I tried to evaluate the system generated summaries using ROUGE. I have used the command line bellow but i get this-bash: ROUGE-1.5.5.pl: command not founderror. what is the problem?
ROUGE-1.5.5.pl -n 4 -w 1.2 -m -2 4 -u -c 95 -r 1000 -f A -p 0.5 -t 0 -a -d rougejk.in
The path to your file "ROUGE-1.5.5.pl" isn't defined in your PATH variable, or your file isn't in a folder defined in PATH :
$> echo $PATH
If you want to add the path to the folder containing "ROUGE-1.5.5.pl" :
PATH="$PATH:/path/to/folder"
Then you will be able to run your command as described.
You can add this line to your .bashrc, if you want this to be permanent.
Else you have to run the command like this (from your script location) :
./ROUGE-1.5.5.pl -n 4 -w 1.2 -m -2 4 -u -c 95 -r 1000 -f A -p 0.5 -t 0 -a -d rougejk.in
Related
I asked about an issue I had with this using a different approach (Having issues running mpi4py on large HPC system. Receving startup errors and sometimes variable errors), however I'm currently attempting two other approaches. With no success. All examples below still put the same task on each of the six resource sets.
Background: I'm attempting to distribute predictions across resource sets on a node. Each resource set contains 1 gpu and 7 cpus and there are six sets per node. Once a RS task completes, it should move on to the next prediction on in a list (part00.lst through part05.lst; in theory one per RS)
First approach looks something like this (a submission bash script calls this using jsrun -r6 -g1 -a1 -c7 -b packed:7 -d packed -l gpu-cpu):
#!/bin/bash
output=/path/ ##where completed predictions will be collected
for i in {0..5}; do
target=part0${i}.lst
........ ##the singularity job script to execute using $target and $output variables
done
The next attempt is using simultaneous jobs steps via UNIX backgrounding (which others have been able to appropriate to do similar things that I wish to do, but for different jobs and tasks). Here I created six separate bash files with each corresponding input file ($target aka part00.lst through part05.lst):
#!/bin/bash
## Various submission flags here
for i in {0..5}; do
jsrun -r 6 -g 1 -a 1 -c 7 -brs -d packed -l gpu-cpu bash batch_run_0${i}.sh &
done
wait
I also attempted just hardcoding the six separate bash files:
#!/bin/bash
jsrun -r 6 -g 1 -a 1 -c 7 -brs -d packed -l gpu-cpu bash batch_run_00.sh &
jsrun -r 6 -g 1 -a 1 -c 7 -brs -d packed -l gpu-cpu bash batch_run_01.sh &
jsrun -r 6 -g 1 -a 1 -c 7 -brs -d packed -l gpu-cpu bash batch_run_02.sh &
jsrun -r 6 -g 1 -a 1 -c 7 -brs -d packed -l gpu-cpu bash batch_run_03.sh &
jsrun -r 6 -g 1 -a 1 -c 7 -brs -d packed -l gpu-cpu bash batch_run_04.sh &
jsrun -r 6 -g 1 -a 1 -c 7 -brs -d packed -l gpu-cpu bash batch_run_05.sh &
wait
Thanks for any help! I'm still quite new to all of this!
Okay, attempt number two using simultaneous job steps/UNIX process backgrounding was nearly correct!
It now works. An example for one node:
Submission script:
#!/bin/bash
## Various submission flags here
for i in {0..5}; do
jsrun -r 6 -g 1 -a 1 -c 7 -brs -d packed -l gpu-cpu bash batch_run_0${i}.sh &
done
wait
It was only a matter of incorrect flags (-n 1 -r 1, not -n 1 -r 6).
I run a few scripts 1 by 1
cat 001.sh
sh /home/mysqldom/da-cron/f_mysqldom_nrd/5_change_nrd_tld.sh
sh /home/mysqldom/da-cron/f_mysqldom_nrd/5_proxy_removed.sh
sh /home/mysqldom/da-cron/f_mysqldom_nrd/6_sync_nrd.sh
The last script wont work... if I run manually it work very well...
the script is
cat 6_sync_nrd.sh
source /home/mysqldom/da-cron/var.sh
cd /home/mysqldom/da-cron/f_mysqldom_nrd/
mysql -u mysqldom_fnrd -p$mysqldom_fnrd_password -D mysqldom_fnrd -e "UPDATE \`$yesterday\` SET sync='$yesterday';"
mysql -u mysqldom_fnrd -p$mysqldom_fnrd_password -D mysqldom_fnrd -e "DELETE FROM \`$yesterday\` WHERE domain_name = 'domain_name';"
sed s/change_database/$yesterday/g update.conf > $yesterday.conf
/usr/share/logstash/bin/logstash -f $yesterday.conf --path.data /var/lib/logstash108
rm -rf nohup.out
The 6 has to be run after 5
any idea whats worn in it
So in the terminal I access the remote host through ssh -p then once I'm in i have to cd /directory1/directory2/. Then I want to find the latest directory which I do using ls -td -- */ | head -n 1 then using this I want to cd into that and tail -n 1 file1
All these commands work in the terminal but I want to automate it to where I can just type ./tailer.sh and have that be output.
