Questions tagged [high-performance-computing]
Questions concerning high performance computing (HPC).
102
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How can I build the wheels necessary for a quick installation of PySCFad on a "compute node"?
The following is the procedure I have been following:
Install PySCFad
...
- 30.8k
7
votes
3
answers
2k
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Running an ORCA calculation from Python
I'm a master's student and recently I started doing computational chemistry calculations using ORCA program.
This program works by command line and I saw that the majority of computational chemistry ...
- 145
5
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2
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916
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How to increase the number of CPUs in my computer?
I'm running my calculations using Quantum ESPRESSO on a 10th generation i7 computer (Dell) with Ubuntu.
When I run any calculation using the command ...
- 727
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0
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Why is my CISD restart failing in PySCF?
A case that works
In my answer to Restarting an FCI calculation in PySCF, I provided a folder full of input and output files that demonstrates saving (as a numpy ...
- 30.8k
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Is PySCF able to print checkpoint files during a CISD calculation?
The problem
I've described how to restart a CISD calculation in my answer to the question: Restarting an FCI calculation in PySCF, but this requires all iterations of the CISD calculation to finish, ...
- 30.8k
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Why is my post-processing calculation using Quantum ESPRESSO not complete after 9 hours?
I'm working on an i7 laptop with the parallel version of Quantum ESPRESSO (8 processors are running). I ran a post-processing calculation by ...
- 727
1
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1
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90
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PySCF: How to do CCSD calculations from an FCIDUMP file in HDF5 format?
Recently my question: Why does CCSD work, but not CCSD(T), after reading an FCIDUMP in PySCF? lead to a bug fix that allows users to do CCSD(T) calculations from an FCIDUMP file in PySCF. That was ...
- 30.8k
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Is this "internal error" reproducible when compiling OpenMolcas on other Intel compilers?
The procedure I've been following to build OpenMolcas with an Intel Fortran compiler in the Compute Canada environment is as follows:
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- 30.8k
2
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0
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CUDA memory Error when using NAMD, mentions cygwin even though cygwin isn't installed?
I've run into some issues with NAMD that cause me to get the following error whenever I try to begin a simulation run:
...
Roshan Pathak
8
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2
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2k
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Why does Quantum ESPRESSO need 13TB of RAM for a (3x3x3)nm supercell?
I made a 3nm×3nm×3nm supercell mesh of pbs atoms which contains about 2000 atoms and QE gave me a 13256 GB requirement of RAM. What am I doing wrong? Many people have already done this calculation, ...
- 83
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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.) &...
- 816
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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 ...
- 661
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149
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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. ...
- 1,641
2
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0
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164
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Gaussian Job File with Variables and Link1
I work now with larger job files and use the --Link1-- keyword to organize up to 10 jobs in one job file. This works very well for me. But I got a lot of job series ...
- 816
5
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1
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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 ...
- 1,915
2
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0
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Why does the GPU version of VASP consume a lot of time on STRESS calculation? [closed]
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 ...
- 1,915
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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
173
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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 ...
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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
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0
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115
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How to save the generated 3d representation of the structure(s) by Viewer3d in Py4vasp?
I used py4vasp to calculate structure from data and then I displayed them in a structure viewer (Viewer3d) by this line: calc.structure[:].plot(). It returns a ...
4
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0
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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 ...
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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 ...
- 1,439
7
votes
1
answer
183
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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
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4
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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 ...
- 773
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661
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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.
...
- 1,644
7
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116
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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.
...
- 1,644
9
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5
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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 ...
- 20.7k
6
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1
answer
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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 ...
- 10.6k
8
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5
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2k
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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
7
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1
answer
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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 ...
- 10.6k
12
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2
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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 ...
- 4,091
5
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222
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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.
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- 3,834
20
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10
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4k
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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 ...
- 1,317
12
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1
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125
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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 ...
- 4,091
17
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3
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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 ...
- 1,644
14
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3
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2k
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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 ...
- 1,915
9
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1
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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
445
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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 ...
- 731
7
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2
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156
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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 ...
- 1,915
6
votes
1
answer
178
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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 ...
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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.
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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 ...
- 1,641
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5
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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 ...
- 1,015
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138
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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 ...
- 1,641
14
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3
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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 ...
- 1,641
7
votes
1
answer
990
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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 ...
- 1,641
16
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2
answers
444
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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,...
- 8,612
25
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6
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3k
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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 ...
- 1,040
8
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1
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556
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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 ...
- 2,481
22
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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