GSoC 2020 wrap-up

Google Summer of Code 2020

Google Summer of Code 2020 wrapped up! It was a very successful GSoC Summer for MDAnalysis with three great projects. Even more importantly, we got to engage with three outstanding students: Hugo MacDermott-Opeskin, Yuxuan Zhuang, and Cédric Bouysset.

You can read more about their projects in their blog posts:

Finally, a big thank-you to our GSoC mentors: @IAlibay, @acpmnv, @fiona-naughton. Their constant and enthusiastic engagement was crucial to the success of our students.

— Org Admins (@richardjgowers, @kain88-de, @orbeckst)

GSoC Report: Trajectory New Generation: the trajectory format for the future of simulation

This is the end?

Well well well, here we are at the end of GSoC! What a ride it has been, giving me a chance to improve my skills and contribute in ways I never thought would be possible. Thanks to all my mentors @acpmnv (Paul), @orbeckst (Oliver) and @richardjgowers (Richard) for all the help and guidance throughout.

Why TNG?

Trajectory storage has proved problematic for the molecular simulation community, due to large file sizes, poor portability and low metadata incorporation. As hardware and software advances enable the creation of larger and more complex datasets, shortcomings in trajectory formats have been highlighted. The Trajectory New Generation (or TNG) format 1,2 designed by GROMACS aims to remove these shortcomings, enabling flexible compression, metadata incorporation small file sizes combined with a lightweight API.

Despite its many advantages, the TNG format has not seen widespread adoption, as tooling to support the format is lacking. Creation of new TNG tooling has been hindered by the current design and implementation of the TNG library in older style C code. My project centered around improving implementation and tooling for the TNG format. Our primary aims were two fold, with the first half of my project working on converting the original library to C++ and the second half on developing some Python bindings so that the format can be read into MDAnalysis.

TNG time!

I started GSoC working on the TNG library with the aim of adding tests, understanding the API and converting the older C style API it to C++. I worked on this for the majority of the bonding period as well as the first and some of the second coding period.

First I added tests in !3 which then revealed problems in the base API that were fixed in !6, !12 and !17. I then made these additional tests into a formal test suite employing GoogleTest in !16, !20 and !21. This revealed some more API elements that could be improved which were touched up in !22, !23 and !25.

Using GoogleTest, a typical regression test looked a lot like this:

TEST_F(ArgonCompressedTest, BoxShapeValues)
    int64_t             stride_length, i;
    tng_function_status read_stat;
    read_stat = tng_util_box_shape_read(traj, &box_shape, &stride_length);
    EXPECT_EQ(read_stat, TNG_SUCCESS);
    // box_shape frame 0
    const std::vector<float> frame_0  = {
        3.60140, 0.00000, 0.000000, 0.000000, 3.60140, 0.000000, 0.000000, 0.000000, 3.60140,
    ASSERT_EQ(frame_0.size(), 9);
    // compare element by element
    for (i = 0; i < 9; i++)
        EXPECT_FLOAT_EQ(box_shape[i], frame_0[i]);


Now you can just make test to ensure your TNG times will be fun times!

Once we had a test suite that could be used to check library correctness on the major routines we started to work on the TNG library itself. Key goals were C++ compilation and in turn modernisation of the library routines to modern C++. I achieved full C++ compilation in a combination of !26, !27, !29, !33 and !34.

Moving the project to C++ appeared simple at the top level:

set_source_properties(SOURCE ... LANGUAGES CXX)

Where all .c files should be renamed to .cpp (primarily so clang will read them as C++ correctly). Then the hard part! Non ISO C then had to be made ISO C++. An example of this is given below:

void DECLSPECDLLEXPORT* Ptngc_warnmalloc_x(size_t size, char* file, int line);
#define warnmalloc(size) Ptngc_warnmalloc_x(size, __FILE__, __LINE__)

Use of this macro performs a void to T implicit cast which has deprecated in C++ as being unsafe. In C++ this requires an explicit cast with static_cast<T>():

//explicitly cast
unsigned int*  dict = static_cast<unsigned int*>(warnmalloc(0x20004 * sizeof *dict));

Also important, although technically ISO compliant, was turning C style casts into explicit (explicitly ugly) C++ casts:

md5_append(md5_state, (md5_byte_t*)str, len);
// to this (wow disgusting)
md5_append(md5_state, reinterpret_cast<md5_byte_t*>(const_cast<char*>(str)), len);

There were loads and loads of these throughout the library, which hopefully look a lot more like C++ now.

