1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64
PRACE Benchmarks for GPAW ========================= GPAW ---- ### Code description [GPAW](https://wiki.fysik.dtu.dk/gpaw/) is a density-functional theory (DFT) program for ab initio electronic structure calculations using the projector augmented wave method. It uses a uniform real-space grid representation of the electronic wavefunctions that allows for excellent computational scalability and systematic converge properties. GPAW is written mostly in Python, but includes also computational kernels written in C as well as leveraging external libraries such as NumPy, BLAS and ScaLAPACK. Parallelisation is based on message-passing using MPI with no support for multithreading. Development branches for GPGPUs and MICs include support for offloading to accelerators using either CUDA or pyMIC/libxsteam, respectively. ### Download GPAW is freely available under the GPL license at: https://gitlab.com/gpaw/gpaw ### Install Generic [installation instructions](https://wiki.fysik.dtu.dk/gpaw/install.html) and [platform specific examples](https://wiki.fysik.dtu.dk/gpaw/platforms/platforms.html) are provided in the [GPAW wiki](https://wiki.fysik.dtu.dk/gpaw/). For accelerators, architecture specific instructions and requirements are also provided for [Xeon Phis](build/build-xeon-phi.md) and for [GPGPUs](build/build-cuda.md). Benchmarks ---------- ### Download The benchmark set is available in the [benchmark](benchmark/) directory or, for download, either directly from the [git repository](https://github.com/mlouhivu/gpaw-benchmarks/tree/prace) or from the PRACE RI website (http://www.prace-ri.eu/ueabs/). To download the benchmarks, use e.g. the following command: ``` git clone -b prace https://github.com/mlouhivu/gpaw-benchmarks ``` ### Benchmark cases #### Case S: Carbon nanotube A ground state calculation for a carbon nanotube in vacuum. By default uses a 6-6-10 nanotube with 240 atoms (freely adjustable) and serial LAPACK with an option to use ScaLAPACK. Expected to scale up to 10 nodes and/or 100 MPI tasks.
Input file: [benchmark/carbon-nanotube/input.py](benchmark/carbon-nanotube/input.py)
#### Case M: Copper filament A ground state calculation for a copper filament in vacuum. By default uses a 2x2x3 FCC lattice with 71 atoms (freely adjustable) and ScaLAPACK for parallelisation. Expected to scale up to 100 nodes and/or 1000 MPI tasks.
Input file: [benchmark/carbon-nanotube/input.py](benchmark/copper-filament/input.py)
#### Case L: Silicon cluster A ground state calculation for a silicon cluster in vacuum. By default the cluster has a radius of 15Å (freely adjustable) and consists of 702 atoms, and ScaLAPACK is used for parallelisation. Expected to scale up to 1000 nodes and/or 10000 MPI tasks.
Input file: [benchmark/carbon-nanotube/input.py](benchmark/silicon-cluster/input.py)
### Running the benchmarks No special command line options or environment variables are needed to run the benchmarks on most systems. One can simply say e.g. ``` mpirun -np 256 gpaw-python input.py ``` #### Special case: KNC For KNCs (Xeon Phi Knights Corner), one needs to use a wrapper script to set correct affinities for pyMIC (see [examples/affinity-wrapper.sh](examples/affinity-wrapper.sh) for an example) and to set two environment variables for GPAW: ```shell GPAW_OFFLOAD=1 # (to turn on offloading) GPAW_PPN=<no. of MPI tasks per node> ``` For example, in a SLURM system, this could be: ```shell GPAW_PPN=12 GPAW_OFFLOAD=1 mpirun -np 256 -bootstrap slurm \
./affinity-wrapper.sh 12 gpaw-python input.py
``` #### Examples Example [job scripts](examples/) (`examples/job-*.sh`) are provided for different systems together with related machine specifications (`examples/specs.*`) that may offer a helpful starting point.