Questions tagged [high-performance-computing]
Questions concerning high performance computing (HPC).
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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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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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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.
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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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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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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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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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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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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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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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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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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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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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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 ...
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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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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 ...
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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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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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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. ...
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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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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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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 ...
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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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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 ...
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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.
user1263
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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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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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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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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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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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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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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, ...
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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 ...
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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, ...
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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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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 ...
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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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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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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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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{...
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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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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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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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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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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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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 ...
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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 ...
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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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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 ...
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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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