Tag: centos

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Apologies for the second post here. I wanted to do a better job of gathering my thoughts but managed to write a short novel in the process. I’m interested in seeing better AI/ML tooling support in Fedora. To be honest, I’ve pretty much given up on using Fedora with the…

Hi team I used slurm cluster on this flavour of Nvidia BCM and it worked but now its showing below mentioned error when running some srun commands . please refer below and let me know if more info is required . [root@master88 ~]# sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST…

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.   Get Started with This Ready-To-Go Azure Solution  This readymade library environment on Windows Server offered by Apps4Rent takes…

Is it normal to get truncated identifiers after applying SQL scema of RegaDB? 0 Hello, everyone I am trying to set up RegaDB on my CentOS system, and I have installed PostgreSQL via conda. I followed the RegaDB installation manual to configure the PostgreSQL database. However, when I have applied…

Hi, I think I might have found a bug in featureCounts from Rsubread (v2.12.3). I am trying to find reads overlapping exon junctions from a personalised reference, using Nanopore long read BAMs. I am afraid I cannot share fully reproducible code as I am using my own reference, but this…

jhill April 19, 2023, 2:00pm 1 When I try to run attached LAMMPS input with:lmp -sf omp -pk omp 12 -in input.datI get a segmentation fault (LAMMPS 28Mar2023). Without OpenMP or on a GPU the calculation runs. There is nothing attached to your message. Please try the KOKKOS package instead…

I’m trying to use Nsight Systems with Julia, but am hitting an issue where it attempts to open the wrong libpcre library. Julia sets its RUNPATH to be $ORIGIN/../lib:$ORIGIN/../lib/julia and the library is in the second of these directories. However when I run LD_DEBUG=libs nsys launch julia I get the…

HelloI’ve got some issues when running pvserver on HPC(Slurm) by singularity. Looking for some help sincerely. VersionParaView-5.11.0-MPI-Linux-Python3.9-x86_64.tar.gz (download from this link) Run EnvHPC Cluster managed by Slurm (CentOS 7) without any mpi QuestionI packet paraview to singularity SIF. Dockerfile like FROM centos:7 COPY paraview /usr/local/paraview RUN yum install -y libXcursor…

seven April 7, 2023, 1:36am 1 jupyterhub:2.2.2system: centos 8the notebook page show nothing when i click new terminal in top menu.the server console: Traceback (most recent call last):File “/usr/local/lib/python3.6/site-packages/ptyprocess/ptyprocess.py”, line 522, in reads = self.fileobj.read1(size)OSError: [Errno 5] Input/output error During handling of the above exception, another exception occurred: Traceback (most…

Dear Community,   This is Pim, a new EPYC user. I just DIYed a workstation as following:     – Supermicro H11DSi     – EPYC 7B12 * 2     – Samsung RECC 3200 32G * 16     –  Samsung 980 Pro 2t     – Centos 7…

Problem with fatsq-dump 0 Hi, I am absolutely new in NGS data analysis and have just started working in centos. I installed sratoolkit with the commands : conda create –n sratoolkit_env –y conda activate sratoolkit_env conda install –c bioconda sra-tools –y Then as given in the Biostar Handbook (Bioinformatics Data…

Hello, am following this page to make multiple R installation available. $ rstudio-server version 2021.09.0+351 (Ghost Orchid) for CentOS 8 Steps I’ve done rstudio-server stop cd /etc/rstudio touch r-versions chmod g+rwx,o+rwx /etc/rstudio/r-versions chmod -t /etc/rstudio/r-versions Modify r-versions with the following lines Path: /opt/R/4.2.2 Label: CRAN R422 Path: /opt/microsoft/ropen/4.0.2/lib64/R Label: MRAN…

GROMACS version:2022.5GROMACS modification: Don’t think soOS -CentOS 7.9cmake 3.17.3local anaconda3 for python3CUDA 11.7 I am looking for help on what i might have missed. Gromacs compiled ok without any reported errors. I had to install openMPI and symlink it for the compiler to see it.All the mdrun tests fail with…

Core Administrative Tasks Configuration Files RStudio Server uses several configuration files all located within the /etc/rstudio directory. Configuration files and folders include: rserver.conf Core server settings rsession.conf Settings related to individual R sessions notifications.conf Notifications to be delivered to user sessions Pro logging.conf Configuration of the logging system including logger…

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Environment: CentOS Linux 7 (Core)LAMMPS version: LAMMPS-15Sep2022Packages:make yes-mc yes-molecule yes-asphere yes-peri yes-sph yes-EXTRA-PAIRmake serialwith fluid membrane package from: data.mendeley.com/datasets/4v53nkv5hc/1(code modified to match 2022 version) Input file: (A modification based on Ballistic impact response of lipid membranes – Nanoscale (RSC Publishing)) # This is LAMMPS input script specifies a CG model…

