Questions tagged [high-performance-computing]

Questions concerning high performance computing (HPC).

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76 votes
6 answers
13k views

Did the 2019 discovery of O(N log(N)) multiplication have a practical outcome?

Some time ago I've read this news article, Mathematicians Discover the Perfect Way to Multiply, reporting a discovery published in 2019, where Harvey and Hoeven[1] found a algorithm able to execute ...
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44 votes
14 answers
6k views

Supercomputers around the world

For a matter modelling person, the most valuable resource is computing power. For many of us, computing power at hand limits the scale of problems we can solve. There are many national supercomputing ...
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36 votes
13 answers
3k views

What is a good programming language for matter modeling?

What is a good programming language for matter (e.g. molecular or materials) modeling? Since this is a broad field, I don't expect there to be only one answer.
26 votes
9 answers
4k views

Which Linux distribution is best for Matter Modeling?

In some science fields there are efforts to provide customized distributions, so you can get a productive environment with minimum set-up overhead. For example, in high energy particle physics, we ...
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26 votes
1 answer
4k views

How does the recent Chinese quantum supremacy claim compare with Google's?

Very recently, China claims achieving 'Quantum Supremacy' with the world's fastest Quantum Computer. Their computer was designed as a circuit of lasers, beam splitters and mirrors (see figure bellow) ...
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24 votes
6 answers
3k views

Are there critical mistakes to avoid when creating a workstation (32-128 cores)?

What are practical concerns for creating a workstation that will likely be expanded in the future to have more workstations/nodes? I am interested in running atomistic and quantum mechanical ...
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24 votes
6 answers
5k views

Is ARM64 the next big thing?

Considering how GPUs in matter modeling was first recognized in gaming devices like PlayStation, it is also interesting to consider whether ARM64 chips, which are the type of chips in modern smart ...
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23 votes
3 answers
7k views

Since MKL is not optimized for AMD hardware, should I use a math library specific to AMD, or would an open-source one be just as good?

The codes for quantum mechanical calculations make heavy use of linear algebra, and it seems most of them delegate this task to time-tested and highly optimized libraries, instead of trying to deploy ...
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22 votes
4 answers
3k views

Solving the Schrödinger equation as a service?

Does anyone know of a company with a cloud-based service which takes some representation of a molecule as an input, and then somehow solves the Schrödinger equation to some level of accuracy and ...
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20 votes
10 answers
4k views

GUIs for Quantum Chemistry... Where are they?

I have a general and maybe a little silly / funny question. Why don't most CompChem or QuantumChem software have a GUI? SIESTA is trying with Simune as far as I know, but even proprietary software ...
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20 votes
3 answers
785 views

Materials Modeling with Raspberry Pi?

Does anyone have any knowledge or direction for creating a homemade Beowolf cluster for materials modeling?I would like to be able to run my own "hobby" simulations at home, so a low energy, ...
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20 votes
2 answers
795 views

What is a chemputer?

I first saw the term "chemputer" when reading about the work of Neil Ostlund (who you may know as one of the authors of the famous book "Modern Quantum Chemistry"). Based on the ...
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19 votes
4 answers
4k views

Should I buy a CPU or a GPU for doing calculations?

A few years ago there was a significant difference between CPUs and GPUs for performing calculations. It was quite clear when to go for a CPU or a GPU. Today there are GPUs with a very large number ...
19 votes
1 answer
141 views

Are there any High-Throughput studies that aim to discover High Tc superconductors?

High-Throughput materials modeling based on Density Functional Theory has become very popular recently. If, for example, we search "High-Throughput Perovskites" in Google Scholar, we get over ~14,000 ...
18 votes
3 answers
2k views

Running Quantum ESPRESSO calculations in Google Colab

So one big problem I experience in doing calculations with Quantum ESPRESSO is that many calculations require a lot of computing power: you need large RAM capacities and powerful processors especially ...
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17 votes
4 answers
4k views

I am considering to purchase a GPU. What calculations would need FP32, and what would need FP64?

I would like to know how to choose the best GPU on the basis of its FP32 or FP64 efficiency, depending on different types of simulations. In brief I would like to know what types of simulations work ...
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17 votes
3 answers
2k views

What does ns/day mean in high-performance computing?

