Skip to main content

Questions tagged [high-performance-computing]

Questions concerning high performance computing (HPC).

Filter by
Sorted by
Tagged with
5 votes
0 answers
43 views

Butina cluster over a 300 million SMILES

I have a dataset with approximately 300 million SMILES strings, for which I want to apply Butina clustering and extract the Tanimoto similarity matrix to visualize the PCA of this matrix. Since I have ...
user avatar
4 votes
0 answers
22 views

Which quantum chemistry codes have the capability use point charges in a QM/MM setting?

I came across a few examples like: NWchem : QM/MM Bq charges PySCF : QM/MM with MM charges GPAW : External Point charge potential I wanted to know of other code examples, which had the same ...
Atom's user avatar
  • 1,005
5 votes
0 answers
24 views

What are good test cases for benchmarking and scaling studies of SIESTA on up to a few thousand cores?

Subject says it all. I'm looking for SIESTA test cases suitable for benchmarking and scaling studies on clusters having up to a few thousand cores.
Gerardo Cisneros's user avatar
1 vote
0 answers
37 views

MPI_Abort error in LAMMPS simulation

I used LAMMPS to simulate the thermal conductance for Al2O3/bilayer graphene/Al2O3 system along the z axis. This is my input file. ...
Kieran's user avatar
  • 753
5 votes
0 answers
68 views

Problem with using VASP with ase on a GPU

I am a newbie using VASP, currently I am trying to calculate the formation energy per atom and pre bandgap using DFT with VASP on a GPU machine. I wrote the following script for calculating the ...
harsh's user avatar
  • 223
6 votes
1 answer
110 views

wannier90 compilation error (MPI)

I tried to build wannier90 for parallel execution in a fedora system. However, I encounter with the following issue repetitively. ...
wenusara satheekshana's user avatar
3 votes
1 answer
69 views

what determines the 'Estimated total dynamical RAM ' in a Quantum Espresso calculation

As per my understandings the computer resources required for a DFT calculation increases by an order of three with the number of atoms. But as you can see in the output files given below the ...
Joyal sunny's user avatar
1 vote
0 answers
42 views

Free Cloud Computing for VASP Simulation

I am looking for suggestions for a free cloud-computing platform for running the VASP simulations. I do have the VASP license. I am also ok, if I am allowed to use for a week or so. I can also install ...
Schrodinger's user avatar
2 votes
1 answer
47 views

How to call VASP input files from parent directory

Let's suppose I want to run the same calculation but for different configurations (= different POSCAR). For all calculations I have the same INCAR, POTCAR and KPOINTS. Those could be stored in a ...
Lukas's user avatar
  • 303
2 votes
0 answers
59 views

Error with running GROMACS with SLURM [closed]

I am running into errors while submitting a job for a basic MD Simulation with HPC on SLURM. My sbatch script reads as follows: ...
Pranoy Ray's user avatar
  • 1,637
3 votes
0 answers
80 views

Need Help Resolving Quantum ESPRESSO Calculation Error Linked to OpenMPI on Desktop

I tried to run my Quantum ESPRESSO calculations as I was used to do in my desktop. But they give me an error message linked to Openmpi, and I don't know how to solve it. Can someone please help me? ...
Camilla's user avatar
  • 2,169
4 votes
0 answers
59 views

OOM Error Calculating ESP Charges with Psi4

I'm trying to create a script to generate partial charges for a given .dat file. As an example of my process, I'm currently using gromacs to run minimization on a box of propane. It outputs a min.gro ...
asquith's user avatar
  • 41
4 votes
1 answer
436 views

Kill or let be: Is this calculation stuck or just very slow?

My question is regarding a medium-to-large DLPNO-UCCSD(T)-F12 calculation. I have a ~250 electron system, an open-shell molecule inside a water droplet, and I'm trying to get the total energy, first ...
epalos's user avatar
  • 4,869
4 votes
1 answer
320 views

Run ASE MD in parallel

I would like to run my MD simulation in parallel on a cluster (16 CPUs per node). From the ASE doc we can see that: ASE will automatically run in parallel, if it can import an MPI communicator from ...
Marco Di Gennaro's user avatar
2 votes
0 answers
87 views

Is memory per core more import than # of memory channels for high performance VASP calculation?

Cross posted on StackOverflow. I ask this question cause recently my department want to purchase a HPC cluster mainly for first principle calculation. For now we have three choices: (1) Per node dual ...
Tieyuan Bian's user avatar
10 votes
2 answers
956 views

What factors could cause a calculation to run successfully on a laptop but encounter issues on an HPC system?

I am performing an SCF Quantum ESPRESSO calculation on an HPC system, but it is taking significantly longer than usual. When I inspect the output file, I notice that it is stuck at a specific line, ...
Camilla's user avatar
  • 2,169
4 votes
0 answers
121 views

Why my scf calculation with 30*30*30 k-points grid is stuck in the same line for more than 6 hours? [closed]

I'm running a scf Quantum ESPRESSO calculation on a cluster to get the optical properties of my material. I noticed that the output file is stuck in the same line for more than 6 hours even though ...
Camilla's user avatar
  • 2,169
6 votes
3 answers
696 views

The meaning of some HPC vocabulary

Bellow is a part from the partitions of an HPC. Can someone please explain to me the meaning of each term ( mix, alloc, adle, node28, bigmem[41-44], gpu[51-52].....) ...
Camilla's user avatar
  • 2,169
6 votes
0 answers
51 views

PC Specifications for a small DFT Research Group [duplicate]

Planning to set up a small research group here at my university to do some DFT/MD work and I'm looking for a nice setup that will cater to that. Will be asking for funding from the university or from ...
tumblewush's user avatar
4 votes
0 answers
32 views

What are the general principles of setting parellelization options in VASP?

