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Resource Managers
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1 TORQUE Resource Manager
The Terascale Open-source Resource and QUEue Manager (TORQUE) is a distributed resource manager providing control over batch jobs and distributed compute nodes. TORQUE can integrate with the Moab Workload Manager to improve overall utilization, scheduling and administration on a HPC-C4 cluster.
1.1 Batch Job (PBS) Variables : bwForCluster
At the time a job is launched into execution, TORQUE defines multiple environment variables, which can be used from within the submission script to define the correct workflow of the job.
Since the work load manager TORQUE on BwForCluster_Chemistry uses the resource manager TORQUE, the following environment variables of TORQUE are added to your environment once your job has started
(excerpt of the most important ones).
| Environment | Brief explanation |
|---|---|
| PBS_O_WORKDIR | Directory where the qsub command is issued (Job's submission directory) |
| PBS_O_SHELL | Script shell |
| PBS_O_PATH | Path variable used to locate executables within job script |
| PBS_O_HOST | Host on which job script is currently running |
| PBS_O_HOME | Home directory of submitting user |
| PBS_O_LOGNAME | Name of submitting user |
| PBS_NODEFILE | File that lists the hosts (compute nodes) on which the job is run. Line delimited. |
| PBS_JOBNAME | User specified jobname |
| PBS_NODENUM | Node offset number |
| PBS_NUM_NODES | Number of nodes allocated to the job |
| PBS_QUEUE | Job queue |
| PBS_NP | Number of execution slots (cores) for the job |
| PBS_NUM_PPN | Number of procs per node allocated to the job |
| PBS_JOBID | Unique number PBS assigns to a job |
| PBS_TASKNUM | Number of tasks requested |
| TMPDIR | Directory on the scratch (local and fast) disk space that is unique to a job |
- PBS_O_WORKDIR is typically used at the beginning of a script to go to the directory where the qsub command was issued, which is frequently also the directory containing the input data for the job, etc. The typical use is
cd $PBS_O_WORKDIR
inside a submission script.
- PBS_NODEFILE is typically used to define the environment for the parallel run, for mpirun in particular. Normally, this usage is hidden from users inside a script (e.g. enable_arcus_mpi.sh), which defines the environment for the user.
- PBS_JOBID is useful to tag job specific files and directories, typically output files or run directories. For instance, the submission script line
myApp > $PBS_JOBID.out
runs the application myApp and redirects the standard output to a file whose name is given by the job id. (NB: the job id is a number assigned by Torque and differs from the character string name given to the job in the submission script by the user.)
- TMPDIR is the name of a scratch disk directory unique to the job. The scratch disk space typically has faster access than the disk space where the user home and data areas reside and benefits applications that have a sustained and large amount of I/O. Such a job normally involves copying the input files to the scratch space, running the application on scratch and copying the results to the submission directory.
See also:
1.2 Job Exit Status
Once a job under TORQUE has completed, the exit_status attribute will contain the result code returned by the job script. This attribute can be seen by submitting a qstat -f command to show the entire set of information associated with a job. The exit_status field is found near the bottom of the set of output lines.
$ msub bwforcluster-quantum-example.moab
760236
$ qstat
Job ID Name User Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
760236.adm01 ...-example.moab kn_l_pop235844 00:00:00 C short
$
$ qstat -f 760236
Job Id: 760236.adm01
Job_Name = bwforcluster-quantum-example.moab
Job_Owner = kn_l_pop235844@adm01
resources_used.cput = 00:00:00
resources_used.mem = 0kb
resources_used.vmem = 0kb
resources_used.walltime = 00:00:11
job_state = C
queue = short
server = adm01
Checkpoint = u
ctime = Fri Jan 15 10:10:23 2016
Error_Path = adm01:/nfs/home1/kn/kn_kn/kn_l_pop235844/src/chem/quantum_esp
resso/4.0.3_epw/bwhpc-examples/bwforcluster-quantum-example.moab.76023
6
exec_host = n0301/0
exec_port = 15003
group_list = kn_kn
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = a
mtime = Fri Jan 15 10:10:44 2016
Output_Path = adm01:/nfs/home1/kn/kn_kn/kn_l_pop235844/src/chem/quantum_es
presso/4.0.3_epw/bwhpc-examples/bwforcluster-quantum-example.moab.7602
36
Priority = 0
qtime = Fri Jan 15 10:10:23 2016
Rerunable = False
Resource_List.mem = 4000mb
Resource_List.nodect = 1
Resource_List.nodes = 1:ppn=1
Resource_List.walltime = 48:00:00
session_id = 1349
Variable_List = MOAB_BATCH=,MOAB_CLASS=short,MOAB_GROUP=kn_kn,
MOAB_JOBID=760236,MOAB_JOBNAME=bwforcluster-quantum-example.moab,
MOAB_MACHINE=torque,MOAB_NODECOUNT=1,MOAB_NODELIST=n0301,
MOAB_PARTITION=Moab,MOAB_PROCCOUNT=1,MOAB_TASKMAP=n0301:1,
MOAB_USER=kn_l_pop235844,PBS_O_QUEUE=short,PBS_O_HOME=/,
PBS_O_PATH=/sbin:/usr/sbin:/bin:/usr/bin,
PBS_O_WORKDIR=/nfs/home1/kn/kn_kn/kn_l_pop235844/src/chem/quantum_esp
resso/4.0.3_epw/bwhpc-examples,PBS_O_HOST=adm01,PBS_O_SERVER=adm01,
MOAB_SUBMITDIR=/home/kn/kn_kn/kn_l_pop235844/src/chem/quantum_espress
o/4.0.3_epw/bwhpc-examples,PATH=/sbin:/usr/sbin:/bin:/usr/bin
euser = kn_l_pop235844
egroup = kn_kn
queue_type = E
etime = Fri Jan 15 10:10:23 2016
--> exit_status = 0
start_time = Fri Jan 15 10:10:33 2016
start_count = 1
fault_tolerant = False
comp_time = Fri Jan 15 10:10:45 2016
job_radix = 0
total_runtime = 14.439113
proxy_user = kn_l_pop235844
submit_host = adm01
job_id = 760236
x = ENVREQUESTED:TRUE;SID:Moab;SJID:760236;SRMJID:760236
This code can be useful in diagnosing problems with jobs that may have unexpectedly terminated.
