oldwiki.scinet.utoronto.ca - User contributions [en-gb]

User Remote

2018-02-12T14:51:22Z

Ashwin: /* Usage */

__FORCETOC__

==Step 0: Some SSH Aliases to Make Life Easier==

<pre>
function p7() {
ssh p7n01-ib0 "$@"
}

function gpc() {
ssh gpc01 "$@"
}
</pre>

==Submitting jobs==
The GPC and P7 job submission commands (<tt>qsub</tt> and <tt>llsubmit</tt>, respectively) do not allow for the submission of multiple job files, leaving the user to have to for-loop through multiple files when batch submission is required. The below bash function automates such looping and can be added to the shell environment

<pre>
function submit() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then # Login node
echo "Can't submit from a login node"
return
fi

if [ $host -eq 1 ]; then # GPC
submitter=qsub
elif [ $host -eq 2 ]; then # P7
submitter=llsubmit
fi

for fpath in "$@"; do
$submitter "$fpath"
done
}

</pre>

===Usage===

<pre>
ashwin@gpc-f101n084-ib0 $ ls
job1.sh job2.sh job3.sh

ashwin@gpc-f101n084-ib0 $ submit job*.sh
# submits all three job files using qsub
</pre>

<pre>
ashwin@gpc-f101n084-ib0 $ ls
job1.ll job2.ll job3.ll

ashwin@ashwin@p7n01 $ submit job*.ll
# submits all three job files using qsub
</pre>

==Canceling jobs==

The GPC and P7 job submission commands (<tt>canceljob</tt> and <tt>llcancel</tt>, respectively) do not allow for the submission of multiple job files, leaving the user to have to for-loop through multiple files when batch submission is required. The below bash function automates such looping and can be added to the shell environment

<pre>
function cancel() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then # Login node
echo "Cannot cancel from Login node"
return
fi

if [ $host -eq 1 ]; then # GPC
canceler=canceljob
elif [ $host -eq 2 ]; then # P7
canceler=llcancel
fi

for jid in "$@"; do
$canceler "$jid"
done

}

</pre>

==Remote/Batch query running jobs==
The GPC and P7 queues may be queried for job status (respectively, with <tt>showq</tt> and <tt>llq</tt>). However, this shows only the job ID and not much else. The following bash functions list the running and queued jobs in much more detail

===Querying multiple queues===
<pre>
function que() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then
p7 que
echo "========================================"
gpc que
fi

if [ $host -eq 1 ]; then #GPC
showq -u "$USER"
elif [ $host -eq 2 ]; then # P7
llq -u "$USER"
fi
}
</pre>

===Getting detailed job information from queues===
<pre>
function columnize() {
array=$1
(for lineno in `seq 0 ${#lines[@]}`; do
line=${lines[lineno]}
echo "$line"
done) | column -t
}

function clearLines() {
for _ in `seq 1 $1`; do
echo -ne "\e[1A"
done
}

function whatare() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`
if [ $host -eq 0 ]; then
echo "============ P7 ============"
p7 whatare
echo ''
echo ''
echo "============GPC ============"
gpc whatare
fi

lines=()
if [ $host -eq 1 ]; then #GPC
echo "-----------RUNNING-----------"
for jobid in `showq -r -u $USER | grep $USER | cut -d' ' -f1 | sort -n`; do
name=`whatis "$jobid" | grep AName | cut -d":" -f2 | tr -d '\n'`
wtime=`checkjob "$jobid" | head | grep "WallTime" | tr -d '\n'`

len=${#lines[@]}
clearLines $len

appendlen=$((len + 1))
line="$jobid $name $wtime"
lines[$appendlen]="$line"
columnize $lines
done

echo "-----------WAITING-----------"
len=${#lines[@]}
appendlen=$((len + 1))
lines[$appendlen]="-----------WAITING-----------"

for jobid in `showq -i -u $USER | grep $USER | cut -d' ' -f1 | sort -n`; do
name=`whatis "$jobid" | grep AName | cut -d":" -f2`
wtime=`checkjob "$jobid" | head | grep "WallTime"`

len=${#lines[@]}
clearLines $len

appendlen=$((len + 1))
line="$jobid $name $wtime"
lines[$appendlen]="$line"
columnize $lines
done

