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#!/usr/bin/env 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.
#
BLD='\033[1m'
GRN='\033[0;32m'
RED='\033[0;31m'
CYN='\033[0;36m'
NC='\033[0m' # No Color
############################################################
# Usage #
############################################################
function usage {
echo ""
# Display usage
echo "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."
echo ""
echo "usage: h5fuse.sh [-f filename] [-h] [-p] [-q] [-r] [-v] "
echo "-f filename Subfile configuration file."
echo "-h Print this help."
echo "-q Quiet all output. [no]"
echo "-p h5fuse.sh is being run in parallel, with more than one rank. [no]"
echo "-r Remove subfiles after being processed. [no]"
echo "-v Verbose output. [no]"
echo ""
}
function gen_mpi {
# Program to determine MPI rank and size if being run in parallel (-p).
cat > "${c_src}" << EOL
#include <mpi.h>
#include <stdio.h>
int main() {
MPI_Init(NULL, NULL);
int world_size;
MPI_Comm_size(MPI_COMM_WORLD, &world_size);
int world_rank;
MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
printf("%d %d", world_rank, world_size);
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
}
EOL
}
function fuse {
# function for fusing the files
mpi_rank=0
mpi_size=1
nstart=1
nend=$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 #
############################################################
############################################################
############################################################
# Process the input options. Add options as needed. #
############################################################
# Get the options
file_config=""
verbose="false"
quiet="false"
rm_subf="false"
parallel="false"
while getopts "hpqrvf:" option; do
case $option in
f) # subfiling configuration file
file_config=$OPTARG;;
h) # display Help
usage
exit;;
p) # HDF5 fused file
parallel="true";;
q) # quiet all output
quiet="true";;
r) # remove completed subfiles
rm_subf="true";;
v) # verbose output
verbose="true";;
\?) # Invalid option
echo -e "$RED ERROR: Invalid option ${BLD}-${OPTARG}${RED} $NC"
usage
exit 1;;
* ) usage
exit 1;;
esac
done
FAILED=1
############################################################
# Configure file checks #
############################################################
#
SUBF_CONFDIR="${H5FD_SUBFILING_CONFIG_FILE_PREFIX:-$PWD}"
# Try to find the config file
if [ -z "$file_config" ]; then
nfiles=$(find "$SUBF_CONFDIR" -maxdepth 1 -type f -iname "*.config" -printf '.' | wc -m)
if [[ "$nfiles" != "1" ]]; then
if [[ "$nfiles" == "0" ]]; then
echo -e "$RED Failed to find .config file in ${SUBF_CONFDIR} $NC"
usage
exit $FAILED
else
echo -e "$RED More than one .config file found in ${SUBF_CONFDIR} $NC"
usage
exit $FAILED
fi
fi
file_config=$(find "${SUBF_CONFDIR}" -maxdepth 1 -type f -iname '*.config')
fi
if [ ! -f "$file_config" ]; then
echo -e "${RED} configuration file ${BLD}$file_config${NC} ${RED}does not exist. $NC"
exit $FAILED
fi
stripe_size=$(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 $FAILED
fi
hdf5_file="$(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 $FAILED
fi
subfile_dir="$(grep "subfile_dir=" "$file_config" | cut -d "=" -f2)"
if test -z "$subfile_dir"; then
echo -e "$RED failed to find subfile directory in $file_config $NC"
exit $FAILED
fi
# For bash 4.4+
subfs=$(sed -e '1,/subfile_dir=/d' "$file_config")
mapfile -t subfiles <<< "$subfs"
if [ ${#subfiles[@]} -eq 0 ]; then
echo -e "$RED failed to find subfiles list in $file_config $NC"
exit $FAILED
fi
nsubfiles=${#subfiles[@]}
# Get the number of local subfiles
subfiles_loc=()
subfiles_size=()
for i in "${subfiles[@]}"; do
subfile="${subfile_dir}/${i}"
if [ -f "${subfile}" ]; then
subfiles_loc+=("$subfile")
subfiles_size+=($(wc -c "${subfile}" | awk '{print $1}'))
else
subfiles_size+=(0)
fi
done
if [ "$quiet" == "false" ]; then
TIMEFORMAT="COMPLETION TIME = %R s"
time fuse
else
fuse
fi
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