HPC/Submitting and Managing Jobs/Advanced node selection
Node Types
Hardware
Carbon has many major node generations, named genN for short, with N being an integer. In some generations, nodes differ further by the amount of memory.
Node Types
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 |
- Compute time is charged as the product of cores reserved × wallclock time × charge rate. The charge rate accommodates nominal differences in CPU speed.
- gen7 nodes have two GPUs each; GPU usage is currently not "charged" (accounted for) separately.
- Virtual memory usage on nodes may reach up to about 2 × the physical memory size. Your processes running under PBS may allocate that much vmem but cannot practically use it all for reasons of swap space size and bandwidth. If a node acitvely uses swap for more than a few minutes (which drastically slows down compute performance), the job will automatically be killed.
Major CPU flags
CPU capabilities grow with each node generation. Executables can be compiled to leverage specific CPU capabilities. Jobs using such executables must use the qsub option -l nodes=...:genX
to be directed to nodes having that capability.
Flag name | gen5 | gen6 | gen7 | gen8 |
---|---|---|---|---|
cat_l2 cdp_l2 cldemote gfni movdir64b movdiri pconfig sha_ni umip vaes vpclmulqdq | – | – | – | x |
avx512_bitalg | – | – | – | x |
avx512_vbmi2 | – | – | – | x |
avx512_vpopcntdq | – | – | – | x |
avx512ifma | – | – | – | x |
avx512vbmi | – | – | – | x |
avx512_vnni | – | – | x | x |
mpx | – | x | x | – |
avx512bw | – | x | x | x |
avx512cd | – | x | x | x |
avx512dq | – | x | x | x |
avx512f | – | x | x | x |
avx512vl | – | x | x | x |
art clwb flush_l1d ibpb mba md_clear ospke pku ssbd stibp tsc_deadline_timer xgetbv1 xsavec | – | x | x | x |
3dnowprefetch abm acpi aes aperfmperf apic arat arch_perfmon bmi1 bmi2 bts cat_l3 cdp_l3 cmov constant_tsc cqm cqm_llc cqm_mbm_local cqm_mbm_total cqm_occup_llc cx16 cx8 dca de ds_cpl dtes64 dtherm dts eagerfpu epb ept erms est f16c flexpriority fpu fsgsbase fxsr hle ht ida invpcid invpcid_single lahf_lm lm mca mce mmx monitor movbe msr mtrr nonstop_tsc nopl nx pae pat pbe pcid pclmulqdq pdcm pdpe1gb pebs pge pln pni popcnt pse pse36 pts rdrand rdseed rdt_a rdtscp rep_good rsb_ctxsw rtm sdbg sep smap smep smx ss sse sse2 sse4_1 ssse3 syscall tm tm2 tpr_shadow tsc tsc_adjust vme vmx vnmi vpid x2apic xsave xsaveopt xtopology xtpr | x | x | x | x |
avx | x | x | x | x |
avx2 | x | x | x | x |
fma | x | x | x | x |
adx | x | x | x | x |
sse4_2 | x | x | x | x |
Selecting node types for jobs
Jobs are directed automatically onto nodes of the same generation, with preference for gen2. 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 :gen6
or :gen8
. For example, to run on 2 nodes with 8 cores each:
Recommendations
- Avoid specifying a node generation unless you have a reason. This widens the pool of nodes suitable to run your job, thus decreasing wait times.
- With
ppn=16
your jobs may run on any node generation.
Advanced control of processeors-per-node (PPN)
Each Carbon node has nodes with different CPU core counts.
A request of ppn=16
in the job submission can get routed onto a node with exactly 16 cores, or the job can get routed to a node with more cores, shareable by other jobs.
You can specify if your application is fine to run on shared nodes or needs nodes for exclusive use, such as 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 $PBS_NODEFILE).
Select an option from the following scenarios.
- Permit other users and jobs
- When a job requires only a few cores and a commensurate fraction of other resources, simply specify
ppn
as needed:
#PBS -l nodes=nnn:ppn=4
- In this case, the remaining cores may be allocated to other jobs, which is the default policy:
#PBS -l naccesspolicy=SHARED
- Permit only your own jobs
#PBS -l nodes=nnn:ppn=2 #PBS -l naccesspolicy=SINGLEUSER -n
- Permit only one job per node, no sharing
- When your job requires only a few cores but a disproportionate fraction of another resource on a node (such as most of its memory or a lot of I/O bandwidth), claim the entire node:
#PBS -l nodes=nnn:ppn=4 #PBS -l naccesspolicy=SINGLEJOB -n
- PBS will reserve the entire node(s), but place each node name only
ppn
times in the$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.
