 91 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt index d27962d..4e42153 100644 --- a/CMakeLists.txt +++ b/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 ${CMAKE_USE_PTHREADS_INIT}) + message (FATAL_ERROR "Subfiling requires pthreads for system thread library") + endif () + CHECK_INCLUDE_FILE("stdatomic.h" HAVE_STDATOMIC_H) if (NOT HAVE_STDATOMIC_H) message (FATAL_ERROR "Subfiling VFD requires atomic operations support. C11 stdatomic.h NOT available.") diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 9818004..3b98874 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1235,7 +1235,7 @@ if (NOT ONLY_SHARED_LIBS) ) if (NOT WIN32) target_link_libraries (${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}") diff --git a/utils/subfiling_vfd/h5fuse.sh b/utils/subfiling_vfd/h5fuse.sh deleted file mode 100755 index 8170586..0000000 --- a/utils/subfiling_vfd/h5fuse.sh +++ /dev/null @@ -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" - - |