How to administer sun grid engine – biowiki

himem_nodes.q – hi-mem nodes/hosts (currently just one node/host, which has 32GB RAM shared by four 2.2GHz Opteron CPUs) – 4 CPUs total Current exec node configuration then you should pipe that to something like tail -n because you only want the end of the massive log that it will spit out. This brings up a template queue configuration file for the new queue, probably using Vim. Data recovery expert Edit it to your liking and save it, then exit. Data recovery jobs Usually, you will just leave everything as the template gave it to you, except: indicating the maximum number of jobs allowed to execute simultaneously on each host (usually that’s just the number of CPUs on that host), plus a leading “1” for no reason that I can readily identify (for all I know, it’s not necessary), e.g.: Disclaimer: the following step is only useful if you have more than one host group… Database concepts 6th edition which we don’t, nor do we explicitly use host groups (as far as I know) for anything. Database kernel So you can probably omit this… Raid 5 data recovery software I followed it just in case. Now, configure the exec host ON THE ACTUAL EXEC HOST/NODE. Data recovery pro Note that if you are installing more than a couple of exec hosts, it might make sense to use a configuration file and do it as described in Step 3 of Sun Grid Engine. Data recovery tools mac The procedure described here is the manual, interactive one, suitable for adding a small number of hosts. Unzip and untar the installation files into your directory of choice (for us, it is /opt/sge/). Z wave database Add the port numbers for SGE to /etc/services, e.g.: Now perform the most idiotic step of the entire installation, and the step which the SGE documentation seems to make no mention of: we must copy your cell directory (for us, it is /opt/sge/default/, because our cell name is “default) from the master host to your exec host (i.e. Database orm you must copy the contents of /opt/sge/default/ from the master to /opt/sge/default/ on the exec host). Database workbench If you don’t, you will get an error during the interactive install telling you that the master node has not been installed. Database best practices If there is a proper way to do this that someone knows, please enlighten me. Accept all defaults, except specify the local spool directory (for us, it is /opt/sge/default/spool/, but can really be anything that sgeadmin is allowed to write to… Database schema I think…). Data recovery external hard drive Another non-default is if you added this host to the appropriate queues on the master already, as described above, you should say no to adding a “default queue instance for this host.” At the end of the interactive installation, SGE will ask you to run the settings script. Database 1 to many For our purposes, ignore the syntax it gives you, and run this instead: Does your job actually get dispatched and run (that is, qstat no longer shows it – because it was sent to an exec host, ran, and exited), but something else isn’t working right? Get more info on what’s wrong with it using: If any of the above have an “access denied” message in them, it’s probably a permissions problem. Data recovery galaxy s6 Your user account does not have the privileges to read from/write to where you told it (this happens with the -e and -o options to qsub often). Os x data recovery software So, check to make sure you do. Database technology Try, for example, to SSH into the node on which the job is trying to run (or just any node) and make sure that you can actually read from/write to the desired directories from there. Database queries definition While you’re at it, just run the job manually from that node, see if it runs – maybe there’s some library it needs that the particular node is missing. To avoid permissions problems, cd into the directory on the NFS where you want your job to run, and submit from there using qsub -cwd to make sure it runs in that same directory on all the nodes. If the “state” column in qstat -f has a big E, that host or queue is in an error state due to… Data recovery mac free well, something. Data recovery phone Sometimes an error just occurs and marks the whole queue as “bad”, which blocks all jobs from running in that queue, even though there is nothing otherwise wrong with it. Database normalization Use qmod -c to clear the error state for a queue. Maybe that’s not the problem, though. Data recovery quote Maybe there is some network problem preventing the SGE master from communicating with the exec hosts, such as routing problems or a firewall misconfiguration.


Database key types You can troubleshoot these things with qping, which will test whether the SGE processes on the master node and the exec nodes can communicate. N.B.: remember, the execd process on the exec node is responsible for establishing a TCP/IP connection to the qmaster process on the master node, not the other way around. Database instance The execd processes basically “phone home”. Data recovery raid 0 So you have to run qping from the exec nodes, not the master node! where 536 is the port that qmaster is listening on, and 1 simply means that I am trying to reach a daemon. Data recovery tools Can’t reach it? Make sure your firewall has a hole on that port, that the routing is correct, that you can ping using the good old ping command, that the qmaster process is actually up, and so on. If the above checks out, check the messages log in /var/log/sge_messages on the submit and/or master node (on our Babylon Cluster, they’re both the node sheridan): before I submit the job, and then submit a job in a different window. Database programming languages The -f option will update the tail of the file as it grows, so you can see the message log change “live” as your job executes and see what’s happening as things take place. (Note that the above is actually a symbolic link I put in to the messages log in the qmaster spool directory, i.e. Super 8 database /opt/sge/default/spool/qmaster/messages.) One thing that commonly goes wrong is permissions. 5 databases Make sure that the user that submitted the job using qsub actually has the permissions to write error, output, and other files to the paths you specified. For even more precise troubleshooting… H data recovery registration code maybe the problem is unique only to some nodes(s) or some queue(s)? To pin it down, try to run the job only on some specific node or queue: Maybe you should also try to SSH into the problem nodes directly and run the job locally from there, as your own user, and see if you can get any more detail on why it fails. • You submit >10,000 jobs to SGE, which uses too much system resources resulting in their inability to get dispatched to exec hosts, and start getting the “failed receiving gdi request” error on something as simple as qstat. Database link You can’t use qdel to wipe the jobs due to the same error. • A job is stuck in the r state (and if you try to delete it, the dr state) despite the fact that the exec host is not running the job, not is even aware of it. Database google This can happen if you reboot a stuck/unresponsive exec host. We are tapping only a fraction of SGE’s features, but as I learn the system more, the pages ( Sun Grid Engine, How To Use Sun Grid Engine, and How To Administer Sun Grid Engine) will grow. Database update Some particular things to look at are: • making the Macs in the lab submit and administartive hosts (so people don’t have to log into sheridan all the time, they can just submit jobs from the Macs directly)

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