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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 after the #BSUB directives should be #!/bin/csh.
 
  
'''Five important job parameters:'''
+
== tamulauncher ==
<pre>
 
#BSUB -n NNN                    # NNN: total number of cpus to allocate for the job
 
#BSUB -R "span[ptile=XX]"      # XX:  number of cores/cpus per node to use
 
#BSUB -R "select[node-type]"    # node-type: nxt, mem256gb, gpu, phi, mem1t, mem2t ...
 
#BSUB -R "rusage[mem=nnn]"      # selects nodes/hosts that each has at least nnn MBs of memory available.
 
#BSUB -M mm                    # sets the per process enforceable memory limit to nnn 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.
 
Note, that without the '''-R "rusage[mem=nnn]" ''' LSF may select nodes/hosts that do not have the specified nnn MB
 
of memory. The ''' -M mm''' option, on the other hand, limits the amount of memory allocated to a process.
 
When this limit is violated the job will abort. Omitting this specification, causes LSF to assume '''the'''
 
'''default memory limit, by configuration, per process to be 2.5 giga-bytes (2500 MB).''' The following examples, with some commentary,  illustrate the
 
use of these options.
 
  
<pre>
+
''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.'' 
#BSUB -n 900                    # 900: number of cpus to allocate for the job
 
#BSUB -R "span[ptile=20]"      # 20:  number of cores/cpus per node to use
 
#BSUB -R "select[nxt]"          # Allocates NeXtScale nodes
 
</pre>
 
  
The above specifications will allocate 45 (=900/20) whole nodes. In many parallel jobs the selection
+
For more information, visit [https://hprc.tamu.edu/wiki/SW:tamulauncher#tamulauncher this page.]
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>
+
[[ Category:Ada ]]
#BSUB -n 900                    # 900: total number of cpus to allocate for the job
 
#BSUB -R "span[ptile=16]"      # 16:  number of cores/cpus per node to use
 
#BSUB -R "select[nxt]"          # allocates exclusively whole NeXtScale nodes
 
#BSUB -R "rusage[mem=58000]"    # schedules on nodes that have at least 58,000 MB avail
 
#BSUB -M 3600                  # lim its (and enforces) 3600 MB memory use per process and/or ~58,000 MB per node
 
</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 cpu per node.
 
#BSUB -R "select[gpu]"        # Make the allocated node have 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=25000] span[ptile=20]} + 300*{ select[gpu] rusage[mem=220000] span[ptile=20] }"
 
#BSUB -M 12000
 
</pre>
 
 
 
The above specification will allocate 30 NeXtScale and 15 iDataPlex nodes, the latter with GPUs, at 20 cores per node. Note
 
that the enforceable memory limit here 12 gb per process. In the '''More Examples''' section, we provide an illustration of the
 
usefulness of inhomogeneous node selection when the MPMD parallelization model is to be used.
 
 
 
====Common BSUB Options====
 
<pre>
 
-J job name          - sets the job name.
 
-q queue              - submits job to the specified queue. Currently (Feb 2015), this specification is needed only
 
                        for high priority queue for privileged access. Currently (Jan 2015) only the special and staff
 
                        queues allow this type of access.
 
-L shell              - uses the Unix Shell specified to initialize the job's execution environment. The setting of
 
                      this option is required for the module system to work correctly. We recommend that the setting
 
                      be /bin/bash. Some application packages setup their own shell. If you encounter a problem, notify
 
                      the help desk.
 
-W hh:mm or -mm      - sets job's runtime wall-clock limit in hours:minutes or just minutes (-mm).
 
-M men_limit          - sets the per process memory limit in mega-bytes (MBs). The job's memory limit then is
 
                        num_cores * men_limit MBs. When this limit is violated the jobs aborts.
 
-R "rusage[mem=memsz]" - schedules job on nodes that have at least num_cores * memsz MBs available
 
-n num_cores          - assigns number of job slots/cores.
 
-x                    - assigns a whole node (same node as above) exclusively for the job. The SUs charged reflect use of
 
                        all the cores in a node.
 
-o filename          - directs the job's standard output to name. The special string, %J, attaches the jobid.
 
-P project_name      - charges the consumed service units (SUs) to the project specified.
 
-u e-mail_addr        - sends email to the specified address (e.g., netid@tamu.edu, myname@gmail.com) with
 
                        information about main job events.
 
</pre>
 
 
 
====Environment Variables====
 
 
 
When LSF selects and activates a node for the running of your job, by default, it duplicates the environment the job was submitted from. That
 
environment in the process of your work may have been altered by you (e.g., by loading some modules or setting up new or changing some standard environment variables)
 
to be different from that the login created. The next job you submit, however, may require a different execution environment. Hence the
 
recommendation that, in submitting jobs, specify the creation of a new login shell and within the job explicitly customize the environment as needed.
 
A new login shell per job is initialized by specifying the '''#BSUB -L /bin/bash''' option.<br>
 
 
 
All the nodes enlisted for the execution of a job carry most of the environment variables the login process created: HOME, PWD, PATH, USER, etc.
 
In addition, LSF defines new ones in the environment of an executing job. Below, we show an abbreviated list.
 
 
 
<pre>
 
LSB_QUEUE        - The name of the queue the job is dispatched from.
 
LSB_JOBNAME      - Name of the job.
 
LSB_JOBID        - Batch job ID assigned by LSF.
 
LSB_ERRORFILE    - Name of the error file specified with a bsub -e.
 
LSB_HOSTS        - The list of nodes (their LSF symbolic names) that are used to run the batch job.
 
                    A node name is repeated as many times as needed to equal the specified ptile value.
 
                        he memory size of LSB_HOSTS variable is limited to 4096 bytes.
 
LSB_MCPU_HOSTS  - The list of nodes (their LSF symbolic names) ) and the specified or default ptile value.
 
                                per node to run the batch job. This can be relied upon to contain the names of all
 
                                the deployed hosts.
 
LS_SUBCWD        - This is the directory the job was submitted from.
 
TMPDIR              - Set to /work/jobid.tmpdir. LSF and some application programs use it for temporary files.
 
</pre>
 
 
 
All of the above are accessible both in a batch script, at the shell level, as well as within a program (see the EXAMPLES subsection).
 
 
 
==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.