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==Job Submission: the bsub command==
+
== Job Submission ==
<pre>
+
Once you have your job file ready, it is time to submit your job. You can submit your job to LSF with the following command:
bsub < jobfile                  # Submits specified job for processing by LSF
+
[ NetID@ada ~]$ '''bsub < ''MyJob.LSF'''''
</pre>
+
Verifying job submission parameters...
 +
Verifying project account...
 +
      Account to charge:  123456789123
 +
          Balance (SUs):      5000.0000
 +
          SUs to charge:        5.0000
 +
Job <12345> is submitted to default queue <sn_regular>.
  
Here is an illustration,
+
== tamubatch ==
  
<pre>
+
'''tamubatch''' is an automatic batch job script that submits jobs for the user without the need of writing a batch script on the Ada and Terra clusters. The user just needs to provide the executable commands in a text file and tamubatch will automatically submit the job to the cluster. There are flags that the user may specify which allows control over the parameters for the job submitted.
$ bsub < sample1.job
 
Verifying job submission parameters...
 
Job <224139> is submitted to default queue <devel>.
 
</pre>
 
  
The first thing LSF does upon submission is to tag your job with a numeric identifier, a job id.
+
''tamubatch is still in beta and has not been fully developed. Although there are still bugs and testing issues that are currently being worked on, tamubatch can already submit jobs to both the Ada and Terra clusters if given a file of executable commands. ''
Above, that identifier is '''224139'''. You will need it in order to track or manage (kill or modify)
 
your jobs. Next, note that the default current working directory for the job is the directory
 
you submitted the job from. If that's not what you need, you must explicitly indicate that, as we
 
do above when we cd into a specific directory. On job completion, LSF will place in the submission
 
directory the file stdout1.224139. It contains a log of job events and other data directed to
 
standard out. Always inspect this file for useful information.<br>
 
  
By default, a job executes under the environment of the submitting process. This you can change
+
For more information, visit [https://hprc.tamu.edu/wiki/SW:tamubatch this page.]
by using the '''-L shell''' option (see below) and/or by specifying at the start of the job script
 
the shell that will execute it. For example, if you want the job to execute under the C-shell, the first
 
command above the #BSUB directives should be #!/bin/csh.
 
  
'''Five important job parameters:'''
+
== tamulauncher ==
<pre>
 
#BSUB -n NNN                    # NNN: total number of cores/jobslots to allocate for the job
 
#BSUB -R "span[ptile=XX]"      # XX:  number of cores/jobslots per node to use. Also, a node selection criterion
 
#BSUB -R "select[node-type]"    # node-type: nxt, mem256gb, gpu, phi, mem1t, mem2t ...
 
#BSUB -R "rusage[mem=nnn]"      # reserves nnn MBs per process/CPU for the job
 
#BSUB -M mmm                    # sets the per process enforceable memory limit to mmm MB
 
</pre>
 
  
We list these together because in many jobs they can be closely related and, therefore, must be
+
'''tamulauncher''' provides a convenient way to run a large number of serial or multithreaded commands without the need to submit individual jobs or a Job array. User provides a text file containing all commands that need to be executed and tamulauncher will execute the commands concurrently. The number of concurrently executed commands depends on the batch requirements. When tamulauncher is run interactively the number of concurrently executed commands is limited to at most 8. tamulauncher is available on terra, ada, and curie. There is no need to load any module before using tamulauncher. tamulauncher has been successfully tested to execute over 100K commands.
consistently set. We recommend their adoption in all jobs, serial, single-node and multi-node.
 
The '''rusage[mem=nnn]''' setting causes LSF to select nodes that can each allocate '''XX * nnn''' MBs for the execution of the job.
 
The '''-M mm''' sets and enforces the process memory size limit. When this limit is violated the job will abort. Omitting this specification, causes LSF to assume '''the'''
 
'''default memory limit, which by configuration is set to 2.5 giga-bytes (2500 MB) per process.''' The following examples, with some commentary,  illustrate the
 
use of these options.
 
  
'''Important:''' if the process memory limit, default (2500 MB)  or specified, is exceeded during execution the job will fail with a '''memory violation''' error.
+
''tamulauncher is preferred over Job Arrays to submit a large number of individual jobs, especially when the run times of the commands are relatively short. It allows for better utilization of the nodes, puts less burden on the batch scheduler, and lessens interference with jobs of other users on the same node.''
  
<pre>
+
For more information, visit [https://hprc.tamu.edu/wiki/SW:tamulauncher#tamulauncher this page.]
#BSUB -n 900                    # 900: number of cores/jobslots to allocate for the job
 
#BSUB -R "span[ptile=20]"      # 20: number of cores per node to use
 
#BSUB -R "select[nxt]"          # Allocates NeXtScale type nodes
 
</pre>
 
  
The above specifications will allocate 45 (=900/20) whole nodes. In many parallel jobs the selection
+
[[ Category:Ada ]]
of NeXtScale nodes at 20 cores per node is the best choice. Here, the maximum memory per process
 
is set to 2500 MB. Here, we're just illustrating what happens when you omit the memory-related options.
 
