HPC/Submitting and Managing Jobs

Directories and Environment

First read: directory configuration.

Applications

We use the environment-modules package to manage user applications. This is similar to places like NERSC or PNNL. The basic CNM-specific user environment is configured automatically in /etc/profile.d/cnm.{sh,csh}.

For now the only applications are the Development tools.

Submitting jobs to Moab/Torque

 qsub [-A accountname] [options] jobfile

For details on options:

 man qsub
 qsub --help

More details are at the Torque Manual, in particular the qsub man page.

The single main queue is batch and need not be specified. All job routing decisions are handled by the scheduler. In particular, short jobs are accommodated by a daily reserved node and by backfill scheduling, i.e. "waving forward" while a big job waits for full resources to become available.

Debug queue

For testing job processing and your job environment, use qsub -q debug or #PBS -q debug. The queue accepts jobs under the following conditions

nodes <= 2
ppn <= 4
walltime <= 1:00:00

Checking job status

Use the command qstat (from PBS) or showq (from Moab):

qstat [-u $USER]

showq [-u $USER]

regular output

qstat -a

showq -n

alternate format (showing job names)

Getting extra information

qstat -n [-1] jobnum

Show nodes where a job runs.

qstat -f [jobnum] [-1]

Full information such as submit arguments and run directories. The "-1" option disables wrapping for long output lines.

checkjob [-v] jobnum

Get extended jobs status information – useful to diagnose problems with "stuck" jobs.

Removing jobs

To retract a queued job or terminate an already running job:

 qdel jobnumber

Example job file

• sample job file for Infiniband interconnect (recommended):

#!/bin/bash

##  Basics: Number of nodes, processors per node (ppn), and walltime (hhh:mm:ss)
#PBS -l nodes=5:ppn=8
#PBS -l walltime=0:10:00
#PBS -N job_name
#PBS -A account

## File names for stdout and stderr.  If not set here, the defaults
## are <JOBNAME>.o<JOBNUM> and <JOBNAME>.e<JOBNUM>
#PBS -o job.out
#PBS -e job.err

## send mail at begin, end, abort, or never (b, e, a, n)
#PBS -m ea

# change into the directory where qsub will be executed
cd $PBS_O_WORKDIR

# count allocated cores
NPROCS=`wc -l < $PBS_NODEFILE`

# start MPI job over default interconnect
mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
        programname

• If your program reads from files or takes options and/or arguments, use and adjust one of the following forms

mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
       programname  < run.in

mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
       programname  -options arguments < run.in

mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
       programname < run.in > run.out 2> run.err

In this form, anything after programname is optional. If you use specific redirections for stdout or stderr as shown (>, 2>), the job-global files job.out, job.err declared earlier will remain empty or only contain output from your shell startup files (which should really be silent), and the rest of your job script.

• Infiniband (OpenIB) is the default (and fast) interconnect mechanism for MPI jobs. This is configured through the environment variable $OMPI_MCA_btl.
• To select ethernet transport (e.g. for embarrasingly parallel jobs), specify an -mca option:

mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
	-mca btl self,tcp \
        programname

The account parameter

The parameter for option -A account is in most cases the CNM proposal, specified as follows:

cnm123

(3 digits) for proposals below 1000

cnm01234

(5 digits, 0-padded) for proposals from 1000 onwards.

user

(the actual string "user", not your user name) for a limited personal startup allocation

staff

for discretionary access by staff.

You can check your account balance in hours as follows:

mybalance -h
gbalance -u $USER -h

Node Types

Hardware

Carbon has two major node types, called gen1 and gen2, and gen2 is further differentiated by the amount of memory.

