Submitting a job on PBS with while loop, changing output file names - loops

I have a (let's call it original) script to parse a file (~1000 lines) line by line, generate arguments to execute a C++ program.
#!/bin/bash
i = 0
while IFS='' read -r line || [[ -n "$line" ]]; do
a="$line" | cut -c1-2
b="$line" | cut -c3-4
c="$line" | cut -c5-6
d="$line" | cut -c7-8
e="$line" | cut -c9-10
f="$line" | cut -c11-12
g="$line" | cut -c13-14
h="$line" | cut -c15-16
i="$line" | cut -c17-18
j="$line" | cut -c19-20
k="$line" | cut -c21-22
l="$line" | cut -c23-24
m="$line" | cut -c25-26
n="$line" | cut -c27-28
o="$line" | cut -c29-30
p="$line" | cut -c31-32
./a.out "$a" "$b" "$c" "$d" "$e" "$f" "$g" "$h" "$i" "$j" "$k" "$l" "$m" "$n" "$o" "$p" > $(echo some-folder/output_${i}.txt)
done < test_10.txt
I want to schedule this job in a batch, so that each run is queued and ran on separate cores.
I checked the PBS and qsub writing styles. I could write a PBS file (simple one, without all options for now. Lets call it callPBS.PBS):
#!/bin/bash
cd $PBS_O_WORKDIR
qsub ./a.out -F "my arguments"
exit 0
I can call this file instead of ./a.out -------- in original script. BUT how do I pass "my arguments"? Problem is they are not fixed.
Secondly I know qsub takes -o as an option for output file. But I want my output file name to be changed. I can pass that as an argument again, but how?
Can I do this in my original script:
callPBS.pbs > $(echo some-folder/output_${i}.txt)
I am sorry if I am missing something here. I am trying to use all that I know!

Related

Bash Add elements to an array does not work [duplicate]

Why isn't this bash array populating? I believe I've done them like this in the past. Echoing ${#XECOMMAND[#]} shows no data..
DIR=$1
TEMPFILE=/tmp/dir.tmp
ls -l $DIR | tail -n +2 | sed 's/\s\+/ /g' | cut -d" " -f5,9 > $TEMPFILE
i=0
cat $TEMPFILE | while read line ;do
if [[ $(echo $line | cut -d" " -f1) == 0 ]]; then
XECOMMAND[$i]="$(echo "$line" | cut -d" " -f2)"
(( i++ ))
fi
done
When you run the while loop like
somecommand | while read ...
then the while loop is executed in sub-shell, i.e. a different process than the main script. Thus, all variable assignments that happen in the loop, will not be reflected in the main process. The workaround is to use input redirection and/or command substitution, so that the loop executes in the current process. For example if you want to read from a file you do
while read ....
do
# do stuff
done < "$filename"
or if you wan't the output of a process you can do
while read ....
do
# do stuff
done < <(some command)
Finally, in bash 4.2 and above, you can set shopt -s lastpipe, which causes the last command in the pipeline to be executed in the current process.
I think you're trying to construct an array consisting of the names of all zero-length files and directories in $DIR. If so, you can do it like this:
mapfile -t ZERO_LENGTH < <(find "$DIR" -maxdepth 1 -size 0)
(Add -type f to the find command if you're only interested in regular files.)
This sort of solution is almost always better than trying to parse ls output.
The use of process substitution (< <(...)) rather than piping (... |) is important, because it means that the shell variable will be set in the current shell, not in an ephimeral subshell.

jq: 1 compile error jq: error: schedule/0 is not defined at <top-level>, line 1: .Christchurch.bus-schedule.from["Weekday"] |= . + ["1646"]

I have a react application which uses a .sh file to generate a part of the application. But I have come across an error which prevents the application from reading the data files.
I've looked at versioning, possible syntax changes in the .sh file which is emap.sh
This is the .sh file
#!/bin/bash
object='{}'
find 'public/data' -type f -name '*.csv' | while read -r filename;
do
filename=$(echo "$filename" | sed 's/public\/data\///' | sed 's/ /\//')
city=$(echo "$filename" | cut -d'/' -f1)
medium=$(echo "$filename" | cut -d'/' -f2)
direction=$(echo "$filename" | cut -d'/' -f3)
date=$(echo "$filename" | cut -d'/' -f4)
time=$(echo "$filename" | cut -d'/' -f5| head -c-5)
object=$(echo $object | jq -c ".$city.$medium.$direction[\"$date\"] |= . + [\"$time\"]")
echo $object > public/available.json
done
It should be successful so that when we yarn the application, it shows up having read the data, but we get a page without data in the area using the information that needs to be processed.
The shell variables should be passed to jq in a more robust manner, e.g. along these lines:
jq -c --arg city "$city" \
--arg medium "$medium" \
--arg direction "$direction" \
--arg date "$date" \
--arg time "$time" \
'.[$city][$medium][$direction][$date] += [$time]'
As #OguzIsmail points out, though, you would probably be better off avoiding all the messiness by doing everything with just find and jq.