We definitely urge that you specify them. '''The memory enforceable limit per process here is 2.5 MB, the default setting.'''
 
 
 
<pre>
 
#BSUB -n 900                    # 900: total number of cores/jobslots to allocate for the job
 
#BSUB -R "span[ptile=16]"      # 16:  number of cores/jobslots per node to use
 
#BSUB -R "select[nxt]"          # allocates NeXtScale type nodes
 
#BSUB -R "rusage[mem=3600]"    # schedules on nodes that have at least 3600 MB per process/CPU avail
 
#BSUB -M 3600                  # enforces 3600 MB memory use per process
 
</pre>
 
 
 
The above specifications will allocate 57 (= ceiling(900/16)) nodes. The decision to only apply XX (here 16) number cores
 
per node, and not the maximum 20, for a computation requires some judgement. The execution profile of the job is
 
important. Typically, some experimentation is required in finding the optimal tile number for a given code.
 
 
 
<pre>
 
#BSUB -n 1                    # Allocate a total of 1 cpu/core for the job, appropriate for serial processing.
 
#BSUB -R "span[ptile=1]"      # Allocate 1 core per node.
 
#BSUB -R "select[gpu]"        # Allocate a node that has gpus (of 64GB or 256GB memory). A "select[phi]"
 
                              # specification would allocate a node with phi coprocessors.
 
</pre>
 
 
 
Omitting the last two options in the above will cause LSF to place the job on any conveniently available
 
core on any node, idle or (partially) busy, of any type, except on those with 1TB or 2TB memory.<br>
 
 
 
It is worth emphasizing that, under the current LSF setup, only the '''-x''' option and a ptile value equal to the node's
 
core limit will prevent LSF from scheduling jobs that match the balance of unreserved cores.
 
 
 
====Inhomogeneous Node Selection====
 
<pre>
 
#BSUB -n 900
 
#BSUB -R "600*{ select[nxt] rusage[mem=3000] span[ptile=20]} + 300*{ select[gpu] rusage[mem=3000] span[ptile=20] }"
 
#BSUB -M 3000
 
</pre>
 
 
 
The above specification will allocate 30 (600/20) NeXtScale and 15 (300/20) iDataPlex nodes, the latter with GPUs, at 20 cores per node. Note that the enforceable memory limit here 3000 MB per process. In the '''Examples''' section, we provide an illustration of the usefulness of inhomogeneous node selection when the MPMD parallelization model is to be used.
 
 
 
===Job tracking and control commands===
 
 
 
<pre>
 
bjobs [-u all or user_name] [[-l] job_id]    # displays job information per user(s) or job_id, in summary or detail (-l) form, respectively.
 
bpeek [-f] job_id                            # displays the current contents of stdout and stderr output of an executing job.
 
bkill job_id                                # kills, suspends, or resumes unfinished jobs. See man bkill for details.
 
bmod [bsub_options]  job_id                # Modifies job submission options of a job. See man bmod for details.
 
lsload [node_name]                          # Lists on std out a node's utilization. Use bjobs -l jobid
 
                                            # to get the names of nodes associated with a jobid. See man lsload for details.
 
</pre>
 
 
 
All of the above have decent man pages, if you're interested in more detail.
 
 
 
'''Examples'''
 
<pre>
 
$ bjobs -u all
 
JOBID      STAT  USER            QUEUE      JOB_NAME            NEXEC_HOST SLOTS RUN_TIME        TIME_LEFT
 
223537    RUN  adinar          long      NOR_Q                1          20    400404 second(s) 8:46 L
 
223547    RUN  adinar          long      NOR_Q                1          20    399830 second(s) 8:56 L
 
223182    RUN  tengxj1025      long      pro_at16_lowc        10        280  325922 second(s) 5:27 L
 
229307    RUN  natalieg        long      LES_MORE            3          900  225972 second(s) 25:13 L
 
229309    RUN  tengxj1025      long      pro_atat_lowc        7          280  223276 second(s) 33:58 L
 
229310    RUN  tengxj1025      long      cg16_lowc            5          280  223228 second(s) 33:59 L
 
. . .            . . .    . . .
 
 
 
$ bjobs -l 229309
 
 
 
Job <229309>, Job Name <pro_atat_lowc>, User <tengxj1025>, Project <default>, M
 
                          ail <czjnbb@gmail.com>, Status <RUN>, Queue <long>, J
 
                          ob Priority <250000>, Command <## job name;#BSUB -J p
 
                          ro_atat_lowc; ## send stderr and stdout to the same f
 
                          ile ;#BSUB -o info.%J; ## login shell to avoid copyin
 
                          g env from login session;## also helps the module fun
 
                          ction work in batch jobs;#BSUB -L /bin/bash; ## 30 mi
 
                          nutes of walltime ([HH:]MM);#BSUB -W 96:00; ## numpro
 
                          cs;#BSUB -n 280; . . .
 
                          . . .
 
