Questions tagged [high-performance-computing]
Questions concerning high performance computing (HPC) as it relates to matter modeling.
33
questions
8
votes
0answers
58 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.
<...
8
votes
0answers
61 views
VASP's NPAR and KPAR for parallelization
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
341 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
67 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
159 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 ...
11
votes
3answers
272 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 ...
19
votes
6answers
4k 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
199 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 ...
7
votes
1answer
277 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
votes
2answers
70 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
54 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
40 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 ...
7
votes
0answers
51 views
What's the largest system we can study based on “fundamental limits to computation”?
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 ...
4
votes
0answers
82 views
Which DMRG package has the easiest learning curve?
I've been meaning to learn how to use DMRG (density matrix renormalization group) for a long time. Which package has the easiest learning curve? I specifically mean it should be easy to actually learn ...
9
votes
1answer
358 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 ...
10
votes
1answer
88 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 ...
8
votes
1answer
72 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 ...
37
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
109 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 ...
63
votes
6answers
7k 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 ...
15
votes
3answers
220 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 ...
23
votes
8answers
3k 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 ...
15
votes
2answers
317 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, ...
14
votes
3answers
273 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 ...
12
votes
1answer
318 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 ...
18
votes
4answers
3k 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 ...
15
votes
3answers
138 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. ...
11
votes
1answer
67 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, ...
10
votes
1answer
82 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 ...
16
votes
1answer
99 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 ...
8
votes
3answers
165 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, ...
10
votes
2answers
115 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, ...
18
votes
1answer
76 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 ...
