Tag: Ubuntu

Index of /ubuntu/ubuntu/pool/universe/f/fastp/

../ fastp_0.20.0+dfsg-1build1.debian.tar.xz 22-Mar-2020 16:49 3892 fastp_0.20.0+dfsg-1build1.dsc 22-Mar-2020 16:49 2004 fastp_0.20.0+dfsg-1build1_amd64.deb 22-Mar-2020 17:11 191764 fastp_0.20.0+dfsg.orig.tar.xz 22-Jul-2019 17:13 64664 fastp_0.20.1+dfsg-1.debian.tar.xz 27-Apr-2020 19:01 3940 fastp_0.20.1+dfsg-1.dsc 27-Apr-2020 19:01 1961 fastp_0.20.1+dfsg-1_amd64.deb 27-Apr-2020 20:21 192944 fastp_0.20.1+dfsg.orig.tar.xz 27-Apr-2020 19:01 64864 fastp_0.23.2+dfsg-2.debian.tar.xz 11-Dec-2021 23:24 8476 fastp_0.23.2+dfsg-2.dsc 11-Dec-2021 23:24 1993 fastp_0.23.2+dfsg-2_amd64.deb 11-Dec-2021 23:24 172754 fastp_0.23.2+dfsg.orig.tar.xz 08-Dec-2021 05:28 82224 …

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Ubuntu Manpage: mothur – sequence analysis suite for research on microbiota

Provided by: mothur_1.48.0-2_amd64 NAME mothur – sequence analysis suite for research on microbiota SYNOPSIS mothur [ batchfile ] DESCRIPTION This manual page documents briefly the mothur command. Mothur seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. It has…

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Ubuntu Manpage: gt-encseq-encode – Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently.

Provided by: genometools_1.6.5+ds-2_amd64 NAME gt-encseq-encode – Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently. SYNOPSIS gt encseq encode sequence_file [sequence_file [sequence_file …]] DESCRIPTION -showstats [yes|no] show compression results (default: no) -ssp [yes|no] output sequence separator positions to file (default: yes) -des [yes|no] output sequence descriptions to file (default: yes) -sds [yes|no]…

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Ubuntu Manpage: samtools-quickcheck – a rapid sanity check on input files

Provided by: samtools_1.19-1_amd64 NAME samtools-quickcheck – a rapid sanity check on input files SYNOPSIS samtools quickcheck [options] in.sam|in.bam|in.cram [ … ] DESCRIPTION Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and…

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Ubuntu Manpage: FastQC – high throughput sequence QC analysis tool

Provided by: fastqc_0.11.9+dfsg-5_all NAME FastQC – high throughput sequence QC analysis tool SYNOPSIS fastqc seqfile1 seqfile2 .. seqfileN fastqc [-o output dir] [–(no)extract] [-f fastq|bam|sam] [-c contaminant file] seqfile1 .. seqfileN DESCRIPTION FastQC reads a set of sequence files and produces from each one a quality control report consisting of…

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Ubuntu Manpage: mash – fast genome and metagenome distance estimation using MinHash

Provided by: mash_2.3+dfsg-1build2_amd64 NAME mash – fast genome and metagenome distance estimation using MinHash SYNOPSIS mash <command> [options] [arguments …] DESCRIPTION mash is the main executable for the Mash software. The actual functionality is provided by the subtools (‘commands’): Commands bounds Print a table of Mash error bounds. dist Estimate…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-azure-5.15/5.15.0.1056.64~20.04.45)

All autopkgtests for the newly accepted linux-meta-azure-5.15 (5.15.0.1056.64~20.04.45) for focal have finished running. The following regressions have been reported in tests triggered by the package: systemd/245.4-4ubuntu3.23 (arm64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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Ubuntu Manpage: Bio::Roary::External::Makeblastdb – Wrapper around NCBIs makeblastdb command

Provided by: roary_3.13.0+dfsg-1_all NAME Bio::Roary::External::Makeblastdb – Wrapper around NCBIs makeblastdb command VERSION version 3.13.0 SYNOPSIS Take in a fasta file and create a temporary blast database. use Bio::Roary::External::Makeblastdb; my $blast_database= Bio::Roary::External::Makeblastdb->new( fasta_file => ‘contigs.fa’, exec => ‘makeblastdb’ ); $blast_database->run(); METHODS output_database Returns the path to the temporary blast database files…

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rstudio – Cannot deploy R-shiny app due to “fribidi was not found”

Local app runs fine, but I keep encountering this error when attempting to publish it. I have already installed fribidi & harfbuzz using brew install fribidi & brew install harfbuzz on my Mac, but I am still encountering the error. I am using: Installing urltools (1.7.3) … Using cached urltools….

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r – How to add a title on the center-left of the plot in ggplot2?

As a very late contribution to TidyTuesday challenge of Bob Ross’s Paintings, I have tried to plot 10 paintings of Bob Ross. Without further background, here is my code; library(tidyverse) library(showtext) library(showtextdb) library(ggthemes) library(ggtext) library(magick) library(ggimage) library(cropcircles) library(cowplot) library(patchwork) font_add_google(“Lora”, bold.wt = 700, family = “plottitle”) font_add_google(“Roboto Slab”, family =…

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Pytorch_all_l Benchmarks – OpenBenchmarking.org

AMD Ryzen 9 5900X 12-Core testing with a ASUS TUF GAMING B550M-PLUS (WI-FI) (1801 BIOS) and MSI NVIDIA GeForce RTX 3080 10GB on Ubuntu 22.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2312292-NE-PYTORCHAL51…

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Generate topology file for glucose – User discussions

horlust December 29, 2023, 10:15am 1 GROMACS version: 2021.4-2GROMACS modification: No Hello everyone! I am fairly new to GROMACS. I’ve been able to successfully run simulations for some small molecules with the OPLS-AA force field. My problem has always been the generation of the topology files. Using pdb2gmx seems impossible…