create arrays from for loop output

I'm trying to understand what I'm doing wrong here, but can't seem to determine the cause. I would like to create a set of arrays from an output for a for loop in bash. Below is the code I have so far:
for i in `onedatastore list | grep pure02 | awk '{print $1}'`;
do
arr${i}=($(onedatastore show ${i} | sed 's/[A-Z]://' | cut -f2 -d\:)) ;
echo "Output of arr${i}: ${arr${i}[#]}" ;
done
The output for the condition is as such:
107
108
109
What I want to do is based on these unique IDs is create arrays:
arr107
arr108
arr109
The arrays will have data like such in each:
[oneadmin#opennebula/]$ arr107=($(onedatastore show 107 | sed 's/[A-Z]://' | cut -f2 -d\:))
[oneadmin#opennebula/]$ echo ${arr107[#]}
DATASTORE 107 INFORMATION 107 pure02_vm_datastore_1 oneadmin oneadmin 0 IMAGE vcenter vcenter /var/lib/one//datastores/107 FILE READY DATASTORE CAPACITY 60T 21.9T 38.1T - PERMISSIONS um- u-- --- DATASTORE TEMPLATE CLONE_TARGET="NONE" DISK_TYPE="FILE" DS_MAD="vcenter" LN_TARGET="NONE" RESTRICTED_DIRS="/" SAFE_DIRS="/var/tmp" TM_MAD="vcenter" VCENTER_CLUSTER="CLUSTER01" IMAGES
When I try this in the script section though I get output errors as such:
./test.sh: line 6: syntax error near unexpected token `$(onedatastore show ${i} | sed 's/[A-Z]://' | cut -f2 -d\:)'
I can't seem to figure out the syntax to use on this scenario.
In the end what I want to do is be able to compare different datastores and based on which on has more free space, deploy VMs to it.
Hope someone can help. Thanks
You can use the eval (potentially unsafe) and declare (safer) commands:
for i in $(onedatastore list | grep pure02 | awk '{print $1}');
do
declare "arr$i=($(onedatastore show ${i} | sed 's/[A-Z]://' | cut -f2 -d\:))"
eval echo 'Output of arr$i: ${arr'"$i"'[#]}'
done
readarray or mapfile, added in bash 4.0, will read directly into an array:
while IFS= read -r i <&3; do
readarray -t "arr$i" < <(onedatastore show "$i" | sed 's/[A-Z]://' | cut -f2 -d:)
done 3< <(onedatastore list | awk '/pure02/ {print $1}')
Better, back through bash 3.x, one can use read -a to read to an array:
shopt -s pipefail # cause pipelines to fail if any element does
while IFS= read -r i <&3; do
IFS=$'\n' read -r -d '' -a "arr$i" \
< <(onedatastore show "$i" | sed 's/[A-Z]://' | cut -f2 -d: && printf '\0')
done 3< <(onedatastore list | awk '/pure02/ {print $1}')
Alternately, one can use namevars to create an alias for an array with an arbitrarily-named array in bash 4.3:
while IFS= read -r i <&3; do
declare -a "arr$i"
declare -n arr="arr$i"
# this is buggy: expands globs, string-splits on all characters in IFS, etc
# ...but, well, it's what the OP is asking for...
arr=( $(onedatastore show "$i" | sed 's/[A-Z]://' | cut -f2 -d:) )
done 3< <(onedatastore list | awk '/pure02/ {print $1}')

How do i echo specific rows and columns from csv's in a variable?

