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comparison bin/_runme_c.sh @ 99:4c65ae2a4bc3

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initialise paths for csing
author Henry S. Thompson <ht@inf.ed.ac.uk>
date Fri, 08 Sep 2023 21:40:52 +0100
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98:93d4915ef797 99:4c65ae2a4bc3
1 #!/bin/bash
2 # This runs on the compute nodes...
3 # Args: [-a i] wd [-d] [-t nthreads] [-b CMDS] [-i input] CMDS
4 # See ug4/azure/notes.txt for documentation
5
6 N=$SLURM_JOB_NUM_NODES
7 n=$SLURM_NTASKS
8 c=$SLURM_CPUS_PER_TASK
9 nodename=$SLURMD_NODENAME
10 local=$SLURM_LOCALID
11 node=$SLURM_NODEID
12 task=$SLURM_PROCID
13
14 if [ "$1" = "-a" ]
15 then
16 shift
17 xarg="$1"
18 shift
19 else
20 xarg=
21 fi
22
23 cd "$1"
24 shift
25
26 if [ "$1" = "-d" ]
27 then
28 shift
29 debug=1
30 fi
31
32 if [ "$1" = "-t" ]
33 then
34 shift
35 threadsPerTask=$1
36 shift
37 else
38 threadsPerTask=2
39 fi
40
41 pjobs=$((c / $threadsPerTask))
42
43 echo $(date) task $n.$task on $nodename:$N.$node start $pjobs jobs 1>&2
44
45 PATH=$W/$USER/bin:$W/shared/bin:$PATH
46 export task PATH n xarg
47
48 if [ "$1" = "-b" ]
49 then
50 shift
51 eval "$1"
52 shift
53 fi
54
55 input="seq 1 $pjobs" # default to make sure something runs
56
57 if [ "$1" = "-i" ]
58 then
59 shift
60 input="$1"
61 shift
62 if [ "$debug" ]
63 then
64 echo $(date) task $n.$task input "|$input|"
65 fi
66 fi
67
68 export cmd="$1"
69 shift
70
71 doit () {
72 arg="$1"
73 echo $(date) start $task $PARALLEL_SEQ "|$cmd|$xarg|$arg|"
74 eval "$cmd"
75 echo $(date) end $task $PARALLEL_SEQ
76 }
77
78 export -f doit
79
80 if [ "$debug" ]
81 then
82 echo $(date) task $n.$task cmd "|$cmd|" doit $(type doit)
83 fi
84
85 source $HOME/.csing_init
86
87 eval "$input" | \
88 if [ "$debug" ]
89 then
90 tee >(cat 1>&2)
91 else
92 cat
93 fi | \
94 if [ $pjobs -le 1 ]
95 then
96 xargs -I ^ -n 1 bash -lc "doit ^"
97 else
98 parallel --line-buffer -j $pjobs doit '{}'
99 fi
100
101 echo $(date) task $n.$task on $nodename:$N.$node end 1>&2
102