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Validating swagger/openapi json using openapi-validations GitHub Action | by Kushal Bhalaik | Dec, 2023

Photo by Maël BALLAND on Unsplash A few months back I had a requirement of checking the APIs for the product I’m working on for breaking changes (Backward Compatibility Check) during CI/CD. As part of that research, I created an action called openapi-validations, which is essentially a wrapper on top…

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Ubuntu Manpage: Bio::Coordinate – Modules for working with biological coordinates

Provided by: libbio-coordinate-perl_1.7.1-4_all NAME Bio::Coordinate – Modules for working with biological coordinates VERSION version 1.007001 SYNOPSIS # create Bio::Coordinate::Pairs or other Bio::Coordinate::MapperIs somehow $pair1; $pair2; # add them into a Collection $collection = Bio::Coordinate::Collection->new; $collection->add_mapper($pair1); $collection->add_mapper($pair2); # create a position and map it $pos = Bio::Location::Simple->new (-start => 5, -end…

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Iterate & Deploy OpenAPI spec files in a repository path. (Github Action)

So I’m trying to iterate through a list of files within a specific path in my repository. Currently using matrix as a for loop but when it iterates through the path, it uses the wildcard ‘*’ when running az import command. Below is my code. name: API Azure Deployment on:…

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Install R and RStudio on Fedora 37

R and RStudio are two popular open-source software packages that are used for statistical analysis, data visualization, and machine learning. R is a programming language and software environment for statistical computing and graphics, while RStudio is an integrated development environment (IDE) for R.  Here at Fixwebnode, we shall look into how to install…

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Index of /ubuntu/pool/universe/g/golang-github-go-openapi-swag

Name Last modified Size Parent Directory   – golang-github-go-openapi-swag-dev_0.0~git20160704.0.1d0bd11-1_all.deb 2017-04-30 03:24 13K golang-github-go-openapi-swag-dev_0.15.0-1_all.deb 2019-10-29 18:46 18K golang-github-go-openapi-swag-dev_0.19.15-1_all.deb 2021-10-19 20:32 26K golang-github-go-openapi-swag-dev_0.21.1-1_all.deb 2022-05-12 00:24 27K golang-github-go-openapi-swag-dev_0.22.4-1_all.deb 2023-10-26 21:32 28K golang-github-go-openapi-swag_0.0~git20160704.0.1d0bd11-1.debian.tar.xz 2017-04-30 02:00 1.6K golang-github-go-openapi-swag_0.0~git20160704.0.1d0bd11-1.dsc 2017-04-30 02:00 2.3K golang-github-go-openapi-swag_0.0~git20160704.0.1d0bd11.orig.tar.xz 2017-04-30 02:00 20K golang-github-go-openapi-swag_0.15.0-1.debian.tar.xz 2019-10-29 18:45 2.7K golang-github-go-openapi-swag_0.15.0-1.dsc 2019-10-29 18:45 2.3K golang-github-go-openapi-swag_0.15.0.orig.tar.gz 2019-10-29…

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Ubuntu Manpage: Bio::EUtilities – BioPerl low-level API for retrieving and storing data from NCBI eUtils

Provided by: libbio-eutilities-perl_1.77-2_all NAME Bio::EUtilities – BioPerl low-level API for retrieving and storing data from NCBI eUtils VERSION version 1.77 SYNOPSIS See Bio::DB::EUtilities for example usage with NCBI. DESCRIPTION This distribution encompasses a low-level API for interacting with (and storing) information from) NCBI’s eUtils interface. See Bio::DB::EUtilities for the query…

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installing R studio server on Ubuntu 22.04 LTS occour dependency problems : Package libclang-dev is not installed – General

I am installing the R studio server on my Ubuntu22.04 LTS, when sudo gdebi rstudio-server-2023.09.1-494-amd64.deb error occours Reading package lists… Done Building dependency tree… Done Reading state information… Done Reading state information… Done RStudio Server RStudio is an integrated development environment (IDE) designed to support multiple languages, including both R…

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Installing Sagemath 10.3 on ubuntu

Installing Sagemath 10.3 on ubuntu – Ask Ubuntu Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Visit Stack Exchange Log in Sign up Ask Ubuntu is a…

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Accepted ugene 49.1+dfsg-1 (source all amd64) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 12 Dec 2023 14:49:53 +0100 Source: ugene Binary: ugene ugene-data ugene-dbgsym Architecture: source all amd64 Version: 49.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Pierre Gruet <p…@debian.org> Description: ugene – integrated bioinformatics toolkit ugene-data – required…

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URI encoding? “.” character in the LDAP authentication – Zero to JupyterHub on Kubernetes

Hello, members. When the user(jupyter.user contains . character) login, Expect behavior: create home jupyter.user Actual behavior: create home jupyter-2euser %2E means ., in the URI encode.So, I suspect Z2JH encodes some characters.Does anyone know how to fix it? hub: config: Authenticator: enable_auth_state: true JupyterHub: authenticator_class: ldapauthenticator.LDAPAuthenticator LDAPAuthenticator: server_address: ldapserver lookup_dn:…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-nvidia-tegra/5.15.0.1020.20)

All autopkgtests for the newly accepted linux-meta-nvidia-tegra (5.15.0.1020.20) for jammy have finished running. The following regressions have been reported in tests triggered by the package: linux-nvidia-tegra/5.15.0-1020.20 (arm64) wireguard/unknown (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions…

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ubuntu – Medaka: unrecognized command ‘tools’ and samtools not found

When trying to run medaka_consensus in ubuntu, I am getting the following error. I installed into a virtualenv to run on ubuntu. (medaka) ubuntu:~/medaka$ medaka_consensus -i combined.fastq -d curated.fasta -t -o ~/medaka 10 -m r941_sup_plant_g610 TF_CPP_MIN_LOG_LEVEL is set to ‘3’ [main] unrecognized command ‘tools’ Attempting to automatically select model version….

