Batch System

For performance and stability reasons, we recommend using qsub and xqsub commands for submitting batch jobs.
Moreover, when submitting multiple jobs, add a sleep delay between jobs or use job arrays for submitting identical jobs.

Be aware the there is a maximum size limit of 64KB for scripts submitted to the queue system. Scripts submitted to the queuing system should mainly consist of parameters for the queuing system and executions of the "real" job.

Batch system

The batch job queuing system on Computerome is based on TORQUE Resource Manager (generally qsub and q... type commands) and Moab Workload Manager (generally msub and m... type commands).Additionally, we have xqsub and xmsub, perl wrapper scripts to qsub and msub respectively, which build a job submission script for you.Extensive documentation is available here:

Batch queues

It is not necessary to use partition or queue options when submitting jobs - however, as described in Working in projects is is required to supply a <group_NAME> corresponding to the project you are currently working in.

Moab Viewpoint

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Submitting batch jobs

On Computerome 2.0, there are three types of machines:

Fat nodes with 40 CPU cores and 1,5TB of memory
Thin nodes with 40 CPU cores and 192 GB of memory
GPU nodes with 40 CPU cores, 192 GB of memory and one NVIDIA Tesla V100 GPU card

You can submit jobs via the command qsub and/or msub. We strongly encourage you to take advantage of modules in your pipelines as it gives you better control of your environment.In order to submit jobs that will run on one node only you will only have to specify the following resources:

How long time you expect the job to run ⇒ '-l walltime=<time>'
How much memory your job requires ⇒ '-l mem=xxxgb'
How many CPUs and GPUs ⇒ '-l nodes=1:ppn=<number of CPUs>:gpus=<number of GPUs>' ; CPU will be from 1 to 40, GPU will be 0 or 1 (':gpus=...' can be left out if not used) .
The <group_NAME> for your current project ⇒ '-W group_list=<group_NAME> -A <group_NAME>' .

To run a job with 23 CPUs, 100GB memory lasting an hour you can use the command:

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=1:ppn=23,mem=100gb,walltime=3600 <your script>

Same job as above, also using GPU:

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=1:ppn=23:gpus=1,mem=100gb,walltime=3600 <your script>

Example using msub:

$ msub -W group_list=<group_NAME> -A <group_NAME> -l nodes=1:ppn=23,mem=100gb,walltime=3600 <your script>

The parameters nodes, ppn, mem is just an example and you should be change to suit your specific job

Interactive jobs

When you want to test something in the batch system, it is strongly recommended to run in an interactive job, by using the following:

$ qsub -W group_list=<group_NAME> -A <group_NAME> -X -I

This will give you access to a single compute node, where you can perform your testing without affecting other users.

iqsub

Computerome is now offering an even more straightforward way to work interactively, the way you do on your own computer or a local linux server, instead of having to submit everything through the queuing system.Just login and type iqsub and the system will ask you 3 simple questions, after which you'll be redirected to a full, private node.

$ iqsub

[ Interactive job ]

  => [ Select group ]

    => [ Select time needed (non extendable) ]

      => [ Enter number of Processors needed (1-40) ]

         => [ Enter number of GPUs needed (0-1) ]

            => [ Enter amount of memory needed ]

Under no circumstances should you ever run jobs or scripts on the Computerome login node.

Script file example

A script for a file to be submitted with qsub might begin with lines like:

#!/bin/sh
### Note: No commands may be executed until after the #PBS lines
### Account information
#PBS -W group_list=pr_12345 -A pr_12345
### Job name (comment out the next line to get the name of the script used as the job name)
#PBS -N test
### Output files (comment out the next 2 lines to get the job name used instead)
#PBS -e test.err
#PBS -o test.log
### Only send mail when job is aborted or terminates abnormally
#PBS -m n
### Number of nodes
#PBS -l nodes=1:ppn=8 
### Memory
#PBS -l mem=120gb
### Requesting time - format is <days>:<hours>:<minutes>:<seconds> (here, 12 hours)
#PBS -l walltime=12:00:00
 
# Go to the directory from where the job was submitted (initial directory is $HOME)
echo Working directory is $PBS_O_WORKDIR
cd $PBS_O_WORKDIR

### Here follows the user commands:
# Define number of processors
NPROCS=`wc -l < $PBS_NODEFILE`
echo This job has allocated $NPROCS nodes

# Load all required modules for the job
module load tools
module load perl/5.20.2
module load <other stuff>

# This is where the work is done
# Make sure that this script is not bigger than 64kb ~ 150 lines, otherwise put in seperat script and execute from here
<your script>

The $PBS... variables are set for the batch job by Torque.