Node names, types	Node generation	Node extra properties	Node count	Cores per node (max. ppn)	Cores total, by type	Account charge rate	CPU model	CPUs per node	CPU nominal clock (GHz)	Mem. per node (GB)	Mem. per core (GB)	GPU model	GPU per node	VRAM per GPU (GB)	Disk per node (GB)	Year added	Note
Login
login5…6	gen7a	gpus=2	2	16	32	1.0	Xeon Silver 4125	2	2.50	192	12	Tesla V100	2	32	250	2019
Compute
n421…460	gen5		40	16	640	1.0	Xeon E5-2650 v4	2	2.10	128	8				250	2017
n461…476	gen6		16	16	256	1.0	Xeon Silver 4110	2	2.10	96	6				1000	2018
n477…512	gen6		36	16	576	1.0	Xeon Silver 4110	2	2.10	192	12				1000	2018
n513…534	gen7	gpus=2	22	32	704	1.5	Xeon Gold 6226R	2	2.90	192	6	Tesla V100S	2	32	250	2020
n541…580	gen8		20	64	2560	1.0	Xeon Gold 6430	2	2.10	1024	16				420	2024
Total			134		4736								48

Benchmarks show that gen2 nodes are about twice as fast as gen1 nodes for memory-intensive applications. (The X5300 series is hampered by a memory bandwidth bottleneck when all 8 cores are active and frequently access memory.) Thus, gen1 nodes are charged at a discounted rate of 50% of the walltime actually used.

Selecting node types for jobs

Jobs are directed automatically onto either gen1 or gen2 nodes, with preference for gen2 if both are available. Unless specifically requested, jobs will never mix generations. This will avoid disparate CPU speeds and MPI communication setup in a job. You can force jobs onto either node set in the job script after #PBS or on the qsub command line by suffixing the nodes= specifier with a property such as :gen1 or :gen2. For example, to run on 2 nodes with 8 cores each:

qsub -l nodes=2:ppn=8:gen1  foo.job	(not recommended for VASP)
qsub -l nodes=2:ppn=8:gen2  foo.job

The following are (as of now) equivalent, since "bigmem" currently implies "gen2":

qsub -l nodes=2:ppn=8:gen2:bigmem  foo.job
qsub -l nodes=2:ppn=8:bigmem       foo.job

See also: http://www.clusterresources.com/torquedocs21/2.1jobsubmission.shtml#resources

Special note for VASP

The following recommendation applies for VASP:

(1) single-node jobs:

• When on gen1 nodes use ppn=4 and disallow sharing

#PBS -l nodes=1:ppn=4:gen1 naccesspolicy=SINGLEJOB

• When on gen2, use ppn=7 or 8

#PBS -l nodes=1:ppn=8:gen2

(2) multi-node jobs: run on gen2 only, by using the following options for qsub or #PBS:

#PBS -l nodes=__:ppn=__:gen2

PPN Tricks

Each Carbon node has 8 cores, and for many jobs users indeed request entire nodes by specififying ppn=8 in the job submission. However, you may need to request fewer cores, e.g. for the following reasons:

• your application is not parallelized,
• your application has limited hardcoded parallelization, e.g. for 2 or 4 cores only,
• your application runs multi-threaded but uses $PBS_NODEFILE to infer the number of processes to start,
• your application runs busy service processes or service threads (e.g. NWChem),
• your application saturates a resource, e.g. memory bandwidth (some large VASP calculations),
• the node's memory is exhausted by fewer application processeses than there are cores available.

Depending on the reason, the node either may be or must not be used by other jobs. In the past, the only way to achieve exclusive but undersubscribed node access was to request ppn=8 and then to thin out a copy of the nodefile before passing it to the application. To eliminate the need to edit the nodefile, use the -l naccesspolicy=… flag to differentiate between resources requested from Moab from those passed to the application (in $PBS_NODEFILE).

Select an option from the following scenarios.