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Index of /ubuntu/pool/universe/libb/libbio-samtools-perl

Name Last modified Size Parent Directory   – libbio-samtools-perl_1.39-1.debian.tar.gz 2013-10-21 00:13 7.7K libbio-samtools-perl_1.39-1.dsc 2013-10-21 00:13 2.1K libbio-samtools-perl_1.39-1_amd64.deb 2013-10-21 00:23 260K libbio-samtools-perl_1.39-1_i386.deb 2013-10-21 00:23 264K libbio-samtools-perl_1.39.orig.tar.gz 2013-10-21 00:13 324K libbio-samtools-perl_1.41-1build1.debian.tar.xz 2015-12-17 16:30 7.6K libbio-samtools-perl_1.41-1build1.dsc 2015-12-17 16:30 2.2K libbio-samtools-perl_1.41-1build1_amd64.deb 2015-12-17 23:10 185K libbio-samtools-perl_1.41-1build1_i386.deb 2015-12-17 23:11 196K libbio-samtools-perl_1.41.orig.tar.gz 2015-06-18 07:19 331K libbio-samtools-perl_1.43-1build3.debian.tar.xz 2017-11-02…

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I am trying to install RStudio on my Ubuntu system (Ubuntu 22.04.1 LTS)

I am trying to install RStudio on my Ubuntu system (Ubuntu 22.04.1 LTS) – Ask Ubuntu Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Visit Stack Exchange…

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PyTorch for JetPack 6.0DP – Jetson Orin Nano

I see that a PyTorch wheel is available for JetPack 6.0DP:developer.download.nvidia.cn/compute/redist/jp/v60dp/pytorch/ However the installation instructions seem to be out of date: NVIDIA Docs Installing PyTorch for Jetson Platform – NVIDIA Docs This guide provides instructions for installing PyTorch for Jetson Platform. The following packages are not generally available for Ubuntu…

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I am trying to install RStudio on my Ubuntu system (Ubuntu 22.04.1 LTS), but I am getting the following error

I am trying to install RStudio on my Ubuntu system (Ubuntu 22.04.1 LTS), but I am getting the following error – Ask Ubuntu Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge,…

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Fix Phonon error after running script – LAMMPS General Discussion

Hello guys,I’m trying to run a script for calculating phonons, after include phonon package within make yes-phonon and recompiling lammps via make serial.There is an unexpected error after run my script via …/lmp_serial -in in.phonon:Reading adp potential file …/…/…/potentials/Ni.adp with DATE: 2011-06-20ERROR: Unrecognized fix style ‘phonon’ is part of the…

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cluster – Slurm nodes randomly dropping

I’ve set up a cluster using Slurm, consisting of a head node, 16 compute nodes, and an NAS with NFS-4 network shared storage. I’ve recently installed Slurm on Ubuntu v22 via apt (sinfo -V reveals slurm-wlm 21.08.5). I’ve tested with some single-node and multi-node jobs, and I can get jobs…

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Too many open files caused by persistent_workers and pin_memory – data

Having some trouble running PyTorch and Lightning with Optuna. After a few trials I run into the following error: OSError: [Errno 24] Too many open files I’ve assembled a script based on Optuna’s example of a PyTorch implementation that very consistently runs into this error on my machine. “”” Optuna…

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Gromacs 2023.3 on Apple M3 chip – User discussions

GROMACS version: 2023.3GROMACS modification: No Hi folks I know that there have been several threads on running Gromacs with Apple M1 and M1 or M2 chips (e.g. Error compiling Gromacs 2023’s checks on Mac M2), but I recently got a MacBook Pro with the M3 chip, so I was interested…

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Sharing some data with each users. (creating symblink or bind mount) – Zero to JupyterHub on Kubernetes

Hello members. 1. Overview This configuration mounts NFS volumes on the following mount points. /home/jovyan /home/shared IIUC, A Z2JH user doesn’t access /home/shared by default.So, I want to create a symlink or bind mount point like /home/jovyan/shared.Does anyone know what configuration file I can set bind mount or symlink? singleuser:…

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python – Pytorch unexpected behaviour after fork

I have an application with PyTorch and Gunicorn. Firstly, I build models(torch Modules) in the Gunicorn Master Worker, and then Gunicorn forks the process, creates workers and serves requests. All the calculations are done on the CPU. The new feature is parallel computation per request, so I fork the Gunicorn…

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Index of /~birch/birchhomedir/dat/tGDE/GDEHELP-linux-intel/dat/GDE/GDEHELP-solaris-sparc/dat/boxshade

Name Last modified Size Description Parent Directory   –   box_dna.grp 1998-12-15 19:27 73   box_dna.par 1998-12-15 19:27 5.2K   box_dna.sim 1998-12-15 19:27 659   box_pep.grp 1998-12-15 19:27 385   box_pep.par 1998-12-15 19:27 5.4K   box_pep.sim 1998-12-15 19:27 658   clust160.grp 1998-12-15 19:27 434   clust160.sim 1998-12-15 19:27 708  …

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Pytorch for JetPack 6.0 – Jetson Orin NX

Hi, I have updated Jetson Orin to Jetpack 6.0, but when I try to install Pytorch with file download from Nvidia “torch-2.1.0a0+41361538.nv23.06-cp38-cp38-linux_aarch64.whl”, it got “ERROR: torch-2.1.0a0+41361538.nv23.06-cp38-cp38-linux_aarch64.whl is not a supported wheel on this platform.” I think the error from Python 3.10 in Ubuntu 22.04. Have any method to build pytorch…

