Submitting your first job
To submit a job to run under SGE, we use the qsub command. qsub (queue submit) takes the commands you give it, and runs it through the scheduler, which finds the optimum place for your job to run. With over 150 nodes and 2500 cores to schedule, as well as differing priorities, hardware, and individual resources, the scheduler's job is not trivial.
There are a few things you'll need to know before running qsub.
- How many cores you need. Note that unless your program is created to use multiple cores (called "threading"), asking for more cores will not speed up your job. This is a common misperception. Beocat will not magically make your program use multiple cores! For this reason the default is 1 core.
- How much time you need. Many users when beginning to use Beocat neglect to specify a time requirement. The default is one hour, and we get asked why their job died after one hour. We usually point them to the FAQ.
- How much memory you need. The default is 1GB. If your job uses significantly more than you ask, your job will be placed on hold until you fix your request.
- Any advanced options. See the AdvancedSGE page for these requests. For our basic examples here, we will ignore these.
So let's now create a small script to test our ability to submit jobs. Create the following file (either by copying it to Beocat or by editing a text file and we'll name it myhost.sh. Both of these methods are documented on our LinuxBasics page.
#!/bin/sh
hostname
Be sure to make it executable
chmod u+x myhost.sh
Now, let's first run it on the headnode. As I write this, I'm logged into the headnode named 'minerva'. When I run it, it looks like this:
% ./myhost.sh minerva
So, now lets submit it as a job and see what happens. Here I'm going to use three options
-l mem=tells how much memory I need. In my example, I'm using our system minimum of 512 MB, which is more than enough. Note that your memory request is per core, which doesn't make much difference for this example, but will as you submit more complex jobs.-l h_rt=tells how much runtime I need. This can be in the form of seconds, or hours:minutes:seconds. This is a very short job, so 60 seconds should be plenty. Note that if you submit a job that needs to run for days or weeks, you'll need to translate that into hours. This can't be changed after the job is started please make sure you have requested a sufficient amount of time.-pe single 1tells SGE that I need only a single core on one machine. The AdvancedSGE page has much more on the "Parallel Environment" switch.
% ls
myhost.sh
% qsub -l h_rt=60 -l mem=512M -pe single 1 ./myhost.sh
INFO: Requested resources for this job: pe=single cores=1 time(HH:MM:SS or SS)=60 mem(per-core)=512M
Your job 1483446 ("myhost.sh") has been submitted
Since this is such a small job, it is likely to be scheduled almost immediately, so a minute or so later, I now see
% ls myhost.sh myhost.sh.po1483446 myhost.sh.pe1483446 myhost.sh.e1483446 myhost.sh.o1483446
The four additional files that were created are in the form scriptname.XX.jjjjjjj - where scriptname is the script you submitted, XX is 'po' (parallel output), 'pe' (parallel error), 'e' (error), or 'o' (output), and jjjjjjj is the job number (which is given when you submitted your job, in this case 1483446).
If everything goes as planned, the po, pe, and e jobs will be blank...
% cat myhost.sh.po1483446 % cat myhost.sh.pe1483446 % cat myhost.sh.e1483446
...and the .o file will show the hostname of the node that ran the job...
% cat myhost.sh.o1483446 mage03
Monitoring Your Job
The kstat perl script has been developed at K-State to provide you with all the available information about your jobs on Beocat. kstat --help will give you a full description of how to use it.
kstat -z This will give you a good summary of your jobs that are running and in the queue.
Hero43
24 of 24 cores
Load 23.4 / 24
495.3 / 512 GB used
daveturner
unafold 1234567
1 core run
127 MB
0 d 5 h 35 m
daveturner
octopus 1234568
16 core run
125 GB
8 d 15 h 42 m
################################## BeoCat Queue ###################################
daveturner
NetPIPE 1234569
2 core
qw
2h
4 GB
killable
0 d 1 h 2 m
kstat produces a separate line for each host. Use kstat -h to see information on all hosts without the jobs. For the example above we are listing our jobs and the hosts they are on.
Host names -
yellow background means reserved,
red background means down,
red means owned by the
group in orange on the right.
Core usage - yellow for empty, cyan for partially used, blue for all cores used.
Load level - yellow or yellow background indicates the node is being inefficiently used. Red just means more threads than cores.
Memory usage - yellow or red means most memory is used. Exceeding memory will show disk swap in background red.
Each job line will contain the username, program name, job ID number, number of cores, maximum memory used, whether the job is killable, and the amount of time the job has run. If the job is still in the queue, it may contain information on the requested run time and memory per core and the time shown is how long the job has been in the queue.
In this case, I have 2 jobs running on Hero43. unafold is using 1 core while octopus is using 16 cores. The most useful information here is the memory being used in each case. While unafold is taking very little memory, octopus is using 125 GB and the red font indicates that it is close to the amount requested. If the memory on a job is over the requested amount it will have a red background and you should request more memory in future runs. If the memory is flashing with a red background, you are more than 50% over your requested amount and your code will be forced to use disk swap which can slow it down enormously. You're usually better off killing the job and restarting with an appropriate memory request. If the code accesses large files, there may be an IO value reported. This number is not very accurate.
kstat -d 7 This will show you information about the jobs that have completed in the last 7 days.
kstat -c This provides a global view of Beocat showing how many cores each person is using.