Shared vs. Exclusive Node Access

Permit other users and jobs

When a job requires only a few cores and a commensurate fraction of other resources, simply specify ppn as needed:

#PBS -l nodes=nnn:ppn=4

In this case, the remaining cores may be allocated to other jobs, which is the default policy:

#PBS -l naccesspolicy=SHARED

Permit only your own jobs

#PBS -l nodes=nnn:ppn=2
#PBS -l naccesspolicy=SINGLEUSER

Permit only one job per node, no sharing

When your job requires only a few cores but a disproportionate fraction of another resource on a node (such as most of its memory or a lot of I/O bandwidth), claim the entire node:

#PBS -l nodes=nnn:ppn=4
#PBS -l naccesspolicy=SINGLEJOB

PBS will reserve the entire node(s), but place each node name only ppn times in the $PBS_NODEFILE. This is also useful for MPI+OpenMP ("hybrid") programming, see below.

Permit only one of your jobs, and permit other user's jobs

#PBS -l nodes=nnn:ppn=4
#PBS -l naccesspolicy=UNIQUEUSER

The node is shared, but limited to one job for any given user.

Different PPN by node

When your first MPI process (the "master" process) requires more memory than your other "worker" processes, give several nodes specifications, separated by a "+" character (which is unusal and born of historical necessity):

#PBS -l nodes=1:ppn=1+2:ppn=4
#PBS -l naccesspolicy=SINGLEJOB

For clarity, the nodes specification in this example reads as follows:

nodes = ( 1:ppn=1 ) + ( 2:ppn=4 )

This will request 3 node exclusively, but the first node will occur only once in the $PBS_NODEFILE, e.g.

n011
n012
n012
n012
n012
n034
n034
n034
n034

In all of the preceding scenarios the following applies:

• The $PBS_NODEFILE seen by the job script will always match ppn.
• For accounting, the job will be billed by the number of cores blocked from use by other users, i.e., ncores=ppn for shared nodes, and ncores=8 otherwise.

Multithreading (OpenMP)

When you wish to use multithreading, you must ensure that the total number of "busy" user threads and processes corresponds to the number of cores requested from PBS. Today, multithreading in applications and libraries is typically programmed using the OpenMP interface and the number of threads is controlled by the environment variable $OMP_NUM_THREADS. Select from the following scenarios.

Pure OpenMP, single entire node

#PBS -l nodes=1:ppn=8

cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=8
...

Pure OpenMP, single node, possibly shared

choose the number of cores n such that 1 ≤ n ≤ 8:

#PBS -l nodes=1:ppn=n
...
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=`uniq -c $PBS_NODEFILE | awk '{print $1; exit}'`
...

Here, the default policy "SHARED" is in effect, and OMP_NUM_THREADS is set automatically by counting the number of times that the first node occurs in $PBS_NODEFILE. This will allow you to vary or override the nodes setting using "qsub -l nodes=…" without having to edit it twice in the job file.

OpenMP/MPI hybrid

Making efficient use of multithreading on multiple nodes which communicate over MPI is fairly involved and is subject to ongoing research. Since OMP_NUM_THREADS is set to 1 by default on MPI satellite nodes, you must export this variable after you altered it in the job file.

#!/bin/bash
#PBS -l nodes=nnn:ppn=4
#PBS -l naccesspolicy=SINGLEJOB

# Calculate number of threads available per MPI process
ppn_mpi=$( uniq -c $PBS_NODEFILE | awk '{print $1; exit}' )
ppn_phys=$( grep -c ^processor /proc/cpuinfo )
OMP_NUM_THREADS=$(( ppn_phys / ppn_mpi ))

mpirun -x OMP_NUM_THREADS \
    -machinefile $PBS_NODEFILE \
    -np `wc -l < $PBS_NODEFILE` \
    …

The -x option is specific to OpenMPI; please consult the documentation to achieve the same behavior in other MPI implementations.

The last example will ensure:

• you get allocated entire nodes (SINGLEJOB policy)
• you do not oversubscribe cores (OMP_NUM_THREADS is calculated from ppn)
• you only have one place to adjust (ppn), and can do so in the command line, or even post submission

Interactive node access

• You can use ssh to interactively access any compute node on which a job of yours is running. As soon as a node no longer runs at least one of your jobs, your ssh session to that node will be terminated.