Questions tagged [high-performance-computing]
Questions concerning high performance computing (HPC) as it relates to matter modeling.
62
questions
6
votes
1answer
98 views
FireWorks for Workflow management or TensorFlow
In computational material science, we need workflows for optimization surrogate models which requires high computation resources. I am actually concerned with why material science community is using ...
8
votes
3answers
129 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.
13
votes
3answers
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 ...
10
votes
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 ...
4
votes
0answers
64 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
votes
3answers
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 ...
7
votes
1answer
166 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
votes
2answers
408 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
votes
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
votes
1answer
128 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
votes
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
votes
5answers
989 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
votes
1answer
114 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
votes
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
votes
1answer
92 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
votes
1answer
202 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
votes
1answer
135 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
votes
1answer
61 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
votes
1answer
286 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
votes
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
votes
2answers
424 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
votes
1answer
404 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
votes
2answers
214 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
votes
1answer
182 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
votes
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.
19
votes
2answers
415 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
votes
1answer
131 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
votes
2answers
310 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
votes
1answer
321 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
votes
0answers
110 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
votes
1answer
393 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
votes
2answers
87 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
votes
1answer
173 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
votes
3answers
552 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
votes
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
votes
2answers
553 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
votes
1answer
401 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 ...
12
votes
3answers
147 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 ...
5
votes
0answers
66 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
votes
1answer
61 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
votes
0answers
79 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 ...
8
votes
0answers
179 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
votes
1answer
464 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
votes
1answer
105 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
votes
1answer
161 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
votes
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
votes
1answer
161 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
votes
6answers
9k 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
votes
4answers
476 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
votes
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 ...