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Slurm REST API in AWS ParallelCluster

This post was contributed by Sean Smith, Sr HPC Solution Architect, and Ryan Kilpadi, SDE Intern, HPC AWS ParallelCluster offers powerful compute capabilities for problems ranging from discovering new drugs, to designing F1 race cars, to predicting the weather. In all these cases there’s a need for a human to…

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Planning to use Kubernetes of a system in which already has SLURM configured – General Discussions

Dear All,Good morningWe have 4 nodes which is already installed with Ubuntu 22.04 , SLURM and we are not usinging much of HPC on this system.In order to make use of the existing hardware we plan to install Kubernetes on the same machine which has SLURM installed , my concern…

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tensorflow – CuDNN using wrong CUDA version

I’m re-doing my CUDA/CuDNN setup on a new profile on Ubuntu 22.04.3 because Keras raised an error with libcublasLT I couldn’t fix. For project compatibility, I need to use TF 12.12 with CUDA 11.8 and CuDNN 8.6. I’m working on a machine with multiple CUDA versions already installed. $ cd…

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Index of /~birch/birchhomedir/dat/tGDE/GDEHELP-linux-x86_64/dat/dGDE/GDEHELP-osx-x86_64/doc/clustalw

Name Last modified Size Description Parent Directory   –   README 1997-04-18 05:21 4.3K   clu2ig.asc 1992-08-13 15:12 1.0K   clustalv.asc 1996-03-15 09:29 74K   clustalw.asc 1996-03-20 05:53 27K   clustalw.doc 2001-11-09 04:45 33K   clustalw.ms 2001-11-09 04:45 43K   clustalw_help 2001-11-09 04:45 31K   clustalx_help 1997-05-19 16:54 51K  …

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is memory suddenly not enough?

Alright, I think I managed to get somewhere with the program’s configuration options: using an older reference config from 2019, shasta doesn’t look to reserve itself unnecessary amounts of memory, and the test should now go through. If this works, we can forget about checking available memory on the host,…

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HPC Kubernetes: AI Training on 3,500 GPUs

To date, Kubernetes has largely steered clear of the high-performance computing (HPC), or supercomputing space. But with such a premium being put on GPUs for large machine learning these days, Kubernetes could provide a more dynamic way for managing vast fleets of GPUs, with the little help from tools that…

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Panic: Could not run ‘torchvision::roi_pool’ with arguments from the ‘CUDA’ backend – Jetson Nano

Hi, Team! I have such errors, when I run my code in docker container: root@de87551d73cf:/app/src# ./main WARN[0032] CUDA is valid WARN[0044] CUDA is valid INFO[0044] Forwarding… [W TensorImpl.h:1156] Warning: Named tensors and all their associated APIs are an experimental feature and subject to change. Please do not use them for…

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Issue with Accessing Thermo Data in Pylammps – LAMMPS Installation

Dear members of the LAMMPS mailing list, I have been attempting to build and install the LAMMPS Python interface (Pylammps) to leverage the advantages of accessing thermos data. However, I am encountering the following error: Based on my understanding from the documentation, if I set up a simulation with a…

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How to Install autodock-vina software package in Ubuntu 16.04 LTS (Xenial Xerus)

How to Install autodock-vina software package in Ubuntu 16.04 LTS (Xenial Xerus) autodock-vina software package provides docking of small molecules to proteins, you can install in your Ubuntu 16.04 LTS (Xenial Xerus) by running the commands given below on the terminal, $ sudo apt-get update $ sudo apt-get install autodock-vina…

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RStudio doesn’t work on Debian 12 with R version 4.3.2 – General

Hello, From the download website, it seems RStudio support Debian 12. I have installed R 4.3.2 R version 4.3.2 (2023-10-31) — “Eye Holes”Copyright (C) 2023 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain…

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Resolving Slurm cgroups Plugin Errors on Ubuntu 22.04 Nodes

I’m working with Slurm and facing issues specifically with the cgroups plugin on Ubuntu 22.04 nodes. Our team is relatively new to Slurm, and we’ve been trying to optimize our resource management for complex computing tasks. However, we’ve encountered a series of errors that are proving difficult to resolve. Here’s…

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Troubleshooting Slurm cgroups Plugin on Ubuntu 22.04

I’m facing a challenging issue with the Slurm cgroups plugin on a system running Ubuntu 22.04. We’re relatively new to Slurm and started using it for better resource management in complex computing tasks. However, we’ve hit a snag with the cgroups plugin, particularly on our Ubuntu 22.04 nodes. Here’s what…

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Automating API Documentation: A Journey from TypeScript to OpenAPI and Schema Governence with Optic

In the previous blog post Documenting and Testing Schemas of Serverless Stacks with Optic & Cypress, we focused on the benefits of schema testing and governance. Briefly, some of the core problems addressed were: Effortless API Documentation: Automating the API documentation creation and update, ensuring that our API documentation evolves…

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systemd autopkgtest regression on arm64 and s390x on mantic

Is seems the container fails to boot. From a bad run: 9109s autopkgtest [10:39:17]: test tests-in-lxd: [———————– 9145s 2023-11-28T10:39:50Z INFO Waiting for automatic snapd restart… 9259s lxd 5.19-8635f82 from Canonical** installed 9288s Creating autopkgtest-prepare-jhI 9475s Retrieving image: metadata: 100% (323.81MB/s) Retrieving image: rootfs: 1% (3.53MB/s) <SNIP> Retrieving image: rootfs: 100%…

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proxy – Failed to Download Packages from Github via Devtools in RStudio

I am just beginning to learn R and have built up an RStudio Server by WSL (Ubuntu 22.04.2)(yes, my PC is on Win11 and just want to use Unix environment). So here it is, I tried to download some packages by devtools::install_github(), yet the console simply showed: Error: Failed to…

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Where is the index command?