echo "-----------BLOCKED-----------"
len=${#lines[@]}
appendlen=$((len + 1))
lines[$appendlen]="-----------BLOCKED-----------"
for jobid in `showq -b -u $USER | grep $USER | cut -d' ' -f1 | sort -n`; do
name=`whatis "$jobid" | grep AName | cut -d":" -f2`
wtime=`checkjob "$jobid" | head | grep "WallTime"`

len=${#lines[@]}
clearLines $len

appendlen=$((len + 1))
line="$jobid $name $wtime"
lines[$appendlen]="$line"
columnize $lines
done

echo "============================="
return
fi

if [ $host -eq 2 ]; then # P7
joblines=`que | tail -n +3 | head -n -2 | sort -t'.' -k2 -n`

echo "---------- RUNNING ----------"
echo "$joblines" | while read jobline; do
status=`echo "$jobline" | awk '$1=$1' | cut -d' ' -f5`

if [[ $status != R ]] ; then
continue
fi

job=`echo $jobline | cut -d' ' -f1 | cut -d'.' -f2`
echo -n `whatis "$job" | grep "Job Name"` && echo
done

echo "---------- WAITING ----------"

echo "$joblines" | while read jobline; do
status=`echo "$jobline" | awk '$1=$1' | cut -d' ' -f5`

if [[ $status != I ]] ; then
continue
fi

job=`echo $jobline | cut -d' ' -f1 | cut -d'.' -f2`
echo -n `whatis "$job" | grep "Job Name"` && echo
done
echo "============================="
return
fi
}

function whatis() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`
if [ $host -eq 0 ]; then
echo "Cannot check from a login node"
#return
fi

if [ $host -eq 1 ]; then #GPC
checker=checkjob
label=AName

elif [ $host -eq 2 ]; then # P7
checker="llq -l"
label="Job Name"
fi

for j in "$@"; do
echo -n "$j " && $checker "$j" | grep "$label"
done
}

</pre>

===Usage===
<pre>
ashwin@gpc-f101n084-ib0 $ whatare
============ P7 ============
---------- RUNNING ----------
# job information about running jobs
---------- WAITING ----------
# job information about waiting jobs
=============================

-----------RUNNING-----------
# job information about running jobs
-----------WAITING-----------
# job information about waiting jobs
-----------BLOCKED-----------
# job information about blocked jobs
=============================
</pre>

<pre>
ashwin@gpc-f101n084-ib0 $ whatare
-----------RUNNING-----------
# job information about running jobs
-----------WAITING-----------
# job information about waiting jobs
-----------BLOCKED-----------
# job information about blocked jobs
=============================
</pre>

User Remote

2018-02-09T15:34:00Z

Ashwin: /* Usage */

__FORCETOC__

==Step 0: Some SSH Aliases to Make Life Easier==

<pre>
function p7() {
ssh p7n01-ib0 "$@"
}

function gpc() {
ssh gpc01 "$@"
}
</pre>

==Submitting jobs==
The GPC and P7 job submission commands (<tt>qsub</tt> and <tt>llsubmit</tt>, respectively) do not allow for the submission of multiple job files, leaving the user to have to for-loop through multiple files when batch submission is required. The below bash function automates such looping and can be added to the shell environment

<pre>
function submit() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then # Login node
echo "Can't submit from a login node"
return
fi

if [ $host -eq 1 ]; then # GPC
submitter=qsub
elif [ $host -eq 2 ]; then # P7
submitter=llsubmit
fi

for fpath in "$@"; do
$submitter "$fpath"
done
}

</pre>

===Usage===

<pre>
ashwin@gpc-f101n084-ib0 $ ls
job1.sh job2.sh job3.sh

ashwin@gpc-f101n084-ib0 $ submit job*.sh
# submits all three job files using qsub
</pre>

<pre>
ashwin@gpc-f101n084-ib0 $ ls
job1.ll job2.ll job3.ll

ashwin@ashwin@p7n01 $ submit job*.ll
# submits all three job files using qsub
</pre>

==Canceling jobs==

The GPC and P7 job submission commands (<tt>canceljob</tt> and <tt>llcancel</tt>, respectively) do not allow for the submission of multiple job files, leaving the user to have to for-loop through multiple files when batch submission is required. The below bash function automates such looping and can be added to the shell environment

