5.USER-OMP package — LAMMPS 15 May 2015 version documentation

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# 5.USER-OMP package

The USER-OMP package was developed by Axel Kohlmeyer at Temple University. It provides multi-threaded versions of most pair styles, nearly all bonded styles (bond, angle, dihedral, improper), several Kspace styles, and a few fix styles. The package currently uses the OpenMP interface for multi-threading.

Here is a quick overview of how to use the USER-OMP package, assuming one or more 16-core nodes. More details follow.

    use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
    make yes-user-omp
    make mpi                                   # build with USER-OMP package, if settings added to Makefile.mpi
    make omp                                   # or Makefile.omp already has settings
    Make.py -v -p omp -o mpi -a file mpi       # or one-line build via Make.py

    lmp_mpi -sf omp -pk omp 16 < in.script                         # 1 MPI task, 16 threads
    mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
    mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task

Required hardware/software:

Your compiler must support the OpenMP interface. You should have one or more multi-core CPUs so that multiple threads can be launched by each MPI task running on a CPU.

Building LAMMPS with the USER-OMP package:

The lines above illustrate how to include/build with the USER-OMP package in two steps, using the “make” command. Or how to do it with one command via the src/Make.py script, described in Section 2.4 of the manual. Type “Make.py -h” for help.

Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must include “-fopenmp”. Likewise, if you use an Intel compiler, the CCFLAGS setting must include “-restrict”. The Make.py command will add these automatically.

Run with the USER-OMP package from the command line:

The mpirun or mpiexec command sets the total number of MPI tasks used by LAMMPS (one or multiple per compute node) and the number of MPI tasks used per node. E.g. the mpirun command in MPICH does this via its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.

You need to choose how many OpenMP threads per MPI task will be used by the USER-OMP package. Note that the product of MPI tasks * threads/task should not exceed the physical number of cores (on a node), otherwise performance will suffer.

As in the lines above, use the “-sf omp” command-line switch, which will automatically append “omp” to styles that support it. The “-sf omp” switch also issues a default package omp 0 command, which will set the number of threads per MPI task via the OMP_NUM_THREADS environment variable.

You can also use the “-pk omp Nt” command-line switch, to explicitly set Nt = # of OpenMP threads per MPI task to use, as well as additional options. Its syntax is the same as the package omp command whose doc page gives details, including the default values used if it is not specified. It also gives more details on how to set the number of threads via the OMP_NUM_THREADS environment variable.

Or run with the USER-OMP package by editing an input script:

The discussion above for the mpirun/mpiexec command, MPI tasks/node, and threads/MPI task is the same.

Use the suffix omp command, or you can explicitly add an “omp” suffix to individual styles in your input script, e.g.

    pair_style lj/cut/omp 2.5

You must also use the package omp command to enable the USER-OMP package. When you do this you also specify how many threads per MPI task to use. The command doc page explains other options and how to set the number of threads via the OMP_NUM_THREADS environment variable.

Speed-ups to expect:

Depending on which styles are accelerated, you should look for a reduction in the “Pair time”, “Bond time”, “KSpace time”, and “Loop time” values printed at the end of a run.

You may see a small performance advantage (5 to 20%) when running a USER-OMP style (in serial or parallel) with a single thread per MPI task, versus running standard LAMMPS with its standard un-accelerated styles (in serial or all-MPI parallelization with 1 task/core). This is because many of the USER-OMP styles contain similar optimizations to those used in the OPT package, described in Section accelerate 5.3.6.

With multiple threads/task, the optimal choice of number of MPI tasks/node and OpenMP threads/task can vary a lot and should always be tested via benchmark runs for a specific simulation running on a specific machine, paying attention to guidelines discussed in the next sub-section.

A description of the multi-threading strategy used in the USER-OMP package and some performance examples are presented here

Guidelines for best performance:

For many problems on current generation CPUs, running the USER-OMP package with a single thread/task is faster than running with multiple threads/task. This is because the MPI parallelization in LAMMPS is often more efficient than multi-threading as implemented in the USER-OMP package. The parallel efficiency (in a threaded sense) also varies for different USER-OMP styles.

Using multiple threads/task can be more effective under the following circumstances:

- Individual compute nodes have a significant number of CPU cores but the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx (Clovertown) and 54xx (Harpertown) quad-core processors. Running one MPI task per CPU core will result in significant performance degradation, so that running with 4 or even only 2 MPI tasks per node is faster. Running in hybrid MPI+OpenMP mode will reduce the inter-node communication bandwidth contention in the same way, but offers an additional speedup by utilizing the otherwise idle CPU cores.
- The interconnect used for MPI communication does not provide sufficient bandwidth for a large number of MPI tasks per node. For example, this applies to running over gigabit ethernet or on Cray XT4 or XT5 series supercomputers. As in the aforementioned case, this effect worsens when using an increasing number of nodes.
- The system has a spatially inhomogeneous particle density which does not map well to the domain decomposition scheme or load-balancing options that LAMMPS provides. This is because multi-threading achives parallelism over the number of particles, not via their distribution in space.
- A machine is being used in “capability mode”, i.e. near the point where MPI parallelism is maxed out. For example, this can happen when using the PPPM solver for long-range electrostatics on large numbers of nodes. The scaling of the KSpace calculation (see the kspace_style command) becomes the performance-limiting factor. Using multi-threading allows less MPI tasks to be invoked and can speed-up the long-range solver, while increasing overall performance by parallelizing the pairwise and bonded calculations via OpenMP. Likewise additional speedup can be sometimes be achived by increasing the length of the Coulombic cutoff and thus reducing the work done by the long-range solver. Using the run_style verlet/split command, which is compatible with the USER-OMP package, is an alternative way to reduce the number of MPI tasks assigned to the KSpace calculation.

Additional performance tips are as follows:

- The best parallel efficiency from omp styles is typically achieved when there is at least one MPI task per physical CPU chip, i.e. socket or die.
- It is usually most efficient to restrict threading to a single socket, i.e. use one or more MPI task per socket.
- IMPORTANT NOTE: By default, several current MPI implementations use a processor affinity setting that restricts each MPI task to a single CPU core. Using multi-threading in this mode will force all threads to share the one core and thus is likely to be counterproductive. Instead, binding MPI tasks to a (multi-core) socket, should solve this issue.

## Restrictions

None.