 
 
RUNLIMIT
 
5760.0 min of nxt1449
 
Tue Nov  4 21:34:43 2014: Started on 280 Hosts/Processors <nxt1449> <nxt1449> <
 
                          nxt1449> <nxt1449> <nxt1449> <nxt1449>  ...
 
                          . . .
 
 
 
Execution
 
                          CWD </scratch/user/tengxj1025/EXTD/pro_atat/lowc/md>;
 
Fri Nov  7 12:05:55 2014: Resource usage collected.
 
                          The CPU time used is 67536997 seconds.
 
                          MEM: 44.4 Gbytes;  SWAP: 0 Mbytes;  NTHREAD: 862
 
 
 
                          HOST: nxt1449
 
                          MEM: 3.2 Gbytes;  SWAP: 0 Mbytes; CPU_TIME: 9004415 s
 
                          econds . . .
 
                          . . .
 
                          . . .
 
 
 
 
 
$ bmod -W 46:00 229309            # resets wall-clock time to 46 hrs for job 229309
 
 
 
 
 
</pre>
 
 
 
 
 
'''Node Utilization.''' It may happen that a job uses its allocated nodes inefficiently.
 
Sometimes this is unavoidable, but many times it is very avoidable. It is unavoidable, for instance, if the
 
amount of memory used per node is a large fraction of the total for that node, and only 1 cpu is used. In
 
that case, cpu utilization will be at best at 5% (1/20) in a regular node. A handy tool, more practical than lsload,
 
for tracking node utilization is the '''lnu''' homegrown command.
 
 
 
<pre>
 
lnu [-h] [-l] -j jobid          # lists on stdout the utilization across all nodes for an executing job. See examples below.
 
</pre>
 
 
 
'''Examples'''
 
 
 
<pre>
 
$ lnu -l -j 795375
 
Job          User                Queue        Status Node  Cpus
 
795375      jomber23            medium            R    4    80 
 
        HOST_NAME      status  r15s  r1m  r15m  ut    pg  ls    it  tmp  swp  mem    Assigned Cores
 
        nxt1417            ok  20.0  21.0  21.0  97%  0.0  0 94976  366M  3.7G 41.6G    20
 
        nxt1764 (L)        ok  19.7  20.0  20.0  95%  0.0  0 95040  366M  3.7G 41.5G    20
 
        nxt2111            ok  20.0  20.0  20.0  98%  0.0  0 91712  370M  4.2G 41.5G    20
 
        nxt2112            ok  20.0  21.1  21.0  97%  0.0  0 91712  370M  4.2G 41.6G    20
 
=========================================================================================================
 
 
 
$ lnu -l -j 753454
 
Job          User                Queue        Status Node  Cpus
 
753454      ajochoa              long              R    1    20 
 
        HOST_NAME      status  r15s  r1m  r15m  ut    pg  ls    it  tmp  swp  mem    Assigned Cores
 
        nxt1222 (L)        ok  4.3  4.5  6.2  20%  0.0  0 54464  422M  4.7G 52.9G    20
 
=========================================================================================================
 
 
 
</pre>
 
 
 
The utilization ('''ut''') and memory paging ('''pg'''), overall, are probably the most significant. Note that the
 
'''tmp, swp,''' and '''mem''' refer to ''available'' amounts respectively.
 

Latest revision as of 14:31, 18 June 2020

Job Submission

Once you have your job file ready, it is time to submit your job. You can submit your job to LSF with the following command:

[ NetID@ada ~]$ bsub < MyJob.LSF
Verifying job submission parameters...
Verifying project account...
     Account to charge:   123456789123
         Balance (SUs):      5000.0000
         SUs to charge:         5.0000
Job <12345> is submitted to default queue <sn_regular>.

tamubatch

tamubatch is an automatic batch job script that submits jobs for the user without the need of writing a batch script on the Ada and Terra clusters. The user just needs to provide the executable commands in a text file and tamubatch will automatically submit the job to the cluster. There are flags that the user may specify which allows control over the parameters for the job submitted.

tamubatch is still in beta and has not been fully developed. Although there are still bugs and testing issues that are currently being worked on, tamubatch can already submit jobs to both the Ada and Terra clusters if given a file of executable commands.

For more information, visit this page.

tamulauncher

tamulauncher provides a convenient way to run a large number of serial or multithreaded commands without the need to submit individual jobs or a Job array. User provides a text file containing all commands that need to be executed and tamulauncher will execute the commands concurrently. The number of concurrently executed commands depends on the batch requirements. When tamulauncher is run interactively the number of concurrently executed commands is limited to at most 8. tamulauncher is available on terra, ada, and curie. There is no need to load any module before using tamulauncher. tamulauncher has been successfully tested to execute over 100K commands.

tamulauncher is preferred over Job Arrays to submit a large number of individual jobs, especially when the run times of the commands are relatively short. It allows for better utilization of the nodes, puts less burden on the batch scheduler, and lessens interference with jobs of other users on the same node.

For more information, visit this page.