In MD simulation benchmarking, you often see performance expressed in terms of ns/day and hours/ns. How do I translate these ...
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16 votes
3 answers
440 views

Job scheduler alternatives

The power of computation required to perform a DFT calculation increases with the size of the system. Therefore, for some systems, is mandatory to use high-performance-computers, clusters, and grids. ...
16 votes
4 answers
710 views

Is there a set of updated, comprehensive benchmarks for speed comparison between different quantum chemistry packages?

I've found a page dedicated to quantum chemistry packages benchmarks, on GitHub, qmspeedtest. But most results there are several years old, and so probably outdated. Is there some place where we can ...
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16 votes
2 answers
433 views

How should I organize and keep track of a huge number of calculations systematically?

Doing matter modeling generates vast amounts of data. We might most probably be working on different projects simultaneously. We definitely will have to revisit old data for revisions, post-processing,...
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16 votes
2 answers
488 views

What's the best way to compare two DFT codes?

What's the most efficient way to compare the two DFT codes in terms of computation time, basis sets (for example, one plane wave vs one atomic orbitals), functional performance, etc.?
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16 votes
1 answer
130 views

What are typical RPA capabilities of plane-wave codes?

Plenty of standard plane-wave codes are able to compute correlation energies on top of DFT solutions using the random-phase approximation (RPA). I was wondering what the typical capabilities are in ...
14 votes
3 answers
2k views

How can I use a GUI on a supercomputer?

I am trying to make plots based to VASP simulation results, but I am struggling with how to download so much data from the server. A lot of examples on the internet are taught using the local desktop ...
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14 votes
2 answers
2k views

High-Performance Computing: What does "Mio CPUh" mean?

Sorry if this question is too simple for the community but I really could not find an explanation. A detailed answer would be appreciated.
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14 votes
1 answer
300 views

DFT Knowledge Check for Posed Problem

Currently I am trying to apply to a graduate program overseas. They require me to include a research proposal in my application. My topic of interest is computational materials science. So, one ...
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13 votes
5 answers
1k views

What are some cloud services for computing?

A group of researchers in my university (including me), started to study the possibility to move to cloud computing services in order to run our simulations. The simulation areas include condensed ...
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13 votes
3 answers
5k views

Should I connect 2-3 laptops to form a supercomputer?

I have recently started to use Quantum ESPRESSO for evaluating different properties of ZnSe Quantum Dots. But I currently don't have access to any cluster and as I am increasing the size of ...
13 votes
2 answers
470 views

How to get potential energy surface from GAMESS?

I'm trying to learn GAMESS and performing a simple PES scan of oxygen molecule. After the completion of the calculations I get a .log file with lots of sections like that: ...
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13 votes
1 answer
154 views

Are nuclear ab-initio methods related to materials ab-initio methods?

I just read this synopsis in Physics where scientists used first-principles nuclear physics calculations to predict the stability of 700 isotopes up to iron. I didn't know that this was possible, ...
13 votes
2 answers
568 views

Deciding the number of CPUs for a DFT calculation for band structure in Quantum ESPRESSO?

If I am using Quantum ESPRESSO for bandstructure calculations, how can I know the number of CPUs necessary for such a calculation? I deal mostly with ternary transition metal oxides which have at ...
13 votes
1 answer
327 views

What is the speed/time required for DFT simulations?

I am currently designing a toy model to calculate an interatomic potential (for an infinite repeating lattice) this toy model needs to scale and perform better than DFT simulations. But sadly I have ...
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12 votes
3 answers
1k views

How can I submit jobs to an HPC scheduler?

It is my first time trying to use an HPC system and I am a bit overwhelmed. I have gone through a course on using HPC systems on Coursera and have a basic idea about using Linux. Could you guys tell ...
12 votes
3 answers
157 views

Citizen science projects in Matter Modeling

According to Wikipedia, Volunteer computing is a type of distributed computing in which people donate their computers' unused resources to a research-oriented project An example of a volunteer ...
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12 votes
3 answers
1k views

External magnetic field in VASP?

I have never found any tags or documentation regarding external magnetic field in VASP but in different well known published articles$^1$, the implementation of the external magnetic field by VASP has ...
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12 votes
2 answers
412 views

What kind of systems do we need to coarse-grain to observe interesting phenomena?

When I go to talks, I hear the statement "coarse-graining is required to access spatio-temporal scales to observe important dynamical behavior for stimuli-responsive systems" before they go ...
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12 votes
1 answer
444 views

Are there examples of ab initio predictions on small molecules without the "major approximations"?

