Questions tagged [high-performance-computing]
Questions concerning high performance computing (HPC).
140
questions
0
votes
0
answers
47
views
Running MD simulations with the xtb program
I am running MD simulations on a HPC cluster via the xtb program (xtb/6.5.0). However, I am only able to run calculations with GFN-FF, and not with GFN2-xTB for some reason.
This works:
...
- 131
4
votes
1
answer
98
views
Choosing Between a Small Cluster and a Workstation for MD Simulations and Quantum Chemistry Calculations
I am part of a research group and we are in the process of deciding on a computing resource for our simulation and data analysis needs.
Our primary tasks include:molecular Dynamics (MD) simulations (...
- 165
4
votes
1
answer
64
views
SLURM job script: Why is the tmp local directory deleted before archiving can occur?
I wrote a SLURM job script to run a computational chemistry calculation using the CREST program (part of the xtb software package). In the script, I create a temporary directory on the local storage ...
- 161
4
votes
0
answers
31
views
How to estimate TFLOPS for calculation in Quantum Espresso?
My question is related to this. But I am more interested in knowing if there is a way to estimate computational requirements in terms of TFLOPS.
I was talking to someone who works in hardware design, ...
- 457
2
votes
1
answer
103
views
Why does SIESTA 5.0.1 fail to run in parallel but working in serial execution?
I am trying out SIESTA for the first time and while it seems to run without any problem for a serial execution, I am encountering an error everytime I am assigning more than 1 processor. So, the ...
2
votes
0
answers
105
views
Can someone please help me with this error associated with slurm workload manager
Whenever it tries to submit a job, it repeatedly gives these errors
...
- 681
2
votes
0
answers
60
views
Latest trends and bench marks for VASP on GPU
I am thinking of getting a server with a GPU system for VASP calculations, and I am interested in learning about the latest benchmarks on these topics. Does anyone have a reference to the latest ...
- 21
2
votes
0
answers
68
views
Issue with hp.x Quantum ESPRESSO Calculation on HPC System
I am trying to run an hp.x Quantum ESPRESSO calculation on an HPC system, but the output is not as expected. The scf calculation runs without any issues. However, ...
- 2,209
5
votes
1
answer
381
views
How may I increase the speed of SCF iterations in SIESTA?
I have experience with VASP and CASTEP, but since I need to use TRANSIESTA to calculate transport properties, I tried to use siesta. I heard that siesta is very fast and can handle large systems, but ...
- 309
2
votes
0
answers
33
views
Can MongoDB/Fireworks run on a supercomputing cluster?
I'm trying to set up MongoDB and Fireworks on a supercomputing cluster, but I've encountered several issues.
OpenSSL and Shared Libraries:
Initially, MongoDB couldn't find the required libcrypto.so.1....
- 21
5
votes
0
answers
66
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 ...
Manuel Ravasqueira
4
votes
0
answers
29
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 ...
- 1,105
5
votes
0
answers
34
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.
1
vote
0
answers
82
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.
...
- 823
5
votes
0
answers
119
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 ...
- 241
6
votes
1
answer
168
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.
...
3
votes
1
answer
141
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 ...
- 794
1
vote
0
answers
71
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 ...
- 484
2
votes
1
answer
78
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 ...
- 313
2
votes
0
answers
78
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:
...
- 1,637
3
votes
0
answers
132
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?
...
- 2,209
8
votes
2
answers
537
views
How can I maximize both CPU and GPU usage when running OpenACC VASP?
I am currently running a fairly large system (NELECT>7400) on the OpenACC GPU port of VASP 6.4.1 on 16 Nvidia A100 GPUs: 4 GPUs x 4 nodes (NCSA Delta 4-Way NVIDIA A100 GPU Compute Nodes). Each of ...
user8097
4
votes
0
answers
70
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 ...
- 41
4
votes
1
answer
497
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 ...
- 4,889
4
votes
1
answer
480
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 ...
- 699
2
votes
0
answers
97
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 ...
- 559
10
votes
2
answers
1k
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, ...
- 2,209
4
votes
0
answers
132
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 ...
- 2,209
6
votes
3
answers
764
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].....)
...
- 2,209
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 ...
- 61
4
votes
0
answers
33
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, ...
- 451
2
votes
1
answer
212
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 ...
- 2,209
1
vote
1
answer
389
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:
...
- 79
8
votes
2
answers
299
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:
...
- 2,209
6
votes
1
answer
822
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 ...
- 381
4
votes
2
answers
396
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 ...
- 2,209
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 ...
- 2,209
5
votes
0
answers
134
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 ...
- 1,007
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 ...
- 2,209
8
votes
1
answer
355
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
...
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 ...
- 165
6
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 ...
- 2,209
3
votes
1
answer
124
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 ...
3
votes
1
answer
193
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, ...
3
votes
0
answers
235
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 ...
- 2,209
1
vote
1
answer
459
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 ...
3
votes
2
answers
267
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:
...
2
votes
0
answers
87
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:
...
Roshan Pathak
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, ...
- 93
3
votes
0
answers
37
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.) &...
- 866