blob: dafaab90fe1557b04dd476c8e5e7c711868856e6 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
|
#!/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'
PUR='\033[0;35m'
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 [-h] [-f filename]"
echo "-h Print this help."
echo "-f filename Subfile configuration file."
echo ""
}
############################################################
############################################################
# Main program #
############################################################
############################################################
############################################################
# Process the input options. Add options as needed. #
############################################################
# Get the options
file_config=""
while getopts ":h:f:" option; do
case $option in
h) # display Help
usage
exit;;
f) # subfiling configuration file
file_config=$OPTARG;;
\?) # Invalid option
echo -e "$RED ERROR: Invalid option ${BLD}-${OPTARG}${RED} $NC"
usage
exit 1;;
* ) usage
exit 1;;
esac
done
FAILED=1
nfiles=1
############################################################
# Configure file checks #
############################################################
if [ -z "$file_config" ]; then
nfiles=$(find . -maxdepth 1 -type f -iname "*.config" -printf '.' | wc -m)
if [[ "$nfiles" != "1" ]]; then
if [[ "$nfiles" == "0" ]]; then
echo -e "$RED Failed to find .config file in current directory. $NC"
usage
exit $FAILED
else
echo -e "$RED More than one .config file found in current directory. $NC"
usage
exit $FAILED
fi
fi
file_config=$(find . -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
subfiles=( $( sed -e '1,/subfile_dir=/d' "$file_config" ) )
#for i in "${subfiles[@]}"; do
# echo "$i"
#done
if [ ${#subfiles[@]} -eq 0 ]; then
echo -e "$RED failed to find subfiles list in $file_config $NC"
exit $FAILED
fi
rm -f "$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
subfile="${subfile_dir}/${i}"
# Verify the file exists
if [ ! -f "${subfile}" ]; then
echo -e "$RED ERROR: file \"${subfile}\" does not exist. $NC"
exit $FAILED
fi
# Verify the file is not being accessed by a process
t_max=60
t_sleep=1
t_elapsed=0
while fuser -s "${subfile}"; do
if [[ $((t_elapsed % 5)) -eq 0 ]]; then
echo -e "$GRN waiting for process to finish accessing file \"${subfile}\" ... [${t_elapsed}s/${t_max}s] $NC"
fi
sleep $t_sleep
t_elapsed=$((t_elapsed+t_sleep))
if [[ $t_elapsed -ge $t_max ]]; then
echo -e "$RED ERROR: file \"${subfile}\" still has process accessing it after ${t_elapsed}s $NC"
exit $FAILED
fi
done
fsize=$(wc -c "${subfile}" | awk '{print $1}')
if [ $((skip*stripe_size)) -le "$fsize" ]; then
EXEC="dd count=1 bs=$stripe_size if=$subfile 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"
|
