Questions tagged [high-performance-computing]
Questions concerning high performance computing (HPC).
118
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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 ...
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4
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1
answer
383
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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 ...
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4
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1
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146
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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 ...
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0
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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 ...
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9
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2
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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, ...
- 1,957
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Why my scf calculation with 30*30*30 k-points grid is stuck in the same line for more than 6 hours?
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 ...
- 1,957
6
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3
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645
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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].....)
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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 ...
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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, ...
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108
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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 ...
- 1,957
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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:
...
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7
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2
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193
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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:
...
- 1,957
5
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1
answer
445
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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 ...
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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 ...
- 1,957
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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 ...
- 1,957
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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 ...
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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 ...
- 1,957
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1
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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
...
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7
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3
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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 ...
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2
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1k
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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 ...
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3
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1
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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 ...
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3
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1
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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, ...
- 33.6k
3
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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 ...
- 1,957
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1
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274
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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 ...
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3
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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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2
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0
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75
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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
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, ...
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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.) &...
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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 ...
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184
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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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579
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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 ...
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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 ...
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357
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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 ...
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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
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1
answer
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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 ...
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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 ...
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7
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1
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319
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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 ...
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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 ...
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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.
...
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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.
...
- 1,674
9
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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 ...
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6
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1
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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 ...
- 10.8k
8
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5
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Suggestions on personal computers 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
4k
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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 ...
- 10.8k
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2
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434
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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 ...
- 4,141
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464
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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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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 ...
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1
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169
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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 ...
- 4,141