Using ssh inside a script to run another script that itself calls ssh

Question

I'm trying to write a script that builds a list of nodes then ssh into the first node of that list and runs a checknodes.sh script which it's self is just a for i loop that calls checknode.sh

The first 2 lines seems to work ok, the list builds successfully, but then I get either get just the echo line of checknodes.sh to print out or an error saying cat: gpcnodes.txt: No such file or directory

MYSCRIPT.sh:

#gets the master node for the job
MASTERNODE=`qstat -t -u \* | grep $1 | awk '{print$8}' | cut -d'@' -f 2 | cut -d'.' -f 1 | sed -e 's/$/.com/' | head -n 1`
#builds list of nodes in job
ssh -qt $MASTERNODE "qstat -t -u \* | grep $1 | awk '{print$8}' | cut -d'@' -f 2 | cut -d'.' -f 1 | sed -e 's/$/.com/'  > /users/issues/slow_job_starts/gpcnodes.txt"

ssh -qt $MASTERNODE cd /users/issues/slow_job_starts/
ssh -qt $MASTERNODE /users/issues/slow_job_starts/checknodes.sh

checknodes.sh

for i in `cat gpcnodes.txt `
do 
    echo "### $i ###"
    ssh -qt $i /users/issues/slow_job_starts/checknode.sh
done

checknode.sh

str=`hostname`
cd /tmp
time perf record qhost >/dev/null 2>&1 | sed -e 's/^/${str}/'
perf report  --pretty=raw | grep % | head -20 | grep -c kernel.kallsyms | sed -e "s/^/`hostname`:/"

You should search for Paramiko... it will make SSHing between various machines/running remote commands a breeze — user11924970
– user11924970, Commented May 9, 2020 at 22:18

Walter A · Accepted Answer · 2020-05-10 09:20:10Z

1

When ssh -qt $MASTERNODE cd /users/issues/slow_job_starts/ is finished, the changed directory is lost. With the backquotes replaced by $(..) (not an error here, but get used to it), the script would be something like

for i in $(cat /users/issues/slow_job_starts/gpcnodes.txt)
do 
    echo "### $i ###"
    ssh -nqt $i /users/issues/slow_job_starts/checknode.sh
done

or better

while read -r i; do 
    echo "### $i ###"
    ssh -nqt $i /users/issues/slow_job_starts/checknode.sh
done < /users/issues/slow_job_starts/gpcnodes.txt

Perhaps you would also like to change your last script (start with cd /users/issues/slow_job_starts)

You will find more problems, like sed -e 's/^/${str}/' (the ${str} inside single quotes won't be replaced by a host), but this should get you started.

EDIT:
I added option -n to the ssh call.
Redirects stdin from /dev/null (actually, prevents reading from stdin).
Without this option only one node is checked.

edited May 10, 2020 at 9:20

answered May 9, 2020 at 22:28

Walter A

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2 Comments

Jetchisel Over a year ago

afaik ssh eats/slurps stdin (this is what I remember from my ssh scripts) , a work around is to use a different fd.

Walter A Over a year ago

@Jetchisel Thanks, I added the option -n.

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