Where is the index command? 1 I unpacked Samtools in Ubuntu using apt install make. The directory is listed below and includes folders and files. There is no index function. I have bam file and am trying to make bai file, not sure what to do next? index command •…

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Problem in installing ‘magick’ R package

Problem in installing ‘magick’ R package 0 Hi everyone: I have attempted to install the R package ‘magick’ on R (version: 4.3.1) using the following command: install.packages(“magick”) However, it turns out that there were some warning messaged popped out in the R console: Installing package into ‘/home/billychan/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is…

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bam or VCF files from GSE75010

bam or VCF files from GSE75010 1 Hi all I’m planning to run a variant calling analysis using Microarray data GSE75010 that contains GSE75010_RAW.tar and GSE75010_complete_dataset.csv.gz. I used to download the .fastq files using SRA Run numbers through Ubuntu/Linux to get .bam and VCF files. However, this is not the…

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finished abnormally, OS return value: 21

SPAdes error: finished abnormally, OS return value: 21 1 I’m having trouble using SPAdes. I’m using SPAdes to do paired end data assembly and I’m getting an unusual stop. error code: finished abnormally, OS return value: 21 Do you know how to resolve this issue? Environment: conda, SPAdes genome assembler…

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AMD brings AI development with PyTorch and ROCm to Radeon RX 7900 XT GPUs

– Advertisement –– In its ongoing effort to make AI more accessible to developers and researchers, AMD added support for Radeon RX 7900 XT GPUs to the AMD ROCm 5.7 open software ecosystem.  Following the recent extension of ROCm support to other AMD RDNA 3 architecture-based GPUs – the AMD Radeon RX…

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Index of /~birch/birchhomedir/dat/mGDE/GDEHELP-osx-x86_64/dat/GDE/GDEHELP-solaris-amd64/dat/fasta2

Name Last modified Size Description Parent Directory   –   blosum50.mat 2008-04-13 19:29 2.1K   bovgh.seq 2008-04-13 19:29 2.5K   bovprl.seq 2008-04-13 19:29 1.0K   codaa.mat 2008-04-13 19:29 1.0K   dna.mat 2008-04-13 19:29 489   egmsmg.aa 2008-04-13 19:29 1.3K   gonnet.mat 2008-04-13 19:29 952   idnaa.mat 2008-04-13 19:29 1.0K  …

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[Kernel-packages] [Bug 2039144] Autopkgtest regression report (linux-meta-laptop/6.5.0.1007.10)

All autopkgtests for the newly accepted linux-meta-laptop (6.5.0.1007.10) for mantic have finished running. The following regressions have been reported in tests triggered by the package: systemd/253.5-1ubuntu6.1 (arm64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-raspi/6.5.0.1008.9)

All autopkgtests for the newly accepted linux-meta-raspi (6.5.0.1008.9) for mantic have finished running. The following regressions have been reported in tests triggered by the package: acpi-call/unknown (arm64) adv-17v35x/unknown (arm64) backport-iwlwifi-dkms/unknown (arm64) bbswitch/unknown (arm64) dahdi-linux/unknown (arm64) ddcci-driver-linux/unknown (arm64) digimend-dkms/unknown (arm64) dm-writeboost/unknown (arm64) dpdk-kmods/unknown (arm64) evdi/unknown (arm64) falcosecurity-libs/unknown (arm64) fwts/unknown (arm64) glibc/unknown…

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Bug in element-wise multiplication of `torch.sparse_csr_tensor`s on GPU – 0’s in result considered significant

🐛 Describe the bug Problem:The problem occurs when using the PyTorch version 2.1.1. The result of element-wise multiplication between two torch.sparse_csr_tensors consider 0s as significant values and retain them in their sparse form. This is not the expected behavior. Moreover, this bug occurs only when the operation is run on…

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AMD uses PyTorch and ROCm to inject AI R&D momentum into Radeon RX 7900 XT graphics cards

5 AMD Expands Support for Developers and Researchers in AI with Radeon RX 7900 XT Graphics Card AMD has once again expanded its support for developers and researchers in the field of artificial intelligence (AI) with the announcement of added support for the Radeon RX 7900 XT graphics card to…

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MinKNOW software installation doubt for MinION Nanopore sequencing

MinKNOW software installation doubt for MinION Nanopore sequencing 0 Hi good people, Recently in lab we have received a Nanopore MinION device and currently trying to figure out installation and other details. I am seeking a few suggestions from users and experts. The running machine spec is AMD Ryzen 9…

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AMD ROCm 5.7 Platform Adds Support for RX 7900 XT – Keep up with CUDA!

0 Create a news article using this content Keep up with CUDA! AMD ROCm platform now supports RX 7900 XT 2023-11-23 14:06:14 Source: Kuai Technology Author: Shang Shang Wen Q Editor: Shang Sang Wen Q Comments () Kuai Technology News on November 23,AMD recently released the ROCm 5.7 version development…

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[slurm-users] Releasing stale allocated TRES

Hi there, I have a recurring problem with allocated TRES, which are not released after all jobs on that node are finished. The TRES are still marked as allocated and no new jobs can’t be scheduled on that node using those TRES. $ scontrol show node node2 NodeName=node2 Arch=x86_64 CoresPerSocket=64 CPUAlloc=0 CPUTot=256…

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Rstudio crashes just before producing a brms model – General

Hello, I am trying to run a brms model with 20000 iterations. After many hours of simulations, and just before being done, Rstudio crashes without any warning. The model compiles successfully with 1000 iterations and, sometimes, with 10000 iterations but several attempts to run the model with 20000 iterations or…

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Bugs : samtools-legacy package : Ubuntu

This bug was fixed in the package samtools-legacy – 0.1.19+dfsg-6ubuntu1 —————samtools-legacy (0.1.19+dfsg-6ubuntu1) noble; urgency=low   * Merge from Debian unstable. (LP: #2044194) Remaining changes:    – Add backport of upstream commit 515f6df as      d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch      in support of fixing ‘zlib: compressBound() returns an incorrect result      on z15′.  * Fixed a couple of spelling errors in the description of    d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch….