Memory constraints
Jobs that do not use all cores on a node are subject to memory contraints,
such that memory on each node is allocated in rough proportion to the number of cores requested.
Specifically, most of Carbon's current nodes have 2 physical memory banks (sets of DIMM slots),
and only one of these is made accessible to jobs that request ppn ≤ nproc/2
,
i.e., half the number of physical cores per node nproc
.
To request access to all memory on a node for jobs with ppn < nproc
use the qsub -n
option, as shown in the solutions above.
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 -n
- 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 matchppn
. - 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, andncores=8
otherwise.
Multithreading using 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
#PBS -l naccesspolicy=SINGLEJOB -n
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=$PBS_NUM_PPN
...
programname …
Choose the number of cores n
such that 1 ≤ n ≤ 8 (or 16)
:
#PBS -l nodes=1:ppn=n
...
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=$PBS_NUM_PPN
...
programname …
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 $PBS_NODEFILE
. This will allow you to vary or override the nodes setting using "qsub -l nodes=…" without having to edit it twice in the job file.
OpenMP/MPI hybrid
Making efficient use of multithreading on multiple nodes which communicate over MPI is fairly involved and is subject to ongoing research. Since OMP_NUM_THREADS
is set to 1 by default on MPI satellite nodes, you must export this variable after you altered it in the job file.
#!/bin/bash
#PBS -l nodes=nnn:ppn=2
#PBS -l naccesspolicy=SINGLEJOB -n
# Calculate number of threads available per MPI process
cores_per_node=$( grep -c ^processor /proc/cpuinfo )
export OMP_NUM_THREADS=$(( cores_per_node / PBS_NUM_PPN ))
mpirun -x OMP_NUM_THREADS -machinefile $PBS_NODEFILE -np $PBS_NP \
programname …
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
It is assumed:
- The number of cores on the first node (running the job script) is the same as on the other nodes.
- All cores on a node will be used.
Advanced: PBS_* Variables
The following environment variables are provided in a job environment, with their value being computed any job runtime.
echo 'env | grep PBS_ | sort' | qsub -N inspect_env
# …
cat ~/inspect_env.o*
PBS_JOBNAME=jobname # from -N option, useful in job script for file names PBS_NP=1 # number of processors requested, automatically used for "mpirun -n …" PBS_NUM_NODES=1 # number of nodes, from resource "-l nodes=…" PBS_NUM_PPN=1 # ppn value, ditto PBS_NODEFILE=/var/spool/torque/aux/… # automatically used as "mpirun -machinefile …" option PBS_GPUFILE=/var/spool/torque/aux/… # file containing GPUs to access, present only with "-l nodes=…:gpus=…" PBS_MICFILE=/var/spool/torque/aux/… # (not applicable on Carbon) PBS_WALLTIME=3600 # requested (or default) walltime, in seconds PBS_ENVIRONMENT # useful for detection in scripts. Usually "PBS_BATCH", but "PBS_INTERACTIVE" under "qsub -I" # PBS internals PBS_JOBCOOKIE=643…31D7 PBS_JOBID=3141593.sched5.carboncluster PBS_MOMPORT=15003 PBS_QUEUE=batch PBS_TASKNUM=1 PBS_NODENUM=0 # usually always 0 (even on daughter nodes!) PBS_VNODENUM=0 # ditto. PBS_VERSION=TORQUE-4.2.10 PBS_O_QUEUE=batch PBS_O_SERVER=sched5 PBS_O_SUBMIT_FILTER=/usr/local/sbin/torque_submitfilter # Unix-like basics PBS_O_HOME=/home/username PBS_O_HOST=n123.carboncluster PBS_O_LANG=C # Unix locale(7) PBS_O_LOGNAME=username PBS_O_MAIL=/var/spool/mail/username PBS_O_PATH=/home/username/bin:… PBS_O_SHELL=/bin/bash PBS_O_WORKDIR=/home/username