GROMACS 4.6: Running on GPUs

I mentioned before that I would write something on running on GPUs. Let’s imagine we want to simulate a solvated lipid bilayer containing 6,000 lipids for 5 µs. The total number of is around 137,000 and the box dimensions are roughly 42x42x11 nm. Although this is smaller than the benchmark we looked at last time, it is still a challenge to run on a workstation. To see this let’s consider running it on my MacPro using GROMACS 4.6.1. The machine is an and has 2 Intel Xeons, each with 4 cores. Using 8 MPI processes gets me 132 ns/day, so I would have to wait 38 days for 5 µs. Too slow!


You have to be careful installing non-Apple supported NVidia GPUs into MacPros, not least because you are limited to 2x6pin power connectors. Taking all this into account, the best I can do without doing something drastic to the power supply is to install an . Since I only have one GPU, I can only run one MPI process, but this can spawn multiple OpenMP threads. For this particular system, I get the best performance with 4 threads (134 ns/day) which is the same performance I get using all 8 cores without the GPU. So when I am using just a single core, adding in the GPU increases the performance by a factor of 3.3x. But as I add additional cores, the increase afforded by the single GPU drops until the performance is about the same at 8 cores.

Now let’s try something bigger. Our lab has a small Intel (Sandy Bridge) computing cluster. Each node has 12 cores, and there are 8 nodes, yielding a maximum of 96 cores. Running on the whole cluster would reduce the time down to 6 days, which is a lot better but not very fair on everyone else in the lab. We could try and get access to Tier-1 or Tier-0 supercomputers but, for this system, that is overkill. Instead let’s look at a Tier-2 machine that uses GPUs to accelerate the calculations.



The University of Oxford, through , has access to the machines owned by the Centre for Innovation. One of these, , is a GPU-based cluster. We shall look at one of the partitions; this has 60 nodes, each with two 6-core Intel processors and 3 NVIDIA M2090 Tesla GPUs. For comparison, let’s run without the GPUs. The data shown are for simulations with only 1 OpenMP thread per MPI process. So now let’s run using the GPUs (which is the point of this cluster!). Again just using asingle OpenMP thread per MPI process/GPU (shown on graph) we again find a performance increase of 3-4x. Since there are 3 GPUs per node, and each node has 12 cores, we could run 3 MPI processes (each attached to a GPU) on each node and each process could spawn 1, 2, 3 or 4 OpenMP threads. This uses more cores,  but since they probably would be sitting idle, this is a more efficient use of the compute resource. Trying 2 or 3 OpenMP threads per MPI process/GPU lets us reach a maximum performance of 1.77 µs per day, so we would get our 5 µs in less than 3 days. Comparing back to our cluster, we can get the same performance of our 96-core local cluster using a total of 9 GPUs and 18 cores on EMERALD.

Finally, let’s compare EMERALD to the Tier-1 PRACE supercomputer CURIE. CURIE was the . For this comparison we will need to use a bigger benchmark, so let’s us . It has 9x the number of lipids, but because I had to add extra water ends up being about 15x bigger at 2.1 million particles. Using 24 GPUs and 72 cores, EMERALD manages 130 ns/day. To get the same performance on CURIE requires 150 cores and ultimately CURIE tops out at 1,500 ns/day on 4,196 cores. Still, EMERALD is respectable and shows how it can serve as a useful bridge to Tier-1 and Tier-0 supercomputers. Interestingly, CURIE also has a “hybrid” partition that contains 144 nodes, each with 2 Intel Westmere processors and 2 NVIDIA M2090 Tesler GPUs. I was able to run on up to 128 GPUs with 4 OpenMP threads per MPI/GPU, making a total of 512 cores. This demonstrates that GROMACS can run on large numbers of GPU/CPUs and that such hybrid architectures are viable as supercomputers (for GROMACS at least).

GROMACS 4.6: Scaling of a very large coarse-grained system

So if I have a particular system I want to simulate, how many processing cores can I harness to run a single version 4.6 job? If I only use a few then the simulation will take a long time to finish, if I use too many the cores will end up waiting for communications from other cores and so the simulation will be inefficient (and also take a long time to finish). In between is a regime where the code, in this case GROMACS, scales well. Ideally, of course, you’d like linear scaling i.e. if I run on 100 cores in parallel it is 100x faster than if I ran on just one.

The rule of thumb for GROMACS 4.6 is that it scales well until there are only ~130 atoms/core. In other words, the more atoms or beads in your system, the larger the number of computing cores you can run on before the scaling performance starts to degrade.

As you might imagine there is a hierarchy of computers we can run our simulations on; this starts at humble workstations, passes through departmental, university and regional computing clusters before ending up at national (Tier 1) and international (Tier 0) high performance computers (HPC).

In our lab we applied for, and , a set of European Tier 0 supercomputers through PRACE. These are currently amongst the . We tested five supercomputers in all: (Paris, France; green lines), (Barcelona, Spain; black line), (Bologna, Italy; lilac), (Munich, Germany; blue) and (Stuttgart, Germany; red ). Each has a different architecture and inevitably some are slightly newer than others. CURIE has three different partitions, called thin, fat and hybrid. The thin nodes constitute the bulk of the system; the fat nodes have more cores per node whilst the hybrid nodes combine conventional CPUs with GPUs.

We tested a coarse-grained 54,000 lipid bilayer (2.1 million beads) on all seven different architectures and the performance is shown in the graph – note that the axes are logarithmic. Some machines did better than others; FERMI, which is an , appears not to be well-suited to our benchmark system, but then one doesn’t expect fast per-core performance on a BlueGene as that is not how they are designed. Of the others, MareNostrum was fastest for small numbers of cores, but its performance began to suffer if more than 256 cores were used. SuperMUC and the Curie thin nodes were the fastest conventional supercomputers, with the Curie thin nodes performing better at large core counts. Interestingly, the Curie hybrid GPU nodes were very fast, especially bearing in mind the CPUs on these nodes are older and slower than those in the thin nodes. One innovation introduced into GROMACS 4.6 that I haven’t discussed previously is one can now run either using purely MPI processes or a . We were somewhat surprised to find, that, in nearly all cases, the pure MPI approach remained slightly faster than the new hybrid parallelisation.

Of course, you may see very different performance using your system with GROMACS 4.6. You just have to try and see what you get! In the next post I will show some detailed results on using GROMACS on GPUs.