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Senior Bioinformatics Support Specialist – it-jobs-switzerland.ch

This is a version of the job ad optimized for mobile devices. Show original job ad The Position ROLE SUMMARY: Creates,  reviews, and maintains training content and training documentation for job-oriented training in cooperation with regional training centers. Training are executed and supported for end customers, first-level support, regional trainers,…

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Unable to launch RStudio on Ubuntu 22.04 – General

Hi, Sorry for the simple question, but I have had some issues getting RStudio to launch on Ubuntu. I am using Ubuntu 22.04.3. I have R installed, and it is running fine. I installed RStudio as below: sudo apt install -f /home/parallels/rstudio-2023.12.0-daily-323-arm64.deb It seems to run fine, but no icon…

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AMD arms three of its gaming GPUs with PyTorch and ROCm support for AI development

AMD announced that three of its RDNA3 desktop graphics cards, the Radeon RX 7900 XT, 7900 XTX, and the Radeon Pro 7900, will now support machine learning development via PyTorch and its ROCm software. PyTorch was originally made by Meta AI but is currently a part of the Linux Foundation….

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Print IP Addresses and Hostnames From Host File on Linux

The host file, located at /etc/hosts on Linux systems, is a crucial part of the networking configuration. It maps hostnames to IP addresses, allowing the system to resolve domain names locally before querying external DNS servers. Sometimes, it becomes necessary to view the entries in this file for troubleshooting or…

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AMD Radeon RX 7900 XT Is The Latest RDNA 3 GPU To Land Support For ROCm 5.7, Accelerated AI With PyTorch

AMD has added the Radeon RX 7900 XT to its list of RDNA 3 consumer-tier GPUs that are supported in the ROCm 5.7 ecosystem including PyTorch. AMD’s Top-Brass of RDNA 3 “Navi 31” GPUs Are Now ROCm 5.7 Supported, PyTorch ML & AI Acceleration Available On Radeon RX 7900 XT…

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AMD extends ROCm 5.7 & PyTorch support to Radeon RX 7900 XT

AMD RX 7900 XT now supported by ROCm 5.7 Three weeks ago, AMD announced that it would support the first RDNA3 GPUs through its ROCm platform for PyTorch. Today, new gaming GPU is being added to this list. AMD is willing to put some money and effort into supporting machine…

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AMD Delivers More Options for AI Developers by Ext…

We recently launched AMD ROCm™ 5.7 for the AMD Radeon™ RX 7900 XTX and Radeon™ PRO W7900 GPUs for Machine Learning (ML) development workflows with PyTorch. We have now extended support to include the Radeon™ RX 7900 XT GPU, introducing even more options for AI developers and researchers.   The…

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[Kernel-packages] [Bug 2007050] Autopkgtest regression report (initramfs-tools/0.142ubuntu15.1)

All autopkgtests for the newly accepted initramfs-tools (0.142ubuntu15.1) for mantic have finished running. The following regressions have been reported in tests triggered by the package: initramfs-tools/0.142ubuntu15.1 (armhf) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-raspi/5.4.0.1099.129)

All autopkgtests for the newly accepted linux-meta-raspi (5.4.0.1099.129) for focal have finished running. The following regressions have been reported in tests triggered by the package: nvidia-graphics-drivers-390/390.157-0ubuntu0.20.04.1 (armhf) openafs/unknown (arm64) openrazer/unknown (arm64) systemd/unknown (arm64) west-chamber/unknown (arm64) wireguard/unknown (arm64) wireguard-linux-compat/unknown (arm64) xtables-addons/unknown (arm64) zfs-linux/unknown (arm64) Please visit the excuses page listed below…

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Run PyTorch Docker Container on Ubuntu with Lambda Stack

Run PyTorch Docker Container on Ubuntu with Lambda Stack Introduction Installing Lambda Stack The One-Line Command Install Installing Nvidia Drivers Installing Deep Learning Libraries and Frameworks Keeping Libraries Up-to-Date Rebooting the System Installing Docker and Nvidia Container Toolkit Installing the Latest Version of Docker Installing the Nvidia Container Toolkit Checking…

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Pflowtts Pytorch – Open Source Agenda

P-Flow: A Fast and Data-Efficient Zero-Shot TTS through Speech Prompting Authors : Sungwon Kim, Kevin J Shih, Rohan Badlani, Joao Felipe Santos, Evelina Bhakturina,Mikyas Desta1, Rafael Valle, Sungroh Yoon, Bryan Catanzaro Affiliations: NVIDIA Status : Generated first sample (Check LJSpeech_Sample_100_epochs.wav) on 11/16/2023. Unofficial implementation of the paper P-Flow: A Fast…

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Installation of DESeq2 package while utilizing free Posit cloud – General

Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager)Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)BiocManager::install(“DESeq2”)‘getOption(“repos”)’ replaces Bioconductor standard repositories,…

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DESeq2 installation failures

DESeq2 installation failures 0 Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager) Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2…

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Index of /ubuntu/pool/universe/r/r-bioc-pwmenrich

