Tag: OpenMP

Unexpected behaviour during hybrid Monte-Carlo simulations (ReaxFF) – LAMMPS Beginners

T.Dem June 25, 2022, 5:41pm #1 Dear LAMMPS users, I am trying to run Monte Carlo simulations using reaxff to study the oxygen coverage on a Pt nanoparticle. I defined my oxygen reservoir using the chemical potential definition for a perfect gas. Initially, the system is very small (350 atoms)…

Continue Reading Unexpected behaviour during hybrid Monte-Carlo simulations (ReaxFF) – LAMMPS Beginners

Convert ONNX RuntimeError: tin_shift_forward_impl: implementation for device cpu not found.

when convert tin to onnx meet this issue: RuntimeError: tin_shift_forward_impl: implementation for device cpu not found. env:sys.platform: linuxPython: 3.8.10 (default, Jun 2 2021, 10:49:15) [GCC 9.4.0]CUDA available: TrueGPU 0,1: Tesla T4CUDA_HOME: /usr/local/cudaNVCC: Cuda compilation tools, release 11.4, V11.4.120GCC: x86_64-linux-gnu-gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0PyTorch: 1.9.1+cu111PyTorch compiling details: PyTorch built with: GCC 7.3…

Continue Reading Convert ONNX RuntimeError: tin_shift_forward_impl: implementation for device cpu not found.

main-i386-default][science/cp2k] Failed for cp2k-9.1.0 in configure

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy17.nyi.freebsd.org/data/main-i386-default/p429f3de9bdcd_s2573e6ced9/logs/cp2k-9.1.0.log Build URL: beefy17.nyi.freebsd.org/build.html?mastername=main-i386-default&build=p429f3de9bdcd_s2573e6ced9 Log: =>> Building science/cp2k build started at Sat Jun 4…

Continue Reading main-i386-default][science/cp2k] Failed for cp2k-9.1.0 in configure

installation of qiime2 on pycharm with anaconda interperter

I’m a relatively new qiime2 (bioinformatics tool based on python language) and python user. So far, I have been using qiime2 inside a virtual machine, which is ok but not great. Since I’m taking a python course and have gotten used to work with pycharm, I’m trying to install the…

Continue Reading installation of qiime2 on pycharm with anaconda interperter

Running rstudio (but not R alone) inside of a conda environment complains about finding Rccp.so

I find that when I try to load some packages in a conda environement, when using rstudio (but not when I’m using R directly), I get an error message about a missing Rcpp.so file. I activate my conda environment (which is running R version 4.1), open RStudio (which I installed…

Continue Reading Running rstudio (but not R alone) inside of a conda environment complains about finding Rccp.so

Nvt.mdp killed in 7 min – User discussions

GROMACS version:2022+cp2k interface basically, my system is small but I couldn’t start nvt job. Can you I help me, what I am doing wrong?Thank you in advance I am taking that error : Command line:gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt Compiled SIMD: AVX_256, but for this host/run AVX2_256 might…

Continue Reading Nvt.mdp killed in 7 min – User discussions

GROMACS – SBGrid Consortium – Supported Software

Usage Notes SBGrid Usage Info GROMACS is GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : sbgrid.org/wiki/gpu CUDA builds of GROMACS are designated by a ‘_cu’ suffix in the version of the application. For example, 2020.2_cu9.2.88 is linked against…

Continue Reading GROMACS – SBGrid Consortium – Supported Software

Issue with segmentation fault – User discussions

GROMACS version: 2021.2, 2019.6GROMACS modification: YesHere post your question I am facing a segmentation fault issue with GROMACS patched with plumed and I was wondering if you could help me. I am trying to run a replica averaged MD simulation by calculating the backbone chemical shifts for a protein (using…

Continue Reading Issue with segmentation fault – User discussions

Simpler explanation of some CREST/xtb environment variables (Conformer searching) : comp_chem

Hi,I am working with CREST/xtb to do some conformer searches. Been reading the docs to understand how to configure the environmental variables. I want to adjust them to suit my system (24 threads workstation) but not sure what to adjust. Wondering if someone can assist in explaining these with simpler…

Continue Reading Simpler explanation of some CREST/xtb environment variables (Conformer searching) : comp_chem

java – GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

I can’t seem to get GATK to recognise the number of available threads. I am running GATK (4.2.4.1) in a conda environment which is part of a nextflow (v20.10.0) pipeline I’m writing. For whatever reason, I cannot get GATK to see there is more than one thread. I’ve tried different…

Continue Reading java – GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

alphafold2: HHblits failed – githubmemory

I’ve tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at github.com/kalininalab/alphafold_non_docker, and both result in the following error: […] E1210 12:01:01.009660 22603932526400 hhblits.py:141] – 11:49:18.512 INFO: Iteration 1 E1210 12:01:01.009703 22603932526400 hhblits.py:141] – 11:49:19.070 INFO: Prefiltering database E1210 12:01:01.009746 22603932526400 hhblits.py:141]…

Continue Reading alphafold2: HHblits failed – githubmemory

Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

Continue Reading Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support