<pre>
function cancel() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then # Login node
echo "Cannot cancel from Login node"
return
fi

if [ $host -eq 1 ]; then # GPC
canceler=canceljob
elif [ $host -eq 2 ]; then # P7
canceler=llcancel
fi

for jid in "$@"; do
$canceler "$jid"
done

}

</pre>

==Remote/Batch query running jobs==
The GPC and P7 queues may be queried for job status (respectively, with <tt>showq</tt> and <tt>llq</tt>). However, this shows only the job ID and not much else. The following bash functions list the running and queued jobs in much more detail

===Querying multiple queues===
<pre>
function que() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then
p7 que
echo "========================================"
gpc que
fi

if [ $host -eq 1 ]; then #GPC
showq -u "$USER"
elif [ $host -eq 2 ]; then # P7
llq -u "$USER"
fi
}
</pre>

===Getting detailed job information from queues===
<pre>
function columnize() {
array=$1
(for lineno in `seq 0 ${#lines[@]}`; do
line=${lines[lineno]}
echo "$line"
done) | column -t
}

function clearLines() {
for _ in `seq 1 $1`; do
echo -ne "\e[1A"
done
}

function whatare() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`
if [ $host -eq 0 ]; then
echo "============ P7 ============"
p7 whatare
echo ''
echo ''
echo "============GPC ============"
gpc whatare
fi

lines=()
if [ $host -eq 1 ]; then #GPC
echo "-----------RUNNING-----------"
for jobid in `showq -r -u $USER | grep $USER | cut -d' ' -f1 | sort -n`; do
name=`whatis "$jobid" | grep AName | cut -d":" -f2 | tr -d '\n'`
wtime=`checkjob "$jobid" | head | grep "WallTime" | tr -d '\n'`

len=${#lines[@]}
clearLines $len

appendlen=$((len + 1))
line="$jobid $name $wtime"
lines[$appendlen]="$line"
columnize $lines
done

echo "-----------WAITING-----------"
len=${#lines[@]}
appendlen=$((len + 1))
lines[$appendlen]="-----------WAITING-----------"

for jobid in `showq -i -u $USER | grep $USER | cut -d' ' -f1 | sort -n`; do
name=`whatis "$jobid" | grep AName | cut -d":" -f2`
wtime=`checkjob "$jobid" | head | grep "WallTime"`

len=${#lines[@]}
clearLines $len

appendlen=$((len + 1))
line="$jobid $name $wtime"
lines[$appendlen]="$line"
columnize $lines
done

echo "-----------BLOCKED-----------"
len=${#lines[@]}
appendlen=$((len + 1))
lines[$appendlen]="-----------BLOCKED-----------"
for jobid in `showq -b -u $USER | grep $USER | cut -d' ' -f1 | sort -n`; do
name=`whatis "$jobid" | grep AName | cut -d":" -f2`
wtime=`checkjob "$jobid" | head | grep "WallTime"`

len=${#lines[@]}
clearLines $len

appendlen=$((len + 1))
line="$jobid $name $wtime"
lines[$appendlen]="$line"
columnize $lines
done

echo "============================="
return
fi

if [ $host -eq 2 ]; then # P7
joblines=`que | tail -n +3 | head -n -2 | sort -t'.' -k2 -n`

echo "---------- RUNNING ----------"
echo "$joblines" | while read jobline; do
status=`echo "$jobline" | awk '$1=$1' | cut -d' ' -f5`

if [[ $status != R ]] ; then
continue
fi

job=`echo $jobline | cut -d' ' -f1 | cut -d'.' -f2`
echo -n `whatis "$job" | grep "Job Name"` && echo
done

echo "---------- WAITING ----------"

echo "$joblines" | while read jobline; do
status=`echo "$jobline" | awk '$1=$1' | cut -d' ' -f5`

if [[ $status != I ]] ; then
continue
fi

job=`echo $jobline | cut -d' ' -f1 | cut -d'.' -f2`
echo -n `whatis "$job" | grep "Job Name"` && echo
done
echo "============================="
return
fi
}

function whatis() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`
if [ $host -eq 0 ]; then
echo "Cannot check from a login node"
#return
fi

if [ $host -eq 1 ]; then #GPC
checker=checkjob
label=AName

elif [ $host -eq 2 ]; then # P7
checker="llq -l"
label="Job Name"
fi

for j in "$@"; do
echo -n "$j " && $checker "$j" | grep "$label"
done
}

</pre>

===Usage===
<pre>
ashwin@gpc-f101n084-ib0 $ whatare
-----------RUNNING-----------
# job information about running jobs
-----------WAITING-----------
# job information about waiting jobs
-----------BLOCKED-----------
# job information about blocked jobs
=============================
</pre>