Any ideas would be appreciated.
The shell script tailer.sh can look something like this
#!/bin/bash
ssh -p <PORT> <HOST_NAME> '( cd /directory1/directory2/ && LATEST_DIR=$(ls -td -- */ | head -n 1) && cd ${LATEST_DIR} && tail -n 1 file1 )'
Then give execute permissions to tailer.sh using chmod u+x tailer.sh
Run the script using ./tailer.sh
I have this bash script code:
#!/bin/bash
FILES=/home/user/Downloads/asd/
for f in $FILES
do
curl -F dir="#/home/user/Downloads/asd;$f" -F Match=3 -F "Name=DrKla" \
-F countNo=1 -F outputFormat=json "http://somelink.com"
done
Inside the asd folder there are 6 files and I want them to be uploaded 1 by 1 with this code as an argument of -F "dir=#...."
When I run my code I get the error:
Warning: skip unknown form field: /home/user/Downloads/asd/
curl: (43) A libcurl function was given a bad argument
Here is a working version of the code for a single file:
curl -F dir="#/home/user/Downloads/asd/count.txt" -F Match=3 -F "Name=DrKla" \
-F countNo=1 -F outputFormat=json "http://somelink.com"
So I want to have all the files in asd folder to be read and uploaded like this. I don't see what's wrong with my do loop.
The issues appear to be that you only give a path, not a reference to all files in the path * and there is a strange semi-colon ; in your path:
#!/bin/bash
FILES=/home/user/Downloads/asd/*
for f in $FILES
do
curl -F dir="#$f" -F Match=3 -F "Name=DrKla" \
-F countNo=1 -F outputFormat=json "http://somelink.com"
done
I'm not sure what the # is for or if it is needed, but $f should already contain the path.
I am trying to make some workaround to solve a problem.
We have a gtk+ program that call a bash script who calls rdesktop.
In a machine, we discover that the rdesktop call need on extra parameter...
Since i didnt write anything of this code, and i can modify the GTK part of the problem, i can only edit the bash script that make the middle call between the calls.
i have a variable called CMD with something that look like:
rdesktop -x m -r disk:USBDISK=/media -r disk:user=/home/user/ -r printer:HP_Officejet_Pro_8600 -a 16 -u -p -d -g 80% 192.168.0.5
i need to "live edit" this line for when the printer parameter exists, it append ="MS Publisher Imagesetter" after the printer name.
The best i accompplish so far is
ladb#luisdesk ~ $ input="rdesktop -x m -r disk:USBDISK=/media -r disk:user=/home/user/ -r printer:HP_Officejet_Pro_8600 -a 16 -u -p -d -g 80% 192.168.0.5"
ladb#luisdesk ~ $ echo $input | sed s/'printer:.*a /=\"MS Publisher Imagesetter\" '/
Which return me:
rdesktop -x m -r disk:USBDISK=/media -r disk:user=/home/user/ -r ="MS Publisher Imagesetter" 16 -u -p -d -g 80% 192.168.0.5
Almost this, but i need to append the string, not replace it.
help?
Edit: i pasted incomplete exemples. fixed
Edit2:
With the help of who respond, i end up with
echo "$input" | sed 's/\(printer:\)\([^ ]*\)/\1\2="MS Publisher Imagesetter"/'
If you want the output to look like:
rdesktop -x m -r disk:USBDISK=/media -r disk:user=/home/user/ -r printer:"HP_Officejet_Pro_8600 MS Publisher Imagesetter" -a 16 -u -p -d -g 80% 192.168.0.5
This sed will do, it matches the printer: part first then the existing printer name and quotes both, if not you can adjust the replacement
variables to put the quotes/spacing where you want:
input="rdesktop -x m -r disk:USBDISK=/media -r disk:user=/home/user/ -r printer:HP_Officejet_Pro_8600 -a 16 -u -p -d -g 80% 192.168.0.5"
echo "$input" | sed 's/\(printer:\)\([^ ]*\)/\1"\2 MS Publisher Imagesetter"/'
output:
rdesktop -x m -r disk:USBDISK=/media -r disk:user=/home/user/ -r printer:"HP_Officejet_Pro_8600 MS Publisher Imagesetter" -a 16 -u -p -d -g 80% 192.168.0.5
You can use this:
sed 's/printer:[^=]\+=/\0 "MS Publisher Imagesetter"/' <<< "$input"
The \0 in the replacement pattern outputs the match itself.