[GE users] Solution to qdel not killing processes

mad margaret_Doll at brown.edu
Fri Mar 13 13:35:07 GMT 2009


I have a Rock 5.3 and RedHat 2.6.18-53.1.14.el.  "qdel" was deleting jobs from the queue manager; the jobs were not showing up in any of the qstat commands or in qmon, but the processes were still running on the compute nodes.

A friend of mine gave me a solution:



libdshconfig-0.20.13 was installed in /usr/local using

configure; make
make install

Then dsh-0.25.9 was installed in /usr/local using

LDFLAGS=-"/usr/local/lib" .configure
make
make check
make install

A list of machines had to be installed in /usr/local/etc/machines.list. The compute nodes which allow queued jobs were included in the file.

/usr/local/etc/dsh.conf was edited to change "remoteshell=rsh" to "remoteshell=ssh". rsh is not a secure process.

qdel-all was installed /opt/gridengine/bin/lx26-amd64 where the other q commands are located. It contains

#!/bin/tcsh
if($#argv != 2) then
echo 2 arguments are required, first the process number followed by the executable
name
exit
endif
qdel $1
/usr/local/dsh-0.25.9/dsh -a "killall -9 $2"


The user runs  "qdel-all queueProcess# jobName"  An example

qdel-all 20492 qserch-1





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