From here I started on modernisation of the library classes and constructs to modern C++. These progressed in !28 which outlined the structure we were aiming for, !32 which defined a specific API for blocks, !35 that updated the trajectory API and !36 which progressed on the IO elements.

An example of a modernisation change to the TNG API involves the use of templates to simplify the definition of TNG data blocks. A complicated struct that carried around a void* array for the data and a tng_datatypes enum to indicate the data type contained in the block could instead be a templated class as is shown below:

template<typename T> // type for data array
TngDataBlock<T>::TngDataBlock(const int64_t&     id,
                            // other stuff
                              T*                 values) :

Template specialization is then used to do the correct operations for each datatype, reducing a lot of very repetitive code paths into a few simpler statements.

Refactoring the TNG library was a huge task, much more so than initially anticipated. Due to this and some changing circumstances, the aforementioned modernisation MRs are all still open with more work required. I plan on working on these into the future but progress will be slow as I do not have solid blocks of time to dedicate.

All the work I have done on TNG itself can be found in my TNG fork as well as open PRs on the TNG library itself.

PyTNG time!

From here I switched focus to PyTNG, a set of Python bindings designed for use by MDAnalysis although technically a separate library. I worked on PyTNG for most of the second half of GSoC. This required changing gears a little bit as well as learning Cython, which was initially a bit of a learning curve for me.

Firstly I changed the TNG libraries exported with PyTNG itself to include the bugfixes obtained as part of the earlier improvements to the TNG library. This was incorporated as part of #28. I then improved the TNG library calls in PyTNG in #29.

Following some design discussions, we then moved towards a newer design for the bindings, so as to be able to read all the blocks available in a TNG file with maximal speed. This was achieved in merging #32 and ongoing work in #38, which are a total redesign of the whole PyTNG API.

The end result of this is a working implementation that can read any TNG block as of #32 with improvements close in #38. I also added docs and examples as part of #38. Profiling and timings indicated high performance of the bindings, with the library largely IO bound at the TNG API (pure C) level.

An example of how to use PyTNG to read a TNG file and extract positions is shown below:

   import pytng
   import numpy as np

   with pytng.TNGFileIterator("traj.tng", 'r') as tng:

      # make a numpy array to hold the data using helper function
      # this array will then be updated in-place 
      positions = tng.make_ndarray_for_block_from_name("TNG_TRAJ_POSITIONS")
      # the TNG API uses regular strides for data deposition,
      # here we stride over the whole trajectory for the
      # frames that have position data
      # where len(tng) is the total number of steps in the file.

      for ts in tng[0:len(tng):tng.block_strides["TNG_TRAJ_POSITIONS"]):
         # read the integrator timestep
         # then, get the data from the requested block by
         # supplying NumPy array which is updated in-place

What can we do now?

  • The TNG library now has a regression-test suite
  • The TNG library can be compiled as C++ 14 with a modern compiler.
  • The groundwork is also laid for further improvements of the library.
  • PyTNG has a (larger) regression-test suite
  • PyTNG is now a set of (more) functional bindings for the TNG format that can read any TNG block!

Looking forward

I plan on extending PyTNG to TNG writing as well as integrating PyTNG into MDAnalysis following GSoC. I have raised issues in PyTNG to make sure things that still need to be completed are apparent to people following on. I also aim to keep working on TNG itself time permitting.

What have I learnt?

Things I have learned in GSoC include

  • C++ class design
  • C++ for binary IO
  • CMake, GoogleTest and how to refactor a large codebase
  • Cython and Python/C integration
  • Working collaboratively on a diverse global team

My experience

GSoC was a fantastic experience for me, as I felt very welcome amongst two communities (MDAnalysis and GROMACS). I hope I was able to give back! I was constantly challenged throughout and this helped me learn and grow with big improvements both in my technical skills and approach to computational problem solving.

Thanks all for having me along!


