Questions tagged [high-performance-computing]
Questions concerning high performance computing (HPC).
90
questions
3
votes
0
answers
17
views
Problem with installation of Multiwell Software package and open mpi
I'm trying to install Multiwell including Thermo. The manual says under 1.4. that I have to install openmpi before. So I followed the instructions from the multiwell manual but get an error at 8.) &...
- 806
5
votes
2
answers
138
views
How to do a loop in Ubuntu?
I want to run multiple Gaussian jobs (one after one). I have a folder which contains more than 30 molecules and I want my calculation to start with molecule 1 then when the job is finished, start the ...
- 441
8
votes
0
answers
128
views
Different Results obtained while doing multiple runs from same inputs in VASP
I have been trying to optimize the parallelization parameters in VASP. By varying the parameters(such as KPAR and NCORE) I am trying to reduce the Elapsed time that is printed at the end of each line. ...
- 1,601
5
votes
1
answer
60
views
How to maximise the parallel efficiency of siesta?
Are there any options I should optimize in the input file to maximize the parallel efficiency? Like in the VASP, there are two options NCORE and ...
- 1,863
2
votes
0
answers
138
views
Why does the GPU version of VASP consume a lot of time on STRESS calculation?
I am trying to compare the CPU and GPU versions of VASP.6.3.0, it seems that the GPU version consumes a lot of time on the STRESS item, does it represent the time for calculation stress tensor?
Here ...
- 1,863
4
votes
0
answers
48
views
Benchmarks for optimised Math Libraries across platforms [closed]
Are there any benchmarks of low-level and high-level math operations from different Math libraries on corresponding architectures?
Here are a few packages:
LAPACK / BLAS + ATLAS (stock version from ...
user784
5
votes
1
answer
123
views
Successfully running parallel gas phase calculation on AMD cloud instance but implicit solvent fails (Local Intel workstation successfully runs both)
I am using an AMD Linux cloud-based instance to ran general optimisation and transition state calculations in parallel. I have noticed that I can run gas phase calculations in parallel but the run ...
- 81
8
votes
1
answer
375
views
How much does it cost (RAM and CPU) to calculate the energy of H2?
I have recently come across this very intriguing paper “The Fundamental Vibration of Molecular Hydrogen”.
I have asked the authors the following naïve questions directly via email:
What was the ...
- 343
4
votes
0
answers
50
views
Recommendation for some papers on simulation of metallic metal
I want to simulate the collision between two gas giants, the inner layer of gas giant contains the layer of metallic hydrogen and a solid core, if two gas giants collide then the abrubt variation of ...
- 41
17
votes
4
answers
4k
views
I am considering to purchase a GPU. What calculations would need FP32, and what would need FP64?
I would like to know how to choose the best GPU on the basis of its FP32 or FP64 efficiency, depending on different types of simulations.
In brief I would like to know what types of simulations work ...
- 1,429
7
votes
1
answer
127
views
Loop calculation in Gaussian
I want to run multiple jobs on Gaussian using windows. I know it is possible to do so on Linux. But can we perform a loop in Gaussian with Windows?
In my calculation, I need to use the optimized ...
- 517
4
votes
4
answers
2k
views
Is there a way to do array broadcasting faster, or without using loops?
I would like to optimize the following code. In real applications, the number of snapshots can be 10000, and for each of them, the lengths can be ...
- 743
8
votes
1
answer
511
views
How to manage disk space for Gromacs XTC (trajectory) file output
I'm running and MD run with this command:
gmx mdrun -v -deffnm md
It also produces trajectory file with .xtc extension.
...
- 1,642
7
votes
0
answers
103
views
How to determine minimum reasonable MD timing for ligand-protein complex [closed]
I am working on protein-ligand complex MD simulation using GROMACS.
Now I'm running the tutorial.
...
- 1,642
9
votes
5
answers
346
views
Recommended software to open NetCDF files?
I found plenty of packages that open .nc files but all specifically catered to climate (meteorological) and geo-maps data. I would like to get suggestions of ...
- 19.9k
6
votes
1
answer
162
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 ...
- 10.3k
8
votes
5
answers
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 ...
user784
6
votes
1
answer
1k
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 ...
- 10.3k
12
votes
2
answers
412
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 ...
- 4,019
5
votes
1
answer
137
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.
...
- 3,729
20
votes
10
answers
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 ...
- 1,266
12
votes
1
answer
111
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 ...
- 4,019
17
votes
3
answers
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 ...
- 1,642
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 ...
- 1,863
9
votes
1
answer
67
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 ...
user784
9
votes
1
answer
333
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 ...
- 721
7
votes
2
answers
147
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 ...
- 1,863
6
votes
1
answer
160
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 ...
- 373
9
votes
3
answers
533
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.
- 1,849
12
votes
3
answers
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 ...
- 1,601
9
votes
5
answers
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 ...
- 995
6
votes
0
answers
133
views
How to run Quantum ESPRESSO on Google Cloud Services or Amazon Web Services [duplicate]
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 ...
- 1,601
13
votes
3
answers
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 ...
- 1,601
7
votes
1
answer
764
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 ...
- 1,601
16
votes
2
answers
433
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,...
- 8,452
24
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 ...
- 1,030
8
votes
1
answer
450
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 ...
- 2,431
22
votes
4
answers
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 ...
- 391
13
votes
5
answers
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 ...
- 19.9k
6
votes
1
answer
221
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, ...
- 5,553
8
votes
4
answers
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 ...
- 1,525
10
votes
1
answer
147
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. ...
- 947
10
votes
1
answer
757
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 ...
- 2,091
13
votes
1
answer
154
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, ...
- 6,459
6
votes
1
answer
134
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 ...
- 317
14
votes
1
answer
300
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 ...
- 313
26
votes
1
answer
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) ...
- 19.9k
16
votes
2
answers
488
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.?
- 1,021
12
votes
1
answer
444
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 ...
- 415
13
votes
2
answers
568
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 ...
- 131