User Remote

2018-02-09T15:33:42Z

Ashwin: /* Getting detailed job information from queues */

__FORCETOC__

==Step 0: Some SSH Aliases to Make Life Easier==

<pre>
function p7() {
ssh p7n01-ib0 "$@"
}

function gpc() {
ssh gpc01 "$@"
}
</pre>

==Submitting jobs==
The GPC and P7 job submission commands (<tt>qsub</tt> and <tt>llsubmit</tt>, respectively) do not allow for the submission of multiple job files, leaving the user to have to for-loop through multiple files when batch submission is required. The below bash function automates such looping and can be added to the shell environment

<pre>
function submit() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then # Login node
echo "Can't submit from a login node"
return
fi

if [ $host -eq 1 ]; then # GPC
submitter=qsub
elif [ $host -eq 2 ]; then # P7
submitter=llsubmit
fi

for fpath in "$@"; do
$submitter "$fpath"
done
}

</pre>

===Usage===

<pre>
ashwin@gpc-f101n084-ib0 $ ls
job1.sh job2.sh job3.sh

ashwin@gpc-f101n084-ib0 $ submit job*.sh
# submits all three job files using qsub
</pre>

<pre>
ashwin@gpc-f101n084-ib0 $ ls
job1.ll job2.ll job3.ll

ashwin@ashwin@p7n01 $ submit job*.ll
# submits all three job files using qsub
</pre>

==Canceling jobs==

The GPC and P7 job submission commands (<tt>canceljob</tt> and <tt>llcancel</tt>, respectively) do not allow for the submission of multiple job files, leaving the user to have to for-loop through multiple files when batch submission is required. The below bash function automates such looping and can be added to the shell environment

<pre>
function cancel() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then # Login node
echo "Cannot cancel from Login node"
return
fi

if [ $host -eq 1 ]; then # GPC
canceler=canceljob
elif [ $host -eq 2 ]; then # P7
canceler=llcancel
fi

for jid in "$@"; do
$canceler "$jid"
done

}

</pre>

==Remote/Batch query running jobs==
The GPC and P7 queues may be queried for job status (respectively, with <tt>showq</tt> and <tt>llq</tt>). However, this shows only the job ID and not much else. The following bash functions list the running and queued jobs in much more detail

===Querying multiple queues===
<pre>
function que() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then
p7 que
echo "========================================"
gpc que
fi

if [ $host -eq 1 ]; then #GPC
showq -u "$USER"
elif [ $host -eq 2 ]; then # P7
llq -u "$USER"
fi
}
</pre>

===Getting detailed job information from queues===
<pre>
function columnize() {
array=$1
(for lineno in `seq 0 ${#lines[@]}`; do
line=${lines[lineno]}
echo "$line"
done) | column -t
}

function clearLines() {
for _ in `seq 1 $1`; do
echo -ne "\e[1A"
done
}

function whatare() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`
if [ $host -eq 0 ]; then
echo "============ P7 ============"
p7 whatare
echo ''
echo ''
echo "============GPC ============"
gpc whatare
fi

lines=()
if [ $host -eq 1 ]; then #GPC
echo "-----------RUNNING-----------"
for jobid in `showq -r -u $USER | grep $USER | cut -d' ' -f1 | sort -n`; do
name=`whatis "$jobid" | grep AName | cut -d":" -f2 | tr -d '\n'`
wtime=`checkjob "$jobid" | head | grep "WallTime" | tr -d '\n'`

len=${#lines[@]}
clearLines $len

appendlen=$((len + 1))
line="$jobid $name $wtime"
lines[$appendlen]="$line"
columnize $lines
done

echo "-----------WAITING-----------"
len=${#lines[@]}
appendlen=$((len + 1))
lines[$appendlen]="-----------WAITING-----------"

for jobid in `showq -i -u $USER | grep $USER | cut -d' ' -f1 | sort -n`; do
name=`whatis "$jobid" | grep AName | cut -d":" -f2`
wtime=`checkjob "$jobid" | head | grep "WallTime"`

len=${#lines[@]}
clearLines $len

appendlen=$((len + 1))
line="$jobid $name $wtime"
lines[$appendlen]="$line"
columnize $lines
done