If you already have loaded some modules in your login environment , you do not need to specify them in the jobscript.

However, we recommend that you do it anyway, since it improves the portability of the jobscript and serves as a reminder of the requirements.

We also strongly advise against the use of the "-V" option, as it makes it hard to debug possible errors during runtime.

The complete list of variables is documented in Exported batch environment variables.Further examples of Torque batch job submission is documented in Job submission

Specifying a different project account

If you run jobs under different projects, for instance pr_12345 and pr_54321, you must make sure that each project gets accounted for separately in the system's accounting statistics.You specify the relevant project account (for example, pr_54321) for each individual job by using these flags to the qsub command:

$ qsub -W group_list=pr_54321 -A pr_54321 ...

or in the job script file, add line like this near the top:

#PBS -W group_list=pr_54321 -A pr_54321

Please use project names only by agreement with your project owner.

Estimating job resource requirements

First time you run your script, you may not have a clear picture of what kind of resource requirements it has. To get a rough estimate, you could submit a job to a full node, with large walltime:

Regular compute node (aka. 'thinnode'):

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=1:ppn=40:thinnode,walltime=99:00:00,mem=180gb -m n <script>

Fat node:

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=1:ppn=40:fatnode,walltime=99:00:00,mem=1200gb -m n <script>

To see the actual resource usage, see output from command qstat

You can add this line to the bottom of your script

qstat -f -1 $PBS_JOBID

It will generate something like the following:

Job Id: <jobid>
    Job_Name = <job_NAME>
    Job_Owner = <user>
    resources_used.cput = 323:00:30
    resources_used.energy_used = 0
    resources_used.mem = 1129928kb
    resources_used.vmem = 3082824kb
    resources_used.walltime = 12:00:35
...
    Resource_List.nodes = 1:ppn=28
    Resource_List.mem = 120gb
    Resource_List.walltime = 12:00:00
    Resource_List.nodect = 1
    Resource_List.neednodes = 1:ppn=28
...

Look at resources_used.xyz for hints.

Requesting a maximum memory size

A number of node features can be requested, see the Torque Job Submission page. For example, you may require a minimum physical memory size by requesting:

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=2:ppn=16,mem=120gb <your script>

i.e.: 2 entire nodes, 16 CPU cores on each, the total memory of all nodes >= 120 GB RAM.

Do not request the maximum physical amount of RAM, since the RAM memory available to users is slightly less than the physical RAM memory.

To see the available RAM memory sizes on the different nodes types see the Hardware page.

Waiting for specific jobs

It is possible to specify that a job should only run after another job has completed succesfully, please see the -W flags in the qsub page.To run <your script> after job 12345 has completed succesfully::

$ qsub -W depend=afterok:12345 <your script>

Be sure that the exit status of job 12345 is meaningful: if it exits with status 0, you second job will run. If it exits with any other status, you second job will be cancelled.It is also possible to run a job if another job fails (``afternotok``) or after another job completes, regardless of status (``afterany``). Be aware that the keyword ``after`` (as in ``-W depend=after:12345``) means run after job 12345 has *started*.

Submitting jobs to 40-CPU fat nodes

The high memory (1536 GB) nodes we define to have a node property of fatnode. You could submit a batch job like in these examples:: 2 entire fatnodes, 32 CPUs each, total 64 CPU cores

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=2:ppn=40:fatnode,mem=1200gb <your script>

Explicitly the g-11-f0042 node, 40 CPU cores:

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=g-11-f0042:ppn=40,mem=120gb <your script>

2 entire fatnodes, each, memory of all nodes => 2000 GB RAM)

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=2:ppn=40:fatnode,mem=2000gb <your script>

Submitting jobs to 40-CPU thin nodes

The standard memory (192 GB) nodes we define to have a node property of thinnode.You could submit a batch job like in these examples::2 entire thinnodes, 40 CPUs each, total 80 CPU cores)

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=2:ppn=40:thinnode,mem=10gb <your script>

Explicitly the g-01-c0052 node, 40 CPU cores

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=g-01-c0052:ppn=40,mem=50gb <your script>

