Questions tagged [high-performance-computing]

Questions concerning high performance computing (HPC).

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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 ...
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.) &...
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 ...
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. ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 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 ...
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. ...
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. ...
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. ...
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 ...
20 votes
3 answers
785 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, ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
8 votes
0 answers
209 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF [closed]

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. ...
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 ...
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 ...
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 ...
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.
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 ...
12 votes
3 answers
157 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 ...
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, ...
20 votes
2 answers
795 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
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. ...
16 votes
3 answers
440 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. ...
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 ...
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 ...
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 ...
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 ...
8 votes
0 answers
253 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 ...
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 ...
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 ...
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 ...
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 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 ...
26 votes
9 answers
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 ...
18 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 ...