Name Last modified Size Parent Directory   – r-bioc-pwmenrich_4.30.0-1.debian.tar.xz 2021-11-25 18:34 2.4K r-bioc-pwmenrich_4.30.0-1.dsc 2021-11-25 18:34 2.1K r-bioc-pwmenrich_4.30.0-1_all.deb 2021-11-25 18:38 1.9M r-bioc-pwmenrich_4.30.0.orig.tar.gz 2021-11-25 18:34 1.6M r-bioc-pwmenrich_4.34.0-1.debian.tar.xz 2022-11-21 18:39 2.4K r-bioc-pwmenrich_4.34.0-1.dsc 2022-11-21 18:39 2.1K r-bioc-pwmenrich_4.34.0-1_all.deb 2022-11-21 18:40 1.9M r-bioc-pwmenrich_4.34.0.orig.tar.gz 2022-11-21 18:39 1.6M r-bioc-pwmenrich_4.36.0-1.debian.tar.xz 2023-07-22 07:34 2.5K r-bioc-pwmenrich_4.36.0-1.dsc 2023-07-22 07:34 2.1K r-bioc-pwmenrich_4.36.0-1_all.deb 2023-07-22…

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DESeq2 design with unbalance data and a multifactor design

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

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DESeq2 with unbalanced dataset and multifactor design

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

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Building from source a pytorch wheel file with all the dependencies and Cuda+Cudnn included; Linux+Python 3.7, Cuda=11.2+Cudnn=8.1

I want to build torch v1.12.1 from source and create wheel with all the dependencies included into the wheel file . Additionally, to force the inclusion of all the Cuda and Cudnn -related stuff from my system into the wheel file. Similar task goes for torchvision v0.13.1.I have Ubuntu 22.04…

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Computation of dipole moment through variable command – LAMMPS General Discussion

Hi!I want to compute dipole moment as sigma(qi*ri) by using variable of atom style however I am getting an error of “Substitution for illegal variable Mnew”. Here are my lines from the code:variable charge atom “q”variable x1 atom “xu”variable y1 atom “yu”variable z1 atom “zu”variable r1 atom “v_x1+v_y1+v_z1”variable Mnew atom…

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PyTorch on ROCm in Docker in QEMU fails – deployment

I know the obvious answer to this is probably that there are just too many layers of jank, and it’s even worse than the title. I’m running PyTorch from the rocm/pytorch Docker container. I’m starting the container by running: docker run -it –network=host –device=/dev/kfd –device=/dev/dri –group-add=video –ipc=host –cap-add=SYS_PTRACE –security-opt seccomp=unconfined…

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AVX error with Deepvariant caller

I installed Deepvariant 1.6.0 on a: Dell poweredge R910, 128 Gb of RAM, 36 cores. The is machine has windows 10 LTSC installed on it. However, also installed on it is: Virtual box 6.0 Ubuntu 20.04 LTS Controller ID: Vboxguestaddtions_6.06 Deepvariant was installed on ubuntu 20.04 LTS using docker: github.com/google/deepvariant…

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Workbench project sharing issue: system error 13 (Permission denied) – NFSv4 on Ubuntu 20.04 – RStudio IDE

Hi there,I have a new Posit Workbench installation on Ubuntu 20.04 and I’m attempting to replicate what I had on my old servers – project sharing working across an NFSv4 share which contains all my user home directories. Both the sharing machine and Workbench machine are running the same version…

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My desktop freezes at random times while training with pytorch – cuDNN

[Environment]OS : Ubuntu 22.04Device : GeForce RTX 4090Nvidia-driver : 535.129.03cuda : cuda_12.1.r12.1 (check with “nvcc -V” command) python : 3.10.12torch : 2.1.0 [Problem that is occurring]While model training, my desktop freezes at random times. Instead of the python process freezing, ubuntu itself freezes completely. It won’t come back on unless…

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Index of /ubuntu/ubuntu/pool/universe/g/golang-github-go-openapi-errors

Name Last modified Size Parent Directory   – golang-github-go-openapi-errors-dev_0.0~git20160704.0.d24ebc2-1_all.deb 2017-04-30 07:43 7.2K golang-github-go-openapi-errors-dev_0.15.0-1_all.deb 2019-10-29 18:46 8.9K golang-github-go-openapi-errors-dev_0.20.1-3_all.deb 2021-12-01 19:13 12K golang-github-go-openapi-errors-dev_0.20.2-1_all.deb 2022-05-12 00:24 12K golang-github-go-openapi-errors_0.0~git20160704.0.d24ebc2-1.debian.tar.xz 2017-04-30 01:54 1.7K golang-github-go-openapi-errors_0.0~git20160704.0.d24ebc2-1.dsc 2017-04-30 01:54 2.3K golang-github-go-openapi-errors_0.0~git20160704.0.d24ebc2.orig.tar.xz 2017-04-30 01:54 14K golang-github-go-openapi-errors_0.15.0-1.debian.tar.xz 2019-10-29 18:45 2.4K golang-github-go-openapi-errors_0.15.0-1.dsc 2019-10-29 18:45 2.3K golang-github-go-openapi-errors_0.15.0.orig.tar.xz 2019-10-29 18:45 14K golang-github-go-openapi-errors_0.20.1-3.debian.tar.xz 2021-12-01…

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Ubuntu Manpage: Bio::Ontology::DocumentRegistry – Keep track of where to find ontologies. Allows lookups

Provided by: libbio-perl-perl_1.7.7-1_all NAME Bio::Ontology::DocumentRegistry – Keep track of where to find ontologies. Allows lookups by name. SYNOPSIS my $registry = Bio::Ontology::DocumentRegistry->get_instance(); my($ont,$def,$fmt) = $registry->documents(‘Sequence Ontology’); my $io = Bio::OntologyIO->new(-url => $ont, -defs_url => $def, -format => $fmt); my $so = $io->next_ontology(); #… DESCRIPTION Do not use this directly, use…

