Monitoring your jobs
There are various ways for you to monitor and check up on your running and completed jobs.
See the status of the nodes
The easiest way to see what is happening on the cluster is to firstly check ganglia. This is a web based monitoring application that displays statistics about the cluster and its nodes. To view this, simply visit;
http://bert.ibers.aber.ac.uk/ganglia
There are a variety of statistics to view. Most useful is probably load_one which shows you the cpu load average on each node. You can also monitor the overall averages along with memory and network usage.
Check on what is running
Once you have submitted your job scripts, you may want to check on the progress of what is running. This is achieved using the qstat command. This will show you your jobs. It might look something like;
[user@bert ~]$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 758061 0.50042 k2bRC-a1.i user r 07/20/2014 14:13:33 amd.q@node010.cm.cluster 1 758062 0.50042 k2bRC-a2.i user r 07/20/2014 14:13:33 amd.q@node009.cm.cluster 1 758063 0.50042 k2bRC-a3.i user r 07/20/2014 14:13:48 amd.q@node009.cm.cluster 1 758064 0.50042 k2bRC-a4.i user r 07/20/2014 14:13:48 amd.q@node008.cm.cluster 1 758065 0.50042 k2bRC-a5.i user qw 07/20/2014 14:14:03 1 758066 0.60208 k2bRC-a6.i user qw 07/20/2014 14:14:18 1
Check a the status of a job
You can use the qstat -j JOB_ID command to get information about a running or queued job. Below is what you might find on a running job.
[user@bert ~]$ qstat -j 758061 ============================================================== job_number: 758061 exec_file: job_scripts/758061 submission_time: Sun Jul 20 14:13:32 2014 owner: user uid: 100000 group: users gid: 100000 sge_o_home: /ibers/ernie/home/user/ sge_o_log_name: user sge_o_path: /ibers/ernie/home/user/perl5/bin:/ibers/ernie/home/user//software/Python/bin:/cm/shared/apps/BLAST/blast-2.2.26/bin:/cm/shared/apps/BLAST/ncbi-blast-2.2.28+/bin sge_o_shell: /bin/bash sge_o_workdir: /ibers/ernie/scratch/user/CGR/dots sge_o_host: bert account: sge cwd: /ibers/ernie/scratch/user/CGR/dots stderr_path_list: NONE:NONE:k2bRC-a1.e hard resource_list: h_stack=512m,h_vmem=20.0G mail_list: user@bert.cm.cluster notify: FALSE job_name: k2bRC-a1.i stdout_path_list: NONE:NONE:k2bRC-a1.o jobshare: 0 hard_queue_list: amd.q env_list: MODULE_VERSION_STACK=3.2.6,MANPATH=:ignore:/cm/local/apps/environment-modules/3.2.6/man:/cm/shared/apps/sge/6.2u5p2/man:/cm/shared/apps/openmpi/open64/64/1.4.4/share/man/,BEDTOOLS=/ibers/ernie/home/user//software/bedtools-2.17.0/bin { eval `/cm/local/apps/environment-modules/3.2.6//Modules/$MODULE_VERSION/bin/modulecmd bash $*` script_file: k2bRC-a1.i usage 1: cpu=22:21:14, mem=967478.88534 GBs, io=4.91085, vmem=13.401G, maxvmem=13.401G scheduling info: queue instance "intel.q@node003.cm.cluster" dropped because it is full queue instance "amd.q@node008.cm.cluster" dropped because it is full queue instance "intel.q@node004.cm.cluster" dropped because it is full queue instance "amd.q@node009.cm.cluster" dropped because it is full queue instance "amd.q@node007.cm.cluster" dropped because it is full queue instance "amd.q@node010.cm.cluster" dropped because it is full