In most textbooks the precise Schrödinger euqation of a molecule is given (and the "beautiful thing" stops here), then born oppenheimer approximation is made, then layers of other ...
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12 votes
1 answer
221 views

Analog computing in matter modeling today: Any applications?

When we think about computers and computing today, almost invariably we think about digital computers, the ever-present objects today. But reading this question in the Chemistry stackexchange, How are ...
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12 votes
1 answer
395 views

Parallelization levels on Quantum ESPRESSO

Quantum ESPRESSO presents several levels of parallelization, including worlds, images, polls, and so on. However, there is a very intricate (and not clear to me) relationship between k-point sampling, ...
12 votes
1 answer
111 views

Benchmarking Monte Carlo simulations of polymers

I have written a simulation engine in C++ to run a Monte Carlo simulation of polymers on a lattice. My code basically plants a polymer on a lattice, and performs certain Monte Carlo moves, including ...
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12 votes
1 answer
373 views

Geometric optimization taking a long time. Are my convergence criteria too tight in CP2K?

I have been having trouble with the VIBRATIONAL_ANALYSIS routine. Namely, the routine keeps timing out. I am trying to find the vibrational modes of Pyridine in a non periodic system, as well as $\ce{...
11 votes
2 answers
1k views

Parallelization in VASP

I have a system that has 1 k-point, 54 atoms, NBANDS=152, and NGZ=80. I'm running an AIMD simulation on VASP version 5.4.4 The ...
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11 votes
1 answer
115 views

Which schedulers are compatible with a virtual machine?

I have an old TORQUE cluster (out of support) with 4 nodes running on Cent OS 6 and I am having trouble using the latest versions of Matter Modelling software. I recently came across Quantum Mobile ...
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11 votes
1 answer
179 views

What are the trade-offs setting DIRSCF to either .TRUE. or .FALSE. (the default) in GAMESS (US)?

The first software I used to run calculations was Gaussian09. When submitting a input, I used to see a pattern of resource usage where the allocated CPU quickly maxed out, remaining high most of the ...
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10 votes
2 answers
248 views

Why is Q-Chem producing a parallel efficiency greater than 1?

The efficiency $E$ of a parallel calculation is defined as \begin{align} E &= \frac{S}{N}, & S &= \frac{T_1}{T_N}, \end{align} where $S$ is the speedup and $N$ is the number of workers, ...
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10 votes
1 answer
757 views

How to understand the wavefunction outputed by QE with HDF5 format?

Following the answer to my question: What is the best program to manipulate numerical DFT wavefunctions to calculate custom matrix elements?, I compiled Quantum ESPRESSO with the hdf5 flag on, and now ...
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10 votes
1 answer
223 views

Are QMC calculations practical for periodic structure calculations?

Even some DFT methods or beyond DFT methods such as MP2 calculations are computationally very expensive today even with clusters. If you compare QMC (quantum monte carlo) calculations with them, are ...
  • 1,889
10 votes
2 answers
196 views

Choosing RAM, CPU time, # of cores, and other parameters for an MD run

I did an AIMD run in VASP using 64 cores (32 cores/node) and 250 GB of memory (125 GB/node) for 5 ps (1 fs time step). The calculation took 12.6 hours to complete. CPU efficiency was 99.7% and memory ...
  • 1,050
10 votes
1 answer
147 views

Is Wannier 90 computationally expensive to run?

I'm extremely new to the Wannier90 code. I was planning to install it on a workstation I have but I would be using the cores to run calculations using Quantum ESPRESSO. I have a few quad core i5 PC's. ...
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10 votes
1 answer
204 views

When running DFT on Q-Chem with an HPC cluster, why is parallelization with OpenMP faster than with MPI?

How to maximize the efficiency/time-to-solution of the calculations in Q-Chem on HPC clusters? MPI parallelization is supposed to improve time-to-solution as compared to OpenMP. The system I tested ...
10 votes
0 answers
136 views

I have access to 1000 cores across 10 nodes, what would be the best way to prallelize an MP2, GW, or RPA calculation for a periodic system in VASP? [closed]

What's the best way for parallelization in VASP for periodic systems? In the documentation, it mostly explains it for the local computer and molecule calculation. Apparently, these explanations don't ...
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