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speech recognition – PyTorch: loss.backward() keeps running for days

I’m using the pretrained model from deepspeech_pytorch (github.com/SeanNaren/deepspeech.pytorch) to do some speech recognition tasks. However, the loss.backward() keeps running for days in training phrase. The code block of training phrase: adversary_model = AdversaryModel( … ) adv_trainset = WavDataset(adv_trainset_wav_path_list, model.labels, adv_train_spect_parser) adv_trainset_dataloader = AudioAdvTrainDataLoader(dataset=adv_trainset, batch_size=FLAGS.batch_size, pin_memory=True, shuffle=True) model.train() # Because my…

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Improve setting up docs – ExecuTorch

escorciav (Victor Escorcia) November 9, 2023, 3:56pm 1 Hi all, Thanks a lot for putting out a quite detailed & easy to navigate documentation & tutorial! Now, Does anyone else feels that the docs jump from 0 to 1?What about linking concepts from How-it-works & High-level-overview into the setting things…

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Index of /ubuntu/ubuntu/pool/universe/g/golang-github-go-openapi-jsonpointer

Name Last modified Size Parent Directory   – golang-github-go-openapi-jsonpointer-dev_0.0~git20160704.0.46af16f-1_all.deb 2017-04-30 03:24 5.4K golang-github-go-openapi-jsonpointer-dev_0.19.5-3_all.deb 2021-12-01 00:25 8.9K golang-github-go-openapi-jsonpointer-dev_0.19.5-4_all.deb 2022-11-25 06:39 8.9K golang-github-go-openapi-jsonpointer-dev_0.19.6-1_all.deb 2023-10-27 02:58 9.4K golang-github-go-openapi-jsonpointer_0.0~git20160704.0.46af16f-1.debian.tar.xz 2017-04-30 02:00 1.8K golang-github-go-openapi-jsonpointer_0.0~git20160704.0.46af16f-1.dsc 2017-04-30 02:00 2.4K golang-github-go-openapi-jsonpointer_0.0~git20160704.0.46af16f.orig.tar.xz 2017-04-30 02:00 12K golang-github-go-openapi-jsonpointer_0.19.5-3.debian.tar.xz 2021-12-01 00:25 2.7K golang-github-go-openapi-jsonpointer_0.19.5-3.dsc 2021-12-01 00:25 2.5K golang-github-go-openapi-jsonpointer_0.19.5-4.debian.tar.xz 2022-11-25 06:39 2.8K golang-github-go-openapi-jsonpointer_0.19.5-4.dsc 2022-11-25…

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rstudio – Emacs is not reading files from other partitions

rstudio – Emacs is not reading files from other partitions – Ask Ubuntu Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Visit Stack Exchange Log in Sign…

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Regarding the error of MD run with CHARMM36 force field – User discussions

Praveen November 9, 2023, 11:28am 1 GROMACS version: 2023GROMACS modification: No Question:I am working in the MD simulation on GROMACS 2023 with Protein+Lipid (as ligand) complex. I have encountered an error, and I already tried all available option to perform MD run with Python version 3.7 and both versions of…

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Cuda error with gromacs 2023.3 (CUDA error #700 an illegal memory access) – User discussions

roozi November 7, 2023, 10:16pm 1 GROMACS version:2023.3GROMACS modification: NoI ‘m getting a CUDA error using the standard Gromacs 2023.3 version on my laptop using:NVIDIA RTX-4060 gpu and 20 OpenMP threads (corei7 generation 13).Cuda version: 12.3 nvidia driver version: 545.84 . Os: Ubuntu 22.4.02 (installed on WSL2 , WINDOWS 11)…

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Index of /ubuntu/pool/universe/p/python-deeptools

Name Last modified Size Description Parent Directory   –   python-deeptools_3.3.2+ds-2.debian.tar.xz 2020-02-08 20:23 5.2K   python-deeptools_3.3.2+ds-2.dsc 2020-02-08 20:23 2.3K   python-deeptools_3.3.2+ds.orig.tar.xz 2020-01-24 14:18 23M   python-deeptools_3.5.0-1.debian.tar.xz 2020-10-28 16:25 5.6K   python-deeptools_3.5.0-1.dsc 2020-10-28 16:25 2.3K   python-deeptools_3.5.0.orig.tar.xz 2020-10-28 16:25 23M   python-deeptools_3.5.1-1.debian.tar.xz 2021-10-18 18:17 5.7K   python-deeptools_3.5.1-1.dsc 2021-10-18 18:17 2.3K  …

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[SOLVED] – AMD GPU 7900XTX passthrough to Ubuntu 22.04 guest vm on proxmox 8.0.2 for PyTorch ROCM.

I got a new machine with AMD CPU 7950x and GPU 7900XTX setup with Proxmox 8.0.2 a few days ago. After successfully make the dedicated GPU passthrough to a Windows11 guest vm and a Ubuntu 22.4 guest vm, I tried to install the latest AMD ROCM support with Pytorch in…

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mv Question during kraken2-build (building database)

mv Question during kraken2-build (building database) 1 Hello all, I’d downloaded and installed Karken2 locally on WSL Ubuntu. After install, I build a standard database with the command: kraken2-build –standard –db databasename here is the out: Downloading nucleotide gb accession to taxon map… done. Downloading nucleotide wgs accession to taxon…

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shiny server running but shiny app does not spawn up from rstudio run button

I have recently launched a new ubuntu 20.04 server on the cloud, installed R, Rstudio and shiny server (all open source). The rstudio is accessible on a remote browser connection. But somehow I am unable to make a simple shiny app to spawn up. Even the sample app /sample-apps/hello/ does…

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