You can also use the 'status' command. By default this command will give you all of your queued and running jobs. If you have no jobs in the queue or running, it will simply quit with no output.
% status Running jobs for user: kylehutson job-ID # name start time running in ------------------------------------------------------------------- 1550047 1 test1.sh 05/22/2014 16:09:34 batch.q Waiting jobs for user: kylehutson job-ID # name submit time -------------------------------------------------------- 1550048 80 test2.sh 05/22/2014 16:09:33
As you can see, this gives the start time for running jobs and submit time for jobs that have not yet started. You can use the '-r' switch to view a relative time.
% status -r Running jobs for user: kylehutson job-ID # name start time running in ------------------------------------------------------------------- 1550047 1 test1.sh -0d 00:00:27 batch.q Waiting jobs for user: kylehutson job-ID # name submit time -------------------------------------------------------- 1550049 80 test2.sh -0d 00:00:03
That leaves you with the question, though - when will my waiting job start? We can't really give an absolute answer to that question, but we can show you where you stand relative to others. The tool for this is 'qstat'.
Here is an edited version (just for space sake) of the jobs on Beocat at the time I'm writing this.
% qstat 0 4:10PM job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 1437729 0.25310 couplings emilieg Rr 04/22/2014 17:22:15 highmem.q@mage11.beocat 60 1457075 0.20816 au9_D2H_MC nvkarimova r 04/30/2014 11:29:03 highmem.q@mage07.beocat 40 1457078 0.20815 au8_C3V_MC nvkarimova r 05/03/2014 04:25:42 highmem.q@mage09.beocat 40 1460509 0.17885 MF_ncbd1 khlee r 04/30/2014 11:13:22 long.q@scout64.beocat 16 1478510 0.13297 TDSE4.scri huiwei r 05/05/2014 19:01:53 highmem.q@mage09.beocat 1 1478511 0.13297 TDSE5.scri huiwei r 05/05/2014 19:01:53 highmem.q@mage09.beocat 1 1488568 0.08904 F_ncbd_270 khlee r 05/15/2014 16:55:20 batch.q@elf61.beocat 24 1488553 0.83423 p.1bxl.10 beugels2 r 05/12/2014 16:08:16 batch.q@elf29.beocat 8 [...] 1550045 0.00093 cufflinks_ wrutter r 05/22/2014 15:33:56 long.q@paladin12.beocat 4 1541856 0.35737 l149h mmohan qw 05/20/2014 11:53:32 8 1 1541857 0.35466 l149h mmohan qw 05/20/2014 11:53:34 8 1 1541858 0.35199 l149h mmohan qw 05/20/2014 11:53:36 8 1 [...] 1541888 0.31023 p.1zy3.43 beugels2 qw 05/20/2014 12:13:38 8 1549982 0.29499 p.1g5j.30 beugels2 qw 05/22/2014 05:25:02 8 1532569 0.04061 H9_310_Bil zhiguang qw 05/18/2014 16:50:14 32 1549979 0.03024 zzz_bwrang blkpawn qw 05/21/2014 23:58:40 80 8-36:1 1549937 0.02694 Mira_denov wrutter qw 05/21/2014 14:15:14 60 1549989 0.02647 zzz_bwrcor blkpawn qw 05/22/2014 11:43:19 80 1-3:1 1451971 0.02127 run.sh zhangs84 hRq 04/25/2014 18:54:21 1 1549913 0.01965 H9_298_Mle zhiguang qw 05/21/2014 10:03:42 32 1549914 0.01965 H9_310_Ml2 zhiguang qw 05/21/2014 10:04:29 32 1549957 0.01741 H_5310BN zhiguang qw 05/21/2014 17:01:46 32 1549915 0.01412 pbwa.sh jpoland qw 05/21/2014 10:11:18 16 1549985 0.01211 H5_298_Bil zhiguang qw 05/22/2014 09:32:34 32 1549987 0.00917 F_1VII khlee qw 05/22/2014 10:40:49 24 1549988 0.00917 C_1VII khlee qw 05/22/2014 10:40:59 24 1550046 0.00239 ni_bulk songliu qw 05/22/2014 15:47:57 8 1489958 0.00000 align liu3zhen hqw 05/12/2014 17:55:43 128
The column I want you to pay attention to first is the 'state'. The two most common statuses you'll see are 'r' ('Running') and 'qw' ('Queued and Waiting'). Generally speaking, those jobs that are higher on the list will start running before the ones lower on the list. This way you can see your relative position. Another useful tool is to see how busy Beocat is. http://gangia.beocat.cis.ksu.edu/ will give you those statistics. Depending on the resources you ask for, a job you submit may start immediately or may take up to several weeks, depending on the priority of your job, the resources available, and the requested resources of the jobs ahead of you in the queue.
If you want to read more, continue on to our AdvancedSGE page.
