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Questions tagged [high-performance-computing]

Questions concerning high performance computing (HPC).

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43 votes
14 answers
7k 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 ...
Thomas's user avatar
  • 9,132
13 votes
5 answers
2k 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 ...
Camps's user avatar
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39 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.
taciteloquence's user avatar
27 votes
9 answers
5k 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 ...
ksousa's user avatar
  • 4,108
12 votes
1 answer
497 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 ...
jw_'s user avatar
  • 405
9 votes
1 answer
613 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 ...
Anibal Bezerra's user avatar
25 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 ...
Wesley's user avatar
  • 1,040
20 votes
3 answers
1k 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, ...
B. Kelly's user avatar
  • 4,366
9 votes
1 answer
515 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....
user14717's user avatar
  • 359
9 votes
3 answers
1k views

What are the advantages of the Davidson diagonalization method over other sparse matrix diagonalization methods?

I am interested to understand the advantages of the Davidson diagonalization method over other sparse matrix diagonalization routines. For instance, Intel MKL.
Wychh's user avatar
  • 2,167
8 votes
5 answers
2k views

Suggestions on personal computers for matter modeling

While there's a lot of good information available out there about choosing laptops, I still find it hard to pick a personal machine for my scientific computing needs. Though most matter modelling ...
user avatar
3 votes
1 answer
103 views

Why is my CISD restart failing in PySCF?

A case that works In my answer to Restarting an FCI calculation in PySCF, I provided a folder full of input and output files that demonstrates saving (as a numpy ...
Nike Dattani - No Free Time's user avatar
24 votes
3 answers
12k 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 ...
ksousa's user avatar
  • 4,108
23 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 ...
Cody Aldaz's user avatar
  • 8,017
20 votes
4 answers
1k 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 ...
ksousa's user avatar
  • 4,108
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 ...
user1420303's user avatar
14 votes
3 answers
7k 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 ...
Parmeet Singh EP 066's user avatar
13 votes
2 answers
791 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: ...
Roman's user avatar
  • 2,373
11 votes
2 answers
2k 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 ...
DoubleKx's user avatar
  • 1,070
8 votes
1 answer
318 views

How can I build the wheels necessary for a quick installation of PySCFad on a "compute node"?

The following is the procedure I have been following: Install PySCFad ...
Nike Dattani - No Free Time's user avatar
8 votes
1 answer
2k 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 ...
Parmeet Singh EP 066's user avatar
19 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 ...
jboy's user avatar
  • 1,151
16 votes
3 answers
1k 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. ...
Anibal Bezerra's user avatar
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 ...
Jack's user avatar
  • 2,057
14 votes
1 answer
284 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 ...
ksousa's user avatar
  • 4,108
12 votes
3 answers
2k 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 ...
Parmeet Singh EP 066's user avatar
12 votes
2 answers
461 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 ...
megamence's user avatar
  • 4,171
11 votes
1 answer
124 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 ...
Thomas's user avatar
  • 9,132
11 votes
1 answer
2k 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 ...
TribalChief's user avatar
  • 2,361
11 votes
1 answer
256 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 ...
ksousa's user avatar
  • 4,108
10 votes
2 answers
389 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, ...
Cody Aldaz's user avatar
  • 8,017
9 votes
1 answer
819 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 ...
Protima Rani Paul's user avatar
9 votes
4 answers
526 views

What programs can do electron integrals and SCF calculations with more than one CPU?

Similar to this question which asks for each answer to provide one software that can do CASSCF: I am interested in software that can do integrals, SCF (Hartree-Fock), and the integral transformation, ...
Eugene Chybisov's user avatar
8 votes
0 answers
93 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 ...
Thomas's user avatar
  • 9,132
6 votes
1 answer
452 views

VASP Memory Estimate

Is there any way to get a memory estimate for VASP calculations either directly or indirectly (based on some example calculation)? For example, I would like to be able to predict based on my settings ...
Tristan Maxson's user avatar
3 votes
1 answer
177 views

Is PySCF able to print checkpoint files during a CISD calculation?

The problem I've described how to restart a CISD calculation in my answer to the question: Restarting an FCI calculation in PySCF, but this requires all iterations of the CISD calculation to finish, ...
Nike Dattani - No Free Time's user avatar
1 vote
1 answer
386 views

PySCF: How to do CCSD calculations from an FCIDUMP file in HDF5 format?

Recently my question: Why does CCSD work, but not CCSD(T), after reading an FCIDUMP in PySCF? lead to a bug fix that allows users to do CCSD(T) calculations from an FCIDUMP file in PySCF. That was ...
Nike Dattani - No Free Time's user avatar