The below script:
#!/bin/bash
otscurrent="
AAA,33854,4528,38382,12
BBB,83917,12296,96213,13
CCC,20399,5396,25795,21
DDD,27198,4884,32082,15
EEE,2472,981,3453,28
FFF,3207,851,4058,21
GGG,30621,4595,35216,13
HHH,8450,1504,9954,15
III,4963,2157,7120,30
JJJ,51,59,110,54
KKK,87,123,210,59
LLL,573,144,717,20
MMM,617,1841,2458,75
NNN,234,76,310,25
OOO,12433,1908,14341,13
PPP,10627,1428,12055,12
QQQ,510,514,1024,50
RRR,1361,687,2048,34
SSS,1,24,25,96
TTT,0,5,5,100
UUU,294,1606,1900,85
"
IFS="," array1=(${otscurrent})
echo ${array1[4]}
Prints:
$ ./test.sh
12
BBB
I'm trying to get it to just print 12... And I am not even sure how to make it just print row 5 column 4
The variable is an output of a sqlquery that has been parsed with several sed commands to change the formatting to csv.
otscurrent="$(sqlplus64 user/password#dbserverip/db as sysdba #query.sql |
sed '1,11d; /^-/d; s/[[:space:]]\{1,\}/,/g; $d' |
sed '$d'|sed '$d'|sed '$d' | sed '$d' |
sed 's/Used,MB/Used MB/g' |
sed 's/Free,MB/Free MB/g' |
sed 's/Total,MB/Total MB/g' |
sed 's/Pct.,Free/Pct. Free/g' |
sed '1b;/^Name/d' |
sed '/^$/d'
)"
Ultimately I would like to be able to call on a row and column and run statements on the values.
Initially i was piping that into :
awk -F "," 'NR>1{ if($5 < 10) { printf "%-30s%-10s%-10s%-10s%-10s\n", $1,$2,$3,$4,$5"%"; } else { echo "Nothing to do" } }')"
Which works but I couldn't run commands from if else ... or atleaste I didn't know how.
If you have bash 4.0 or newer, an associative array is an appropriate way to store data in this kind of form.
otscurrent=${otscurrent#$'\n'} # strip leading newline present in your sample data
declare -A data=( )
row=0
while IFS=, read -r -a line; do
for idx in "${!line[#]}"; do
data["$row,$idx"]=${line[$idx]}
done
(( row += 1 ))
done <<<"$otscurrent"
This lets you access each individual item:
echo "${data[0,0]}" # first field of first line
echo "${data[9,0]}" # first field of tenth line
echo "${data[9,1]}" # second field of tenth line
"I'm trying to get it to just print 12..."
The issue is that IFS="," splits on commas and there is no comma between 12 and BBB. If you want those to be separate elements, add a newline to IFS. Thus, replace:
IFS="," array1=(${otscurrent})
With:
IFS=$',\n' array1=(${otscurrent})
Output:
$ bash test.sh
12
All you need to print the value of the 4th column on the 5th row is:
$ awk -F, 'NR==5{print $4}' <<< "$otscurrent"
3453
and just remember that in awk row (record) and column (field) numbers start at 1, not 0. Some more examples:
$ awk -F, 'NR==1{print $5}' <<< "$otscurrent"
12
$ awk -F, 'NR==2{print $1}' <<< "$otscurrent"
BBB
$ awk -F, '$5 > 50' <<< "$otscurrent"
JJJ,51,59,110,54
KKK,87,123,210,59
MMM,617,1841,2458,75
SSS,1,24,25,96
TTT,0,5,5,100
UUU,294,1606,1900,85
If you'd like to avoid all of the complexity and simply parse your SQL output to produce what you want without 20 sed commands in between, post a new question showing the raw sqlplus output as the input and what you want finally output and someone will post a brief, clear, simple, efficient awk script to do it all at one time, or maybe 2 commands if you still want an intermediate CSV for some reason.

store the values from command into an array bash

svn mergeinfo --show-revs eligible http://svn.test.com/INT_1.0.0/ http://svn.test.com/DEV/ | cut -d"r" -f2 | cut -d" " -f1
6097
6099
when i put this in a script, i get only last value but not all:
#!/usr/bin/bash
src_url="http://svn.test.com/INT_1.0.0/"
target_url="http://svn.test.com/DEV/"
eligible_revs=(`svn mergeinfo --show-revs eligible $src_url $target_url | cut -d"r" -f2 | cut -d" " -f1`)
echo ${eligible_revs[#]}
output:
6099
If you are running Cygwin the line endings can mess it up
$ foo=(`printf 'bar\r\nbaz'`)
$ echo ${foo[*]}
baz

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