CP2K MPI/OpenMP-hybrid Execution (PSMP)

Overview

CP2K's grid-based calculation as well as DBCSR's block sparse matrix multiplication (Cannon algorithm) prefer a square-number for the total rank-count (2d communication pattern). This is not to be obfuscated with a Power-of-Two (POT) rank-count that usually leads to trivial work distribution (MPI).

It can be more efficient to leave CPU-cores unused in order to achieve this square-number property rather than using all cores with a "non-preferred" total rank-count (sometimes a frequency upside over an "all-core turbo" emphasizes this property further). Counter-intuitively, even an unbalanced rank-count per node i.e., different rank-counts per socket can be an advantage. Pinning MPI processes and placing threads requires extra care to be taken on a per-node basis to load a dual-socket system in a balanced fashion or to setup space between ranks for the OpenMP threads.

Because of the above-mentioned complexity, a script for planning MPI/OpenMP-hybrid execution (plan.sh) is available. Here is a first example for running the PSMP-binary on an SMP-enabled (Hyperthreads) dual-socket system with 24 cores per processor/socket (96 hardware threads in total). At first, a run with 48 ranks and 2 threads per core comes to the mind (48x2). However, for instance 16 ranks with 6 threads per rank can be better for performance (16x6). To easily place the ranks, Intel MPI is used:

mpirun -np 16 \
  -genv I_MPI_PIN_DOMAIN=auto -genv I_MPI_PIN_ORDER=bunch \
  -genv OMP_PLACES=threads -genv OMP_PROC_BIND=SPREAD \
  -genv OMP_NUM_THREADS=6 \
  exe/Linux-x86-64-intelx/cp2k.psmp workload.inp

NOTE: For hybrid codes, I_MPI_PIN_DOMAIN=auto is recommended as it spaces the ranks according to the number of OpenMP threads (OMP_NUM_THREADS). It is not necessary and not recommended to build a rather complicated I_MPI_PIN_PROCESSOR_LIST for hybrid codes (MPI plus OpenMP). To display and to log the pinning and thread affinization at the startup of an application, I_MPI_DEBUG=4 can be used with no performance penalty. The recommended I_MPI_PIN_ORDER=bunch ensures that ranks per node are split as even as possible with respect to sockets (e.g., 36 ranks on a 2x20-core system are put in 2x18 ranks instead of 20+16 ranks).

To achieve a similar placement with OpenMPI, ranks are mapped to "execution slots" (--map-by slot) along with specifying the number of processing elements (PE). By default, execution slots are counted in number of physical cores which yields --map-by slot:PE=3 for the same system (mentioned above).

mpirun -np 16 --map-by slot:PE=3 \
  -x OMP_PLACES=threads -x OMP_PROC_BIND=SPREAD \
  -x OMP_NUM_THREADS=6 \
  exe/Linux-x86-64-intelx/cp2k.psmp workload.inp

NOTE: Intel MPI's I_MPI_PIN_ORDER=bunch to balance the number of ranks between sockets (see above) appears hard to achieve with OpenMPI therefore an undersubscribed system may not be recommended. To display and to log the pinning and thread affinization at the startup of an application, mpirun --report-bindings can be used.

The end of the next section continues with our example and extends execution to multiple nodes of the above-mentioned system.

Plan Script

To configure the plan-script, the metric of the compute nodes can be given for future invocations so that only the node-count is required as an argument. The script's help output (-h or --help) initially shows the "system metric" of the computer the script is invoked on. For a system with 48 cores (two sockets, SMP/HT enabled), setting up the "system metric" looks like (plan.sh <num-nodes> <ncores-per-node> <nthreads-per-core> <nsockets-per-node>):

./plan.sh 1 48 2 2

The script is storing the arguments (except for the node-count) as default values for the next plan (file: $HOME/.xconfigure-cp2k-plan). This allows to supply the system-type once, and to plan with varying node-counts in a convenient fashion. Planning for 8 nodes of the above kind yields the following output (plan.sh 8):