GSoC Report: Serialize Universes for parallel

As we approach the exascale barrier, researchers are handling increasingly large volumes of molecular dynamics (MD) data. Whilst MDAnalysis is a flexible and relatively fast framework for complex analysis tasks in MD simulations, implementing a parallel computing framework would play a pivotal role in accelerating the time to solution for such large datasets. In this Google Summer of Code project, we tried to touch on the basics to make sure the fundamental data structure of MDAnalysis—Universe can be serialized, and also streamlined the parallel framework.

Why and how do we serialize a Universe

A very short answer is: for multiprocessing. You know, processes don’t share memory in python. The pythonic way to share information between processes is called serialization—“Pickler” converts the objects into bytestream; “Unpickler” deciphers the bytestream into objects again. During serialization, states are conserved! But it does not sound as simple as it is; and of course, data structures as complex as Universe cannot be serialized easily. What we did in MDAnalysis, is taking the advantage of object composition in python and managing to serialize all the pieces and bits—topology and trajectory—that are crucial for reconstituting a parallel Universe.

One of the fundamental features of MDAnalysis is its ability to create a trajectory reader without loading the file into memory. It provides users with the ability not to ramp up their memory with huge trajectory files, but only loading the current frame into memory (and also random accessing all the frames). It is troublesome in the sense that the I/O Reader of python for such functionality is not picklable. One of the main achievements in PR #2723 is creating a pickling interface for all the trajectory readers.

Another key component of the Universe is its attached AtomGroup. Serializing AtomGroup before was error-prone. Users had to be super-cautious to first recreate/serialize a Universe then AtomGroup. Besides AtomGroup could not be serialized alone; when adding a reference from another Universe, it could only be the positions of the atoms but not AtomGroup itself. After the change in PR #2893, AtomGroup can be serialized alone; if it is pickled with its bound Universe, it will be bound to the same one after serialization; if multiple AtomGroup are serialized together, they will recognize if they are bound to the same Universe or not.

Finally, one of the coolest features that were introduced in version 0.19.0 is on-the-fly transformations (also as a previous GSoC project). You might wonder if you can perform a parallel analysis on a trajectory with the on-the-fly transformation present. Yes, you can…after PR #2859 is merged! You may want to find your favorite collective variables, and guide your further simulations, but most analysis has to be done on an ensemble of aligned trajectories. With the change, you can write a script to run the analysis directly on the supercomputer on-the-fly without jumping into the “trjconv hell”…and in parallel!

Okay enough technical terms talking. More information on serialization can be found in the online docs of MDAnalysis 2.0.0-dev; we also provide some notes on what a developer should do when a new format is implemented into MDAnalysis.

Parallelizing Analysis

So what’s possible now in MDAnalysis? Well you still cannot do since the AnalysisBase API is too broad and we don’t really want to ruin your old scripts. What you can do now is use your favorite parallel tool freely (multiprocessing, joblib, dask, and etc.) on your personal analysis script. But before that, we should point out that per-frame parallel analysis normally won’t reach the best performance; all the attributes (AtomGroup, Universe, and etc) need to be pickled. This might even take more time than your lightweight analysis! Besides, e.g. in dask, a huge amount of time is needed overhead to build a comprehensive dask graph with thousands of tasks. The strategy we take here is called split-apply-combine fashion (Read more about this here Fan, 2019), in which we split the trajectory into multiple blocks, analysis is performed separately and in parallel on each block, then the results are gathered and combined. Let’s have a look.

As an example, we will calculate the radius of gyration. It is defined as:

def radgyr(atomgroup, masses, total_mass=None):
    # coordinates change for each frame
    coordinates = atomgroup.positions
    center_of_mass = atomgroup.center_of_mass()
    # get squared distance from center
    ri_sq = (coordinates-center_of_mass)**2
    # sum the unweighted positions
    sq = np.sum(ri_sq, axis=1)
    sq_x = np.sum(ri_sq[:,[1,2]], axis=1) # sum over y and z
    sq_y = np.sum(ri_sq[:,[0,2]], axis=1) # sum over x and z
    sq_z = np.sum(ri_sq[:,[0,1]], axis=1) # sum over x and y
    # make into array
    sq_rs = np.array([sq, sq_x, sq_y, sq_z])
    # weight positions
    rog_sq = np.sum(masses*sq_rs, axis=1)/total_mass
    # square root and return
    return np.sqrt(rog_sq)

We will load the trajectory first.

u = mda.Universe(adk.topology, adk.trajectory)
protein = u.select_atoms('protein')

Split the trajectory.

n_frames = u.trajectory.n_frames
n_blocks = n_jobs   #  it can be any realistic value (0<n_blocks<=n_jobs, n_jobs<=n_cpus)

frame_per_block = n_frames // n_blocks
blocks = [range(i * frame_per_block, (i + 1) * frame_per_block) for i in range(n_blocks-1)]
blocks.append(range((n_blocks - 1) * frame_per_block, n_frames)) 

Apply the analysis per block.