Submitting 1-CPU jobs

You could submit a batch job like in this example:

$ qsub -W group_list=<group_NAME> -A <group_NAME> -l nodes=1:ppn=1 <your script>

Running parallel jobs using MPI

#!/bin/sh
### Note: No commands may be executed until after the #PBS lines
### Account information
#PBS -W group_list=pr_12345 -A pr_12345
### Job name (comment out the next line to get the name of the script used as the job name)
#PBS -N test
### Output files (comment out the next 2 lines to get the job name used instead)
#PBS -e test.err
#PBS -o test.log
### Only send mail when job is aborted or terminates abnormally
#PBS -m n
### Number of nodes, request 240 cores from 6 nodes
#PBS -l nodes=6:ppn=40
### Requesting time - 720 hours
#PBS -l walltime=720:00:00

### Here follows the user commands:
# Go to the directory from where the job was submitted (initial directory is $HOME)
echo Working directory is $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
# NPROCS will be set to 240, not sure if it used here for anything.
NPROCS=`wc -l < $PBS_NODEFILE`
echo This job has allocated $NPROCS nodes
 
module load moab torque openmpi/gcc/64/1.10.2 gromacs/5.1.2-plumed

export OMP_NUM_THREADS=1
# Using 236 cores for MPI threads leaving 4 cores for overhead, '--mca btl_tcp_if_include ib0' forces InfiniBand interconnect for improved latency
mpirun -np 236 $mdrun -s gmx5_double.tpr -plumed plumed2_path_re.dat -deffnm md-DTU -dlb yes -cpi md-DTU -append --mca btl_tcp_if_include ib0

In order to optimize performance, the queuing system is configured to place jobs on nodes connected to the same InfiniBand switch (30 nodes per switch) if possible.

To get nodes close to each other, use procs=<number_of_procs> and leave out node= and ppn=.To avoid interference with other jobs, procs= should be a multiple of cores per node (ie. 28 for mpinode).

Job Arrays

Submitting multiple identical jobs can be done using job arrays. Job arrays can be created by using the -t option in the qsub submission script. The -t option allows many copies of the same script to be submitted at once. Additional information about -t option can be found in the qsub command reference. Moreover, PBS_ARRAYID environmental variable allows to differentiate the different jobs in the array. The amount of resources required in the qsub submission script is the amount of resources that each job will get.
For instance adding the line:

  #PBS -t 0-14%5

in the qsub script will cause running the job 15 times with not more than 5 actives jobs at any given time.

Please, please, please, use the %# option for limiting the number of active jobs.

PBS_ARRAYID values will run from 0 to 14, as shown below:

 ( perl process.pl dataset${PBS_ARRAYID} )
  
  perl process.pl dataset0
  perl process.pl dataset1
  perl process.pl dataset2
  ….
  perl process.pl dataset14

Jobs in jobs array are run independently and not in any specific order.

Monitoring batch jobs

The Torque command qstat is used to inquire about the status of one or more jobs:

$ qstat -f <jobid>     (Inquire about a particular jobid)
$ qstat -r             (List all running jobs)
$ qstat -a             (List all jobs)

In addition, the Moab scheduler can be inquired using the showq command:

$ showq -r             (List all running jobs)
$ showq -i             (List all idle jobs. Idle jobs are ordered from highest priority to lowest priority)   
$ showq                (List all jobs)

If you want to check the status of a particular jobid use checkjob command:

$ checkjob <jobid>

Adding -v flag(s) to this command will increase the verbosity.

Badly behaving jobs

pestat has not been maintained since 2018 and is unsupported.

As a result, it may not be up to date with current Moab and Torque versions, and you should only use the results as a quideline and pointer to further investigation using standard queueing system tools, such as checkjob, showq and qstat.

Another useful command for monitoring batch jobs is pestat, available as a module. Show status of badly behaving jobs, with bad fields marked by star (*)

$ module load tools pestat
$ pestat -f
Listing only nodes that are flagged by *e
  node state  load    pmem ncpu   mem   resi usrs tasks  jobids/users
  risoe-r01-f002  free     2* 1034109  32 1046397   8017  1/1    1    103125 s147214
  risoe-r01-f010  free  0.53* 1034109  32 1046397   8451  0/0    0
  risoe-r01-f012  free  0.55* 1034109  32 1046397   8019  0/0    0
  risoe-r02-f019  offl* 0.27  1034107  64 1046395   6590  0/0    0
  risoe-r02-f024  free     1* 1034109  32 1046397   8730  0/0    0
  risoe-r03-cn001  excl    29* 128946  28 133042   8266  1/1    1    100096 qyli
...

