wiki:qsub.1.html
Last modified 9 years ago Last modified on 09/16/13 18:00:44

       qsub [<options>] <executable> [<executable options>]


DESCRIPTION

       qsub submits a job to the queue manager for execution.

       JOBID EXPANSION ($jobid or $COBALT_JOBID):

       If  $jobid  or $COBALT_JOBID is specified in any jobid expansion option
       then it will be converted to the actual jobid.

       Example: qsub ... --env myenv=\$jobid_myval ...

       If the jobid is 123 then myenv will be set to '123_myval'

       jobid expansion options: --env, --jobname, -o, -e, -O, --debuglog

       Note: Remember to escape appropriately "\$jobid" or "\$COBALT_JOBID"

       SCRIPT JOB DIRECTIVES (#COBALT):

       Command options can be  entered  in  a  script  job  by  using  #COBALT
       <options>.   You  can  enter  all  in one directive or directives.  The
       #COBALT tag should be right after the first line of the  script.   qsub
       will  continue  to  read  directives until it reads the first line that
       does not contain the tag #COBALT.

       The command line options will take precedence over  the  Cobalt  script
       jobx directives.

       Note:  An error will occur if in the script the --mode option is speci‐
       fied and it is not "script"

       Example:

         script.sh:

           #!bin/bash
           #COBALT -t 50 -n 30
           echo "SCRIPT JOB WITH DIRECTIVE"

         or

           #!bin/bash
           #COBALT -t 50
           #COBALT -n 30
           echo "SCRIPT JOB WITH DIRECTIVE"

         qsub script.sh sargs
         is equivalent to
         qsub -t 50 -n 30 --mode script script.sh sargs

         qsub -t 75 script.sh sargs

       --version
              Displays client revision and Cobalt version

       -A --project [project]
              Associate the job with the allocation for project project.  This
              is used to properly account for machine usage.

       --attrs [<attr1=val1>:<attr2=val2>:...]
              Set  a list of attributes for a job that must be fulfilled for a
              job to run.  For instance, --attrs location=[blocklocation] will
              force a job to run on a specific block.

       --cwd [directory]
              Tell  the job to use the specified directory as the default cur‐
              rent working directory while running the job.

       --debuglog [path to file] - (jobid expansion)
              Send debugging information from cobalt to file specified.

       --dependencies [<jobid1>:<jobid2>:...]
              Set the dependencies for the  job  being  submitted.   This  job
              won't  run  until  all jobs in the dependency list have finished
              and exited with a status of 0.

       --disable_preboot
              If --mode script is specified, this will cause Cobalt to run the
              job  script  without  booting  the  block first.  By default the
              script is executed after the requested block is booted.

       -e --error [path to file] - (jobid expansion)
              Send job stderr to file specified.

       --env [<var1=value1>:<var=value2>] - (jobid expansion)
              Set environment variables that will be  passed  into  the  job's
              environment.   If  the the characters ":" and "=" are within the
              value, right hand side (rhs) of a environment  variable  assign‐
              ment,  then  need to quote the entire string and precede any ":"
              and "=" characters that are in the rhs with "\".  runtime.

              If multiple --env options are specified then qsub will take  the
              union.

              e.g.  qsub  ...  --env  "A=B:C=x\=1\:y\=2\:z\=3:D=ABC" ... --env
              "MY_NAME=cobalt' ...

              A would equal B

              C would equal x=1:y=2:z=3

              D would equal ABC

              and
              Submit job and immediately place it in the user hold state

       -i --inputfile [path to file]
              Send file to job's stdin.

       -I (NOT IMPLEMENTED)
              Run  an  interactive  command. During job execution, the current
              tty will be connected with the running job.  (Not  available  on
              Blue Gene systems.)

       -M --notify [email address]
              Send  an  email notification at the start and stop of the job to
              the specified email address.

       -n --nodecount [nodecount]
              Specifies the node count for a job

       -o --output [path to file] - (jobid expansion)
              Send job stdout to file specified.

       -O --outputprefix [output prefix] - (jobid expansion)
              Use the specified prefix for both .output, .error  and  debuglog
              files.  This will only take effect if -o or -e or --debuglog not
              supplied.

       --proccount [process count]
              Specify the number of processes to start.

       -q --queue [queue]
              Submit the job to the specified queue.

       --run_users --user_list [<user1>:<user2>:...]
              Sets a colon-separated list of users for the job  being  submit‐
              ted.  All users in this list will be able to execute cobalt com‐
              mands to control the job. The submitting user is always able  to
              run commands on a submitted job.

       --run_project
              Appends  the  list  of  users  in a project to the list of users
              authorized to run commands on the submitted job.

       -u --umask
              set umask: octal number default(022)

       -t --time [wallclock time]
              Specify the runtime for a job. If the job runs over this  limit,
              it  will be killed. The time may be specified as eitehr an inte‐
              ger number of minutes or a colon-delimited value of the  format:
              HH:MM:SS. Enter 0 to get the max allowed walltime.

              Run  the  job  with the specified IO Node kernel profile. (Blue‐
              Gene/Q only)

       --ion_kerneloptions [kernel options]
              Run the job with the specified IO Node kernel  options.   (Blue‐
              Gene/Q only)

       --mode [mode]
              This is a platform-dependent setting that controls the execution
              mode of the submitted job and the division of cores  and  memory
              on  the  compute  nodes.  Valid values are dependent on the spe‐
              cific BlueGene platform:

       BG/L: Valid values  are  "co"  (coprocessor),"vn"  (virtual  node)  and
       "script".
                    The default is co.

       BG/P:  Valid  values  are  "smp",  "dual",  "vn" and "script".   "smp",
       "dual" and
                    "vn" correspond to the modes within mpirun. The default is
              "smp"

       BG/Q:   Valid  values  are  "c1","c2","c4","c8","c16","c32","c64",  and
       "script".
                    The c(n) modes correspond to the "ranks-per-node" flag  of
              runjob and
                    governs  the  MPI  ranks  started  per node on the compute
              nodes.  Node memory
                    is divided evenly between  all  processes.   n/64  threads
              will be available
                    to each MPI process as well. If this option is not set the
              default is "c1"

       On all platforms, the "script" mode causes the job to be routed through
       the
              script-forker,  and  will  allow  the  execution  of script jobs
              allows the user to


NOTE

       The only thing printed to STDOUT is  the  jobid,  any  other  error  or
       informational messages are printed to STDERR.


SEE ALSO

       qstat(1),  qdel(1),  qhold(1),  qrls(1),  qalter(1),  qmove(1), cqm(1),
       cqwait(1)


BUGS

                                                                       qsub(1)