A simple version of split-apply-combine code looks like this, it is decorated by dask.delayed, so it won’t be executed immediately:

def analyze_block(blockslice, func, *args, **kwargs): 
    result = [] 
    for ts in u.trajectory[blockslice.start:blockslice.stop]: 
        A = func(*args, **kwargs) 
    return result

We then create a dask job list; the computed results will be an ordered list.

jobs = []
for bs in blocks:
    jobs.append(analyze_block(bs, radgyr, protein, protein.masses, total_mass=np.sum(protein.masses)))
jobs = dask.delayed(jobs)


results = jobs.compute()

How tasks are divided can be visualized by jobs.visualize() and a detailed task stream can be viewed from dask dashboard—Each green bar here represents a block analysis job.

Visualize dask graph

Task stream

Combine the results.

result = np.concatenate(results)
result = np.asarray(result).T

labels = ['all', 'x-axis', 'y-axis', 'z-axis']
for col, label in zip(result, labels):
    plt.plot(col, label=label)
plt.ylabel('Radius of gyration (Å)')

Radius of gyration results

A detailed UserGuide on how to parallelizing your analysis scripts can also be found here: User Guide: Parallelizing Analysis.

Future of parallel MDAnalysis

Of course, we don’t want to limit ourselves to some simple scripts. In Parallel MDAnalysis (PMDA), we are trying out what might be possible (PR #128, #132, #136 with this new feature to build a better parallel AnalysisBase API for the users. After PR #136, you will be able to use native features from dask to build complex analysis tasks and run multiple analyses in parallel as well:

u = mda.Universe(TPR, XTC)
ow = u.select_atoms("name OW")
D = pmda.density.DensityAnalysis(ow, delta=1.0)

# Option one (, n_jobs=2)

#  Option two
D.compute(n_jobs=2)   #  or dask.compute(D)

#  furthermore
dask.compute(D_1, D_2, D_3, D_4...)  #  D_x as an individual analysis job.


These three months of GSoC project have been fun and fruitful. Thanks to all my mentors, @IAlibay, @fiona-naughton, @orbeckst, and @richardjgowers, (also @kain88-de and other developers) for their help, reviewing PRs, and providing great advice for this project. Now MDAnalysis has a more streamlined way to build parallel code for the trajectory analysis. What’s left to do is reaching a consensus on what the future parallel analysis API should look like, optimizing the dask worker footprint, reducing the time for the serialization process, and conducting conclusive benchmarks on different parallel engines.



The benchmark below was run with four AMD Opteron 6274 (64 cores in total) on a single node. The test trajectories (9000 frames, 111815 atoms) were available at the YiiP Membrane Protein Equilibrium Dataset.

Three test cases were conducted under the latest MDAnalysis and PMDA code (PR #136)—RMSD analysis, a more compute-intensive RDF analysis, and the newly supported RMSD analysis with on-the-fly transformation (fit-rot-trans transformation in this case). All these cases show a strong scaling performance before 16 cores.


(Black dash line: ideal strong scaling performance; Blue: parallel performance (the number of blocks being splitted ie equal to the number of cores being used)

Major merged PRs

  • #2723 Basic implementation of Universe and trajectory serialization. Tests and documents.
  • #2815 Refactor ChainReader and make it picklable
  • #2893 Make AtomGroup picklable
  • #2911 Fix old serialization bugs to DCD and XDR formats

PRs to be merged

  • #2859 Serialization of transformations
  • #132 Refactor PMDA with the new picklable Universe
  • #136 New idea on how to refactor PMDA with dask.DaskMethodsMixin.
  • #102 UserGuide on how users can write their own parallel code.