================================================================================
384 cores: 8 node(s) with 2x24 core(s) per node and 2 thread(s) per core
================================================================================
[48x2]: 48 ranks per node with 2 thread(s) per rank (14% penalty)
[24x4]: 24 ranks per node with 4 thread(s) per rank (14% penalty)
[12x8]: 12 ranks per node with 8 thread(s) per rank (33% penalty)
--------------------------------------------------------------------------------
[32x3]: 32 ranks per node with 3 thread(s) per rank (34% penalty) -> 16x16
[18x5]: 18 ranks per node with 5 thread(s) per rank (25% penalty) -> 12x12
[8x12]: 8 ranks per node with 12 thread(s) per rank (0% penalty) -> 8x8
[2x48]: 2 ranks per node with 48 thread(s) per rank (0% penalty) -> 4x4
--------------------------------------------------------------------------------

The first group of the output displays POT-style (trivial) MPI/OpenMP configurations (penalty denotes potential communication overhead), however the second group (if present) shows rank/thread combinations with the total rank-count hitting a square number (penalty denotes waste of compute due to not filling each node). For the given example, 8 ranks per node with 12 threads per rank is chosen (8x12) and MPI-executed:

mpirun -perhost 8 -host node1,node2,node3,node4,node5,node6,node7,node8 \
  -genv I_MPI_PIN_DOMAIN=auto -genv I_MPI_PIN_ORDER=bunch -genv I_MPI_DEBUG=4 \
  -genv OMP_PLACES=threads -genv OMP_PROC_BIND=SPREAD -genv OMP_NUM_THREADS=12 \
  exe/Linux-x86-64-intelx/cp2k.psmp workload.inp

NOTE: For Intel MPI as well as OpenMPI, mpirun's host-list (mpirun -host) is setup with unique node-names, and this is the only style that is explained in this article. There is a competing style where nodes names are duplicated for the sake of enumerating available ranks (or "execution slots" in case of OpenMPI), which is not exercised in this article.

For OpenMPI, the quantity (per node) of the previously mentioned "execution slots" (measured in number of physical cores) are sometimes not known to OpenMPI (depends on cluster/scheduler setup). For instance, mpirun may be complaining about an attempt to use too many execution slots simply because OpenMPI believes all systems represent a single such slot (instead of 2x24 cores it only "sees" a single core per system). In such case, it is not recommended to "oversubscribe" the system because rank/thread affinity will likely be wrong (mpirun --oversubscribe). Instead, the list of unique nodes names (-host) may be augmented with the number of physical cores on each of the nodes (e.g., ":48" in our case).

mpirun -npernode 8 -host node1:48,node2:48,node3:48,node4:48,node5:48,node6:48,node7:48,node8:48 \
  --map-by slot:PE=6 --report-bindings \
  -x OMP_PLACES=threads -x OMP_PROC_BIND=SPREAD -x OMP_NUM_THREADS=12 \
  exe/Linux-x86-64-intelx/cp2k.psmp workload.inp

NOTE: It can be still insufficient to augment the nodes with the expected number of slots (:48). If OpenMPI's mpirun is still complaining, it might be caused and solved by the job scheduler. For example, qsub (PBS) may be instructed with -l select=8:mpiprocs=48 in the above case (mpirun in this job can use less than 48 ranks per node).

The plan-script also suggests close-by configurations (lower and higher node-counts) that can hit the square-property ("Try also the following node counts"). The example (as exercised above) was to illustrate how the script works, however it can be very helpful when running jobs especially on CPUs with not many prime factors in the core-count. Remember, the latter can be also the case for virtualized environments that reserve some of the cores to run the Hypervisor i.e., reporting less cores to the Operating System (guest OS) when compared to the physical core-count.

References

https://github.com/hfp/xconfigure/raw/master/config/cp2k/plan.sh
https://xconfigure.readthedocs.io/cp2k/
https://software.intel.com/content/www/us/en/develop/articles/pinning-simulator-for-intel-mpi-library.html