If TORQUE was unable to start the job, this field will contain a negative number produced by the pbs_mom.
Otherwise, if the job script was successfully started, the value in this field will be the return value of the script.
1.2.1 TORQUE Supplied Exit Codes
| Name | Value | Description |
|---|---|---|
| JOB_EXEC_OK | 0 | job exec successful |
| JOB_EXEC_FAIL1 | -1 | job exec failed, before files, no retry |
| JOB_EXEC_FAIL2 | -2 | job exec failed, after files, no retry |
| JOB_EXEC_RETRY | -3 | job execution failed, do retry |
| JOB_EXEC_INITABT | -4 | job aborted on MOM initialization |
| JOB_EXEC_INITRST | -5 | job aborted on MOM init, chkpt, no migrate |
| JOB_EXEC_INITRMG | -6 | job aborted on MOM init, chkpt, ok migrate |
| JOB_EXEC_BADRESRT | -7 | job restart failed |
| JOB_EXEC_CMDFAIL | -8 | exec() of user command failed |
2 Slurm Resource Manager
The Slurm Resource and Workload Manager (formerly known as Simple Linux Utility for Resource Management (see: SLURM)) is a free and open-source job scheduler.
2.1 Batch Job (Slurm) Variables : bwUniCluster
Since the work load manager MOAB on bwUniCluster uses the resource manager Slurm, the following environment variables of Slurm are added to your environment once your job has started (only an excerpt of the most important ones).
| Environment | Brief explanation |
|---|---|
| SLURM_JOB_CPUS_PER_NODE | Number of processes per node dedicated to the job |
| SLURM_JOB_NODELIST | List of nodes dedicated to the job |
| SLURM_JOB_NUM_NODES | Number of nodes dedicated to the job |
| SLURM_MEM_PER_NODE | Memory per node dedicated to the job |
| SLURM_NPROCS | Total number of processes dedicated to the job |
| SLURM_CLUSTER_NAME | Name of the cluster executing the job |
| SLURM_CPUS_PER_TASK | Number of CPUs requested per task |
| SLURM_JOB_ACCOUNT | Account name |
| SLURM_JOB_ID | Job ID |
| SLURM_JOB_NAME | Job Name |
| SLURM_JOB_PARTITION | Partition/queue running the job |
| SLURM_JOB_UID | User ID of the job's owner |
| SLURM_SUBMIT_DIR | Job submit folder. The directory from which msub was invoked. |
| SLURM_JOB_USER | User name of the job's owner |
| SLURM_RESTART_COUNT | Number of times job has restarted |
| SLURM_PROCID | Task ID (MPI rank) |
| SLURM_NTASKS | The total number of tasks available for the job |
| SLURM_STEP_ID | Job step ID |
| SLURM_STEP_NUM_TASKS | Task count (number of PI ranks) |
See also:
- Slurm input and output environment variables
- Additional bwUniCluster Configurations
- Additional bwUniCluster Slrum Environments
2.2 Job Exit Codes
A job's exit code (aka exit status, return code and completion code) is captured by SLURM and saved as part of the job record.
Any non-zero exit code will be assumed to be a job failure and will result in a Job State of FAILED with a reason of "NonZeroExitCode".
The exit code is an 8 bit unsigned number ranging between 0 and 255. While it is possible for a job to return a negative exit code, SLURM will display it as an unsigned value in the 0 - 255 range.
2.2.1 Displaying Exit Codes and Signals
SLURM displays a job's exit code in the output of the scontrol show job and the sview utility. SLURM displays job step exit codes in the output of the scontrol show step and the sview utility.
When a signal was responsible for a job or step's termination, the signal number will be displayed after the exit code, delineated by a colon(:).
