Questions tagged [high-performance-computing]
Questions concerning high performance computing (HPC).
75
questions
6
votes
0answers
29 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 ...
7
votes
5answers
1k views
Suggestions on laptops 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 ...
5
votes
1answer
107 views
How to properly define %maxcore in ORCA
The %maxcore parameter in ORCA gives the memory per core needed for a calculation, however it is unclear to me if this should be the entire memory available to the ...
12
votes
2answers
379 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 ...
5
votes
0answers
26 views
Case study: KPOINT and band parallelization in Quantum ESPRESSO
I am testing Quantum ESPRESSO with different values for Npool and bands in order to calculate run time.
...
20
votes
10answers
4k views
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 ...
6
votes
0answers
35 views
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 ...
17
votes
3answers
2k views
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 ...
15
votes
3answers
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 ...
8
votes
1answer
55 views
Is there a standard file format for storing one and two electron integrals?
Is there any standard file format (.txt, .dat etc) for storing one and two electron integrals (generated from ab initio packages) which doesn't compromise on precision and is convenient for reading ...
6
votes
0answers
75 views
How to "Fill the CPU with OpenMP threads" to run QE-GPU
I am trying to run GPU enabled QE (QE 6.8 running on Ubuntu 18.04.5 LTS (GNU/Linux 4.15.0-135-generic x86_64) System Configuration: Processor: Intel Xeon Gold 5120 CPU 2.20 GHz (2 Processor) RAM: 96 ...
6
votes
2answers
87 views
Check the syntax of the VASP input file before running
I am a rookie in the DFT calculation area, I found that I could often make mistakes when writing a new input file, so I'd like to ask if there is a tool for checking the syntax and consistency of ...
6
votes
1answer
107 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
187 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
3k 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
99 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 ...
14
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
239 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
417 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,...
24
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
179 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
1k 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
126 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
100 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. ...
10
votes
1answer
304 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
138 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
78 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
289 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
437 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
407 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
262 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
204 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
448 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
138 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
331 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
373 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
121 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
400 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
94 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
179 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 ...
8
votes
0answers
128 views
Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF
I would like to use "fix deposit" with ReaxFF to add atoms to a simulation in which I deposit molecules on a surface.
I have built working scripts for my system with other force fields. ...
12
votes
3answers
631 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 ...
23
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
729 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
423 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 ...