I am doing the computation of a perovskite system of 20 atoms in a supercell. I know that options like NPAR and KPAR, and the numbers of cores used for computations can greatly affect the efficiency, ...
蕭力諶's user avatar
  • 441
2 votes
1 answer
162 views

Why are my HPC calculations not running in SLURM?

Question I submitted 2 jobs for the first time in a HPC to test it. It's a very light calculation that takes almost 5 minutes or less in my desktop. But it has been almost 1 hour since I submitted the ...
Camilla's user avatar
  • 2,169
1 vote
1 answer
307 views

MPI error in Quantum ESPRESSO during optimization of particularly large molecules

I have been recently trying to optimize a particularly large system Mo2C in QE using the pw.x executable and encountering the following MPI errors: ...
Avrana's user avatar
  • 79
8 votes
2 answers
255 views

How to get the directives of a slurm for my Quantum ESPRESSO calculations?

Context I saw some examples of SLURM scripts on the internet like the one below: ...
Camilla's user avatar
  • 2,169
5 votes
1 answer
659 views

Running multinode parallel Orca calculation without a work load manager (scheduler)

I wonder, if someone has run (runs) parallel Orca calculations on at least two nodes without a work load manager (scheduler)? I am asking because I have several interconnected servers (nodes) I'd like ...
EvGeniy's user avatar
  • 371
4 votes
2 answers
368 views

Does loging out from the server stop my Quantum ESPRESSO calculations?

I'm doing simulation with Quantum ESPRESSO, and it's my first time to run it on a server using ssh. I ran some calculations yesterday then I logout using the command ...
Camilla's user avatar
  • 2,169
2 votes
0 answers
100 views

Why I can't access my account using ssh? [closed]

When I try to acess my account in a workstation remotely using my laptop by ssh using the following command: ssh [email protected] I get the following message in ...
Camilla's user avatar
  • 2,169
5 votes
0 answers
128 views

How realistic is the use of classical analog electronic computers in solving the Schrödinger, Hartree-Fock, and Kohn-Sham equations?

Classical binary computer The classical binary computers, on which a Hartree-Fock (or density functional theory) calculation can be executed, already allows seeing a limit in their progress, mainly in ...
SFriendly's user avatar
  • 927
5 votes
2 answers
2k views

How can I run my calculations on a remote server?

I'm going to use a more powerful server to run my simulations on it using a remote control software (The server is in another building). It's my first time to try that. What are the things that I ...
Camilla's user avatar
  • 2,169
8 votes
1 answer
318 views

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 ...
Nike Dattani - No Free Time's user avatar
7 votes
3 answers
3k views

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 ...
Al1010's user avatar
  • 165
5 votes
2 answers
1k views

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 ...
Camilla's user avatar
  • 2,169
3 votes
1 answer
103 views

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 ...
Nike Dattani - No Free Time's user avatar
3 votes
1 answer
177 views

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, ...
Nike Dattani - No Free Time's user avatar
3 votes
0 answers
207 views

Why is my post-processing calculation using Quantum ESPRESSO not complete after 9 hours? [closed]

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 ...
Camilla's user avatar
  • 2,169
1 vote
1 answer
386 views

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 ...
Nike Dattani - No Free Time's user avatar
3 votes
2 answers
260 views

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: ...
Nike Dattani - No Free Time's user avatar
2 votes
0 answers
83 views

CUDA memory Error when using NAMD, mentions cygwin even though cygwin isn't installed? [closed]

I've run into some issues with NAMD that cause me to get the following error whenever I try to begin a simulation run: ...
user avatar
9 votes
2 answers
2k views

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, ...
LEO PHYSICS's user avatar
3 votes
0 answers
34 views

Problem with installation of Multiwell Software package and open mpi [closed]

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.) &...
Andrea's user avatar
  • 856
6 votes
3 answers
772 views

How to run multiple Gaussian jobs one after another in Linux

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 ...
diamond999's user avatar
9 votes
0 answers
222 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. ...
Parmeet Singh EP 066's user avatar
2 votes
0 answers
774 views

Gaussian Job File with Variables and Link1 [closed]

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 ...
Andrea's user avatar
  • 856
5 votes
1 answer
235 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 ...
Jack's user avatar
  • 2,057
2 votes
0 answers
395 views

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 ...
Jack's user avatar
  • 2,057
4 votes
0 answers
75 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 ...
user avatar
5 votes
1 answer
388 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 ...
learner254's user avatar
8 votes
1 answer
400 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 ...
Omar Shehab's user avatar
4 votes
0 answers
54 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 ...
吴yuer's user avatar
  • 141
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 ...
NickZ's user avatar
  • 1,499
7 votes
1 answer
404 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 ...
sarra6's user avatar
  • 579