echo "-----------BLOCKED-----------"
len=${#lines[@]}
appendlen=$((len + 1))
lines[$appendlen]="-----------BLOCKED-----------"
for jobid in `showq -b -u $USER | grep $USER | cut -d' ' -f1 | sort -n`; do
name=`whatis "$jobid" | grep AName | cut -d":" -f2`
wtime=`checkjob "$jobid" | head | grep "WallTime"`

len=${#lines[@]}
clearLines $len

appendlen=$((len + 1))
line="$jobid $name $wtime"
lines[$appendlen]="$line"
columnize $lines
done

echo "============================="
return
fi

if [ $host -eq 2 ]; then # P7
joblines=`que | tail -n +3 | head -n -2 | sort -t'.' -k2 -n`

echo "---------- RUNNING ----------"
echo "$joblines" | while read jobline; do
status=`echo "$jobline" | awk '$1=$1' | cut -d' ' -f5`

if [[ $status != R ]] ; then
continue
fi

job=`echo $jobline | cut -d' ' -f1 | cut -d'.' -f2`
echo -n `whatis "$job" | grep "Job Name"` && echo
done

echo "---------- WAITING ----------"

echo "$joblines" | while read jobline; do
status=`echo "$jobline" | awk '$1=$1' | cut -d' ' -f5`

if [[ $status != I ]] ; then
continue
fi

job=`echo $jobline | cut -d' ' -f1 | cut -d'.' -f2`
echo -n `whatis "$job" | grep "Job Name"` && echo
done
echo "============================="
return
fi
}

function whatis() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`
if [ $host -eq 0 ]; then
echo "Cannot check from a login node"
#return
fi

if [ $host -eq 1 ]; then #GPC
checker=checkjob
label=AName

elif [ $host -eq 2 ]; then # P7
checker="llq -l"
label="Job Name"
fi

for j in "$@"; do
echo -n "$j " && $checker "$j" | grep "$label"
done
}

</pre>

===Usage===

ashwin@gpc-f101n084-ib0 $ whatare
-----------RUNNING-----------
# job information about running jobs
-----------WAITING-----------
# job information about waiting jobs
-----------BLOCKED-----------
# job information about blocked jobs
=============================

User Remote

2018-02-09T15:32:07Z

Ashwin:

User Remote

2018-02-09T15:25:16Z

Ashwin:

__FORCETOC__

==Submitting jobs==
The GPC and P7 job submission commands (<tt>qsub</tt> and <tt>llsubmit</tt>, respectively) do not allow for the submission of multiple job files, leaving the user to have to for-loop through multiple files when batch submission is required. The below bash function automates such looping and can be added to the shell environment

<pre>
function submit() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then # Login node
echo "Can't submit from a login node"
return
fi

if [ $host -eq 1 ]; then # GPC
submitter=qsub
elif [ $host -eq 2 ]; then # P7
submitter=llsubmit
fi

for fpath in "$@"; do
$submitter "$fpath"
done
}

</pre>

===Usage===

<pre>
ashwin@gpc-f101n084-ib0 $ ls
job1.sh job2.sh job3.sh

ashwin@gpc-f101n084-ib0 $ submit job*.sh
# submits all three job files using qsub
</pre>

<pre>
ashwin@gpc-f101n084-ib0 $ ls
job1.ll job2.ll job3.ll

ashwin@ashwin@p7n01 $ submit job*.ll
# submits all three job files using qsub
</pre>

==Canceling jobs==

The GPC and P7 job submission commands (<tt>canceljob</tt> and <tt>llcancel</tt>, respectively) do not allow for the submission of multiple job files, leaving the user to have to for-loop through multiple files when batch submission is required. The below bash function automates such looping and can be added to the shell environment

<pre>
function cancel() {
host=`hostname | awk '/^scinet/ {print 0} /^gpc/ {print 1} /^p7/ {print 2}'`

if [ $host -eq 0 ]; then # Login node
echo "Cannot cancel from Login node"
return
fi

if [ $host -eq 1 ]; then # GPC
canceler=canceljob
elif [ $host -eq 2 ]; then # P7
canceler=llcancel
fi

for jid in "$@"; do
$canceler "$jid"
done

}

</pre>

==Remote/Batch query running jobs==

User Remote

2018-02-09T14:43:38Z

Ashwin:

__FORCETOC__

==Remote submitting jobs==

==Remote cancel jobs==

==Remote query running jobs==

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