diff options
Diffstat (limited to 'utils/subfiling_vfd')
-rwxr-xr-x | utils/subfiling_vfd/h5fuse.sh.in | 206 |
1 files changed, 105 insertions, 101 deletions
diff --git a/utils/subfiling_vfd/h5fuse.sh.in b/utils/subfiling_vfd/h5fuse.sh.in index c6d715f..82d497e 100755 --- a/utils/subfiling_vfd/h5fuse.sh.in +++ b/utils/subfiling_vfd/h5fuse.sh.in @@ -13,7 +13,6 @@ BLD='\033[1m' GRN='\033[0;32m' RED='\033[0;31m' -PUR='\033[0;35m' CYN='\033[0;36m' NC='\033[0m' # No Color @@ -58,6 +57,106 @@ EOL } +function fuse { + +# function for fusing the files + +mpi_rank=0 +mpi_size=1 +nstart=1 +nend=$nsubfiles + +if [ "$parallel" == "true" ]; then + + hex=$(hexdump -n 16 -v -e '/1 "%02X"' /dev/urandom) + c_exec="h5fuse_"${hex} + c_src=${c_exec}.c + + # Generate and compile an MPI program to get MPI rank and size + if [ ! -f "${c_src}" ]; then + gen_mpi + CC=@CC@ + ${CC} "${c_src}" -o "${c_exec}" + fi + wait + rank_size=$(./"${c_exec}") + read -r mpi_rank mpi_size <<<"$rank_size" + + rm -f "${c_src}" "${c_exec}" + + # Divide the subfiles among the ranks + iwork1=$(( nsubfiles / mpi_size )) + iwork2=$(( nsubfiles % mpi_size )) + min=$(( mpi_rank < iwork2 ? mpi_rank : iwork2 )) + nstart=$(( mpi_rank * iwork1 + 1 + min )) + nend=$(( nstart + iwork1 - 1 )) + if [ $iwork2 -gt "$mpi_rank" ]; then + nend=$(( nend + 1 )) + fi +fi + +############################################################ +# COMBINE SUBFILES INTO AN HDF5 FILE # +############################################################ +icnt=1 +skip=0 +seek=0 +seek_cnt=0 +for i in "${subfiles[@]}"; do + + subfile="${subfile_dir}/${i}" + + # bs=BYTES read and write up to BYTES bytes at a time; overrides ibs and obs + # ibs=BYTES read up to BYTES bytes at a time + # obs=BYTES write BYTES bytes at a time + # seek=N skip N obs-sized blocks at start of output + # skip=N skip N ibs-sized blocks at start of input + + status=1 + fsize=${subfiles_size[icnt-1]} + if [ "$fsize" -eq "0" ]; then + seek_cnt=$((seek_cnt+1)) + seek=$seek_cnt + if [ "$rm_subf" == "true" ]; then + if [ -f "${subfile}" ]; then + \rm -f "$subfile" + fi + fi + else + if [ $icnt -ge "$nstart" ] && [ $icnt -le "$nend" ]; then + records_left=$fsize + while [ "$status" -gt 0 ]; do + if [ $((skip*stripe_size)) -le "$fsize" ] && [ "$records_left" -gt 0 ]; then + EXEC="dd count=1 bs=$stripe_size if=$subfile of=$hdf5_file skip=$skip seek=$seek conv=notrunc" + if [ "$verbose" == "true" ]; then + echo -e "$GRN $EXEC $NC" + fi + err=$( $EXEC 2>&1 1>/dev/null ) + if [ $? -ne 0 ]; then + echo -e "$CYN ERR: dd Utility Failed $NC" + echo -e "$CYN MSG: $err $NC" + exit $FAILED + fi + records_left=$((records_left-stripe_size)) + skip=$((skip+1)) + seek=$((seek_cnt+skip*nsubfiles)) + else + status=0 + skip=0 + fi + done; wait + if [ "$rm_subf" == "true" ]; then + \rm -f "$subfile" + fi + fi + seek_cnt=$((seek_cnt+1)) + seek=$seek_cnt + fi + icnt=$(( icnt +1 )) +done; wait + +} + ############################################################ ############################################################ # Main program # @@ -166,104 +265,9 @@ for i in "${subfiles[@]}"; do fi done -START="$(date +%s%N)" - -mpi_rank=0 -mpi_size=1 -nstart=1 -nend=$nsubfiles - -if [ "$parallel" == "true" ]; then - - hex=$(hexdump -n 16 -v -e '/1 "%02X"' /dev/urandom) - c_exec="h5fuse_"${hex} - c_src=${c_exec}.c - - # Generate and compile an MPI program to get MPI rank and size - if [ ! -f "${c_src}" ]; then - gen_mpi - CC=@CC@ - ${CC} "${c_src}" -o "${c_exec}" - fi - wait - rank_size=$(./"${c_exec}") - read -r mpi_rank mpi_size <<<"$rank_size" - - rm -f "${c_src}" "${c_exec}" - - # Divide the subfiles among the ranks - iwork1=$(( nsubfiles / mpi_size )) - iwork2=$(( nsubfiles % mpi_size )) - min=$(( mpi_rank < iwork2 ? mpi_rank : iwork2 )) - nstart=$(( mpi_rank * iwork1 + 1 + min )) - nend=$(( nstart + iwork1 - 1 )) - if [ $iwork2 -gt "$mpi_rank" ]; then - nend=$(( nend + 1 )) - fi -fi - -############################################################ -# COMBINE SUBFILES INTO AN HDF5 FILE # -############################################################ -icnt=1 -skip=0 -seek=0 -seek_cnt=0 -for i in "${subfiles[@]}"; do - - subfile="${subfile_dir}/${i}" - - # bs=BYTES read and write up to BYTES bytes at a time; overrides ibs and obs - # ibs=BYTES read up to BYTES bytes at a time - # obs=BYTES write BYTES bytes at a time - # seek=N skip N obs-sized blocks at start of output - # skip=N skip N ibs-sized blocks at start of input - - status=1 - fsize=${subfiles_size[icnt-1]} - if [ "$fsize" -eq "0" ]; then - seek_cnt=$((seek_cnt+1)) - seek=$seek_cnt - if [ "$rm_subf" == "true" ]; then - if [ -f "${subfile}" ]; then - \rm -f "$subfile" - fi - fi - else - if [ $icnt -ge "$nstart" ] && [ $icnt -le "$nend" ]; then - records_left=$fsize - while [ "$status" -gt 0 ]; do - if [ $((skip*stripe_size)) -le "$fsize" ] && [ "$records_left" -gt 0 ]; then - EXEC="dd count=1 bs=$stripe_size if=$subfile of=$hdf5_file skip=$skip seek=$seek conv=notrunc" - if [ "$verbose" == "true" ]; then - echo -e "$GRN $EXEC $NC" - fi - err=$( $EXEC 2>&1 1>/dev/null ) - if [ $? -ne 0 ]; then - echo -e "$CYN ERR: dd Utility Failed $NC" - echo -e "$CYN MSG: $err $NC" - exit $FAILED - fi - records_left=$((records_left-stripe_size)) - skip=$((skip+1)) - seek=$((seek_cnt+skip*nsubfiles)) - else - status=0 - skip=0 - fi - done; wait - if [ "$rm_subf" == "true" ]; then - \rm -f "$subfile" - fi - fi - seek_cnt=$((seek_cnt+1)) - seek=$seek_cnt - fi - icnt=$(( icnt +1 )) -done; wait - -END=$(( $(date +%s%N) - START )) -DURATION_SEC=$(awk -vp="$END" -vq=0.000000001 'BEGIN{printf "%.4f" ,p * q}') if [ "$quiet" == "false" ]; then - echo -e "$PUR COMPLETION TIME = $DURATION_SEC s $NC" -fi
\ No newline at end of file + TIMEFORMAT="COMPLETION TIME = %R s" + time fuse +else + fuse +fi |