Questions tagged [high-performance-computing]

Questions concerning high performance computing (HPC) as it relates to matter modeling.

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10
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5answers
2k views

Is Ubuntu the best option for DFT calculations?

I have just started studying DFT. I did some basic calculations using a Windows system. How will Ubuntu help me if I install it on my system? How much space should I allocate on drive for the Ubuntu ...
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0answers
45 views

How to run Quantum ESPRESSO on Google Cloud Services or Amazon Web Services

As I am exploring material simulations one really hard truth that I have realized is that my gaming laptop is not at all going to cut it for my research work. Currently I am trying to find the ...
13
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3answers
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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 ...
7
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1answer
129 views

Running Quantum ESPRESSO on a GPU in Windows

I have been using BURAI GUI for Quantum ESPRESSO for the calculation of optical properties of ZnSe. While running calculations I observed that my laptop's GPU was not even being used and I am a bit ...
16
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2answers
399 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,...
23
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6answers
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 ...
8
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1answer
98 views

Can I run an nscf calculation in Quantum ESPRESSO with disk_io='none'?

I had run an SCF calculation on a crystal system in Quantum ESPRESSO and had collected the converged charge density. However, during the NSCF calculation, there is the generation of ...
19
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3answers
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 ...
14
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5answers
971 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 ...
6
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1answer
90 views

What is the best setting for this workstation to speed up VASP calculations?

I am working on HP workstation with : 128 GB of RAM INTEL(R) XEON E5-2620 V3 with 12 cores What are the best settings of NCORE, ...
8
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4answers
2k views

How do I search for a particular string in Linux?

I want to search for a value in the VASP OUTCAR file i.e the format of the line should be Volume of Typ 1: 98.5 % What ...
10
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1answer
80 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. ...
7
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1answer
152 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 ...
13
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1answer
133 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, ...
6
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1answer
52 views

Understanding QuantumEspresso Toolbox through Maestro

Anyone here uses Quantum Espresso through Maestro can tell me a bit more about the calculation panel setting: I understand that -npools option must be divisible by ...
14
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1answer
285 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 ...
25
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1answer
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) ...
16
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2answers
412 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.?
12
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1answer
400 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 ...
13
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2answers
194 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 ...
12
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1answer
166 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{...
14
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2answers
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.
18
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2answers
396 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 ...
10
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1answer
120 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 ...
13
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2answers
287 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: ...
9
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1answer
290 views

Why does my calculation using GROMACS get stuck at step 0?

I have been using the HPCE on our campus for MD simulations using GROMACS. However, when I use the following script, after the job starts to run on the cluster, gets stuck at Step 0 in the log file. <...
10
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0answers
103 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 ...
9
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1answer
390 views

High precision helium energy

In the paper "High Precision Theory of Atomic Helium", Drake lists the then best-known ground state energy of the Schrödinger equation for helium to 22 digits as: $$\lambda_0 \approx -2....
10
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2answers
84 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 ...
10
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1answer
171 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 ...
12
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3answers
494 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 ...
22
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6answers
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 ...
11
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2answers
469 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 ...
9
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1answer
382 views

Is it possible to do TD-DFT/6-31G+(d,p) calculations on a laptop?

In the recent publication: "Density Functional Theory Calculation on the Structural, Electronic, and Optical Properties of Fluorene-Based Azo Compounds", the author claimed to have used ...
8
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2answers
91 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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0answers
65 views

Parallel algorithms on unstructured closed graphs [closed]

Some of the work I do in the study of discrete dislocation dynamics (a branch of materials modeling) involves topological changes on a graph: changes in the connectivity of nodes, as well as deletion ...
3
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1answer
59 views

How to simulate a furnace computationally

I am trying to synthesize MoSe$_2$ crystals in a furnace with two temperature zones. The problem is that the oven is not very wide, so the temperature of the hottest zone influences the temperature of ...
8
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0answers
77 views

What's the largest system we can study based on “fundamental limits to computation”? [closed]

If we have a (classical) computer about the size of a room and if its computational power is only limited by fundamental limits to computation, what is the largest system we can study using different ...
7
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0answers
155 views

What are some DMRG packages with an easy learning curve?

I've been meaning to learn how to use DMRG (density matrix renormalization group) for a long time. Which packages have an easy learning curve? I specifically mean it should be easy to actually learn ...
9
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1answer
459 views

Supercomputers around the world, which allow access for researchers outside the country

In a previous question it has been shown the computation capabilities of the countries all over the world. However, if I didn't miss something, the use of such supercomputers is limited to researchers ...
11
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1answer
103 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 ...
12
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1answer
157 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 ...
40
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14answers
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 ...
13
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1answer
153 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 ...
70
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6answers
8k 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 ...
16
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4answers
446 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 ...
27
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9answers
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 ...
17
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2answers
524 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, ...
16
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3answers
796 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 ...
21
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3answers
2k 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 ...