One of the most common bad behaviors of batch jobs is exhausting of available RAM memory.

An example of usage of pestat:

$ pestat | grep -e node -e 263945
  node state  load    pmem ncpu   mem   resi usrs tasks  jobids/users
  q008  excl  4.08    7974   4  18628   1275  1/1    4    263945 user
  q037  excl  4.02    7974   4  18628   1285  1/1    4    263945 user

The example job above is behaving correctly. Please consult the script located at `which pestat` for the description of the fields. The most important fields are:state = Torque state (second column)node can be free (not all the cores used), excl (all cores used) or down.load = CPU load average (third column)pmem = Physical memory (fourth column)amount of physical RAM installed in the nodencpu = total number of CPU cores (fifth column)resi = Resident (used) memory (seventh column)total memory in use on the given node (the one reported under RES by the "top" command),If used memory exceeds physical RAM on the node, or CPU load is significantly lower than number of CPU cores, the job becomes a candidate to be killed.An example of a job exceeding physical memory:

$ pestat -f | grep 128081
m016  busy* 4.00    7990   4  23992   9937* 1/1    4    128081 user
m018  excl  4.00    7990   4  23992   9755* 1/1    4    128081 user

An example of a job with incorrect CPU load:

$ pestat -f| grep 129284
a014  excl  7.00*  24098   8  72097   2530  1/1    8    129284 user

Searching for free resources

Show what resources are available for immediate use (see `Batch_jobs#batch-job-node-properties`_ for more options):Fatnode:

$ showbf -f fatnode

Thinnode:

$ showbf -f fatnode

pestat can also be used to check what resources are free:

$ pestat | grep free
  risoe-r01-f006  free    29* 1034109  32 1046397  13226  1/1    1    100074 user 1
  risoe-r01-f010  free   2.4* 1034109  32 1046397  79972  2/1    1*   20078 user 2
  risoe-r01-f013  free  0.84  1034109  32 1046397   8395  0/0    1    102268 user 3
  risoe-r02-f015  free  0.81  1034109  32 1046397   8212  0/0    1    102268 user 4
  risoe-r02-f017  free  0.15* 1034109  32 1046397   8489  0/0    1    102268 user 5
  risoe-r02-f023  free  0.56  1034109  32 1046397   8313  0/0    1    102268 user 5
  risoe-r02-f024  free  0.08* 1034109  32 1046397   8101  0/0    1    102268 user 5
  risoe-r02-f025  free  0.02* 1034109  32 1046397   7984  0/0    1    102268 user 5
  risoe-r08-cn289  free   1.4  128946  28 133042   3117  1/1    1    102536 user 5
  risoe-r08-cn300  free   1.5  128943  56 133039   6995  3/2    1*   102406 user 6
  risoe-r12-cn527  free   1.3  128946  28 133042   2741  1/1    1    10047 user 7
  risoe-r02-f018  free    29* 1034110  64 1046398  15376  1/1    1    99432 user 7

The node risoe-r01-f010 is occupied by 1 job (9th column) and two users (8th column) each requesting 1 core. The node risoe-r02-f024 is totally free.

Job control

Some commands only work for privileged accounts. Please contact Computerome support if you need to run these.

Canceling a given job:

Cancel job

$ mjobctl -c <jobid>

$ canceljob <jobid>

Force cancel job - try this if regular cancel fails

$ mjobctl -F <jobid>

Canceling all jobs of a given user (privileged command):

# mjobctl -c -w user=<someuser>

Re-queue a job (privileged command):

# mjobctl -R <jobex>

Change walltime (privileged command):

Changing the wallclock limit of a job by 10 hours 11 minutes and 12 seconds (request Computerome Support in good time to extend walltime for running job):

# mjobctl -m wclimit+=10:11:12 <jobex>

<jobex> is a regex(7) regular expression preceeded by x: e.g. "x:abc12[0-9]"

$ diagnose -f

Check resource usage of completed job (privileged command):

# tracejob -v <jobid>

Check job status:

$ checkjob -v <jobid>

Check when job will run:

$ showstart <jobid>

Special Solution for CPR users