R programming is a software program supported by R basis for statistical computing and non-profit making group. Being a statistical software program package deal, it has elevated in recognition amongst information scientists and information miners who use R for information mining surveys and information evaluation. Its supply code was primarily…

sam123 February 8, 2023, 5:01pm 1 Hi, there, I rebuild Hub docker image based on amazon linux2. When I tried to run it locally, I got error:For the sqlite version error: sqlalchemy.exc.NotSupportedError: (sqlite3.NotSupportedError) deterministic=True requires SQLite 3.8.3 or higher The default SQLite coming with amazon linux2 is 3.7.17. However, I…

I’m using LAMMPS version 23 Jun 2022, on Centos 6. I have installed the reaxFF package bundled with lammps and ECHEMDID-23jun2022 Hello, I’m trying to simulate the behavior of 1M of LiPF6 in Ethylene Carbonate under an electric field in order to establish a baseline for my future simulations. In…

Mo_O January 27, 2023, 5:18pm #1 Dear all, i have some struggle with PyTorch. I upgraded CryoSPARC from 3.3.2 to 4.1.1. After that i installed the patch 230110The problem is if someone run a 3DFlexReconstructionModuleNotFoundError: No module named ‘torch’ I´ve tried to install it on the worker nodes acording to…

============================================================================== Magnitude Simba Google BigQuery ODBC Data Connector Release Notes ============================================================================== The release notes provide details of enhancements, features, known issues, and workflow changes in Simba Google BigQuery ODBC Connector 2.4.1, as well as the version history. 2.4.1 ======================================================================== Released 2021-08-26 Enhancements & New Features [GAUSS-1279] Multi-statement transactions support The…

wandb –version && python –version && uname Weights and Biases version: 0.8.21 Python version: Python 3.6.8 :: Anaconda, Inc. Operating System: CentOS Linux release 7.7.1908 (Core) Description I’m using wandb on the GPU cluster with slurm to run jobs. After the script finishes, wandb prints the following: wandb: Waiting for…

Sample preparation We ordered the GIAB samples from the Coriell Institute (NA24385, NIST ID HG002; NA24149, NIST-ID HG003 and NA24143, NIST-ID HG004). DNA concentration was measured by Qubit. The library was constructed according to Illumina TruSeq DNA PCR Free Library Prep protocol HT (Illumina Inc., San Diego, CA, USA) for…

parallel downloads from SRA with SRA toolkit or other ways to speed up downloads 0 Is there a way to parallelize downloads from NCBI using SRAToolkit on a HPC cluster? I tried using GNU parallel but I can not actually tell if the downloads are doing anything: cat < /home/ptellier/scratch/phillip/data/escc_data/SRA_accessions.txt…

Hello, I am currently trying to install AnnotationHub but I am running into problems. I use R 4.0.4, renv (version 0.15.4) and BiocVersion 3.12. When I run BiocManager::install(“AnnotationHub”), I get the following error: Warning message: This project is configured to use R version ‘4.1.1’, but ‘4.0.4’ is currently being used….

A) GIT/SVN :- We need to set-up a git or svn repository and client systems. Following are the gist – 1) The (Git/SVN) repository will run in CentOS 7 based server. 2) Multiple (GIT/SVN) clients will run from same machine and access this repository. Will source/submit to them. This is…

Hello, I’m trying to setup my first CycleCloud cluster, but I keep getting error in the initialization phase. In particular, it complains about not finding nodes for “nodearray hpc”. The full error message: CycleCloud Version: 8.2.0-1616 Cluster: Test2 (version 8.2.x) ============================== Status: Error [Software Configuration] (retrying) Start Time: 2022-03-13T17:31:29.377Z Description:…

Dear LAMMPS experts, I am trying to build lammps with cmake command with cmake3 by using this command line: cmake3 -C ../cmake/presets/most.cmake ../cmake It seemed that installation was successful according to the below report: — <<< Build configuration >>> Operating System: Linux CentOS Linux 7 Build type: RelWithDebInfo Install path:…

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Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source). I have a conda environment, and I installed traviz from conda, but it cannot be used – when I do library(traviz) R just crashes and quits without any message. So I tried to install…

The program handily beat all competitors, in what one . This will allow us to run alphafold only using CPU ( which is what our VM has). From the developers’ original publication: “The provided inference . The AlphaFold method. Found insideThis book constitutes the refereed proceedings of the First International…

Hi, every one. I find a werid MAplot or volcano plot of DESeq reuslt. I am wondering whether you can give me some advice. This diff result is from two cell type bulk RNA-seq. I use two specific marker to get these two cell type using Flow cytometer. I alreadly…