Tag: centos

python – Reading files asynchronously hangs within Pytorch Dataset when DataLoader.num_workers > 1

I’m training a classifier on raw-bytes in binary files. Each file can be several megabytes long. I have a dataset with several millions of binaries in it. Loading all this data at once and keeping it all in memory is very expensive, so I wanted to write an IterableDataset to…

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gcc – Error compiling giac (inside SageMath) in poly.h function

Environment: CentOS 7.9 GCC 13.1.0 SageMath 10.0 When compiling SageMath, the compilation gets to the “giac” program and fails. The failure occurs in the “poly.h” function. I’m on a closed network so I cannot upload the logfile. Here is the last part of the error: modpoly.cc:16082:1: internal compiler error: Aborted…

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Dihedral atom missing error on lammps – LAMMPS

Dear All, I have a linear coarse-grained polymer system, with nonbonded, bond, angle, and dihedral interactions as a tabulated potential. My simulations consist of 1000 polymer chains, each chain has 200 monomers. The simulations sometimes crash because of dihedral atom missing errors in some processors. I am running the latest…

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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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Jupyterhub z2jh ingress not working – Zero to JupyterHub on Kubernetes

bpfrd December 15, 2023, 6:54pm 1 Hi, I deployed z2jh on a single-node microk8s cluster on a server and it is supposed to be used in production. The problem is ingress address is missing. here is some details: # config.yaml ingress part ingress: annotations: kubernetes.io/tls-acme: “true” enabled: true hosts: -…

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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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Why is DMRcate not available for Bioconductor version 3.18?

Why is DMRcate not available for Bioconductor version 3.18? 0 @daniel-e-weeks-10677 Last seen 22 hours ago Pittsburgh, Pennsylvania, United States… According to the Bioconductor web page for DMRcate, it looks like it is available for Bioconductor version 3.18 but this installation fails: > BiocManager::install(“DMRcate”) Bioconductor version 3.18 (BiocManager 1.30.22), R…

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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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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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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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Deploy CP2K on an Azure virtual machine

This article describes the steps for running a CP2K application on a virtual machine (VM) deployed on Azure. It also presents the performance results of running CP2K on single-node and multi-node VM configurations. CP2K is a quantum chemistry and solid-state physics software package that can perform atomistic simulations of solid…

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Bioinformatics Specialist I | MGH Cancer Center

!*! GENERAL SUMMARY/ OVERVIEW STATEMENT: In Gulhan Lab, we develop statistical and machine learning methods for cancer genomics to improve patient classification and early cancer detection strategies. We aim to decipher the broad spectrum of genomic instabilities that dictate the evolution of cancer genomes, and to understand how best to…

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epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data | GigaScience

Abstract Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5–8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new…

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list index out of range” error while running BETA (Cistrome)

“IndexError: list index out of range” error while running BETA (Cistrome) 0 Dear all, I am getting the error “indexError: list index out of range” while running BETA basic on centos server. Please find the error and input files screenshot attached with this message. Command used: BETA basic -p hcleaf.27me3.final_peaks_macs3_5col.bed…

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[slurm-users] How to delay the start of slurmd until Infiniband/OPA network is fully up?

I’m fighting this strange scenario where slurmd is started before the Infiniband/OPA network is fully up. The Node Health Check (NHC) executed by slurmd then fails the node (as it should). This happens only on EL8 Linux (AlmaLinux 8.8) nodes, whereas our CentOS 7.9 nodes with Infiniband/OPA network work without…

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Error in Gviz (actually, rtracklayer)

Error in Gviz (actually, rtracklayer) | IdeogramTrack 0 @25075190 Last seen 7 minutes ago South Korea When I run this code (below) iTrack <- IdeogramTrack(genome = “hg19”, chromosome = “chr2”, name = “”) then I get the error Error: failed to load external entity “http://genome.ucsc.edu/FAQ/FAQreleases” Did someone else encounter this…

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r – unable to install Tidyverse in RStudio / Chromebook

I have been trying to install tidyverse via RStudio (R 4.3.1) on my Acer chromebook, but keep having error messages. I have been working my way through these messages with the help of previously asked questions on stackoverflow as well as google and chatGPT I have tried various things and…

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Installing ‘tidyverse’ package for R/RStudio – General Help

With help from this forum, I was able to get R and RStudio working on Zorin 16 Lite. I now need to install the ‘tidyverse’ package for R, but attempting the install gives this error: $ sudo R (R starts up) > install.packages(“tidyverse”) Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is…

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[slurm-users] SLURM disregards LDAP configured via SSSD

Hi, I have an issue with SLURM (20.11.9) in conjunction with LDAP user accounts. Both the scheduler node, where slurmctld is running, and the worker nodes that are spun up by slurm are running the SSSD, which fetches user accounts from an external LDAP server. This works fine: I can log into…

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pytorch – torch.cuda.is_available() is False, when correct CUDA is installed. What could be wrong?

I’m having some trouble getting pytorch to access the GPU. I know that there is an agreement of the CUDA version (11.8). I leave some additional information below, does anyone know what is going on? In case it is relevant, I am working on an HPC. When connecting to the…

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DiffBind dba.count() crash/can’t finish problems

I am using Diffbind for an ATAC-Seq analysis. My peak caller is MACS2, and here is my sample sheet: I run Diffbind with the following codes, but it crashed every time on dba.count . it can finished Computing summits… Recentering peaks… Reads will be counted as Paired-end. But have this…

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Write up of installation of JupyterHub on CentOS 8 server – JupyterHub

I recently set up a JupyterHub on a CentOS 8 server on Azure. I would normally set up a hub on Kubernetes (with Zero to JupyterHub) but I was helping a team that had an internal CentOS 8 bare metal server at their institute and wanted to set up a…

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Intel To Further Collaborate With Red Hat, Canonical & SUSE For Intel-Optimized Linux Distros

Show Your Support: This site is primarily supported by advertisements. Ads are what have allowed this site to be maintained on a daily basis for the past 19+ years. We do our best to ensure only clean, relevant ads are shown, when any nasty ads are detected, we work to…

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issue with qiime dada2 denoise-ccs – Technical Support

Hi,I have 24 clean CCS read datasets and i want to get amplicon sequence variants by running dada2.I got one issue when running dada2 denoise-ccs with QIIME2. When i am running dada2 in qiime2 with all 24 samples:The command I used was: qiime dada2 denoise-ccs –i-demultiplexed-seqs reads_qza/ccs_reads.qza –p-min-len 1200 –p-max-len…

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After installing Jupyter Hub and Jupyter Lab on CentOS 7, how do I use them on Windows?

After installing Jupyterhub in CentOS 7 Master account, I want to set up analysis environments and use Jupyter Lab in each account. I want to connect with Jupyter lab from windows-based computer, so people don’t need to log-in to CentOS 7, they just need to write password in Jupyter Lab…

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htseq-count reports count values for deleted genes

htseq-count reports count values for deleted genes 0 I am using htseq-count on BAM files from a bacterial species. We are comparing WT strains as well as two strains with genes knocked out. The knockouts have been verified with whole genome sequencing, but do retain the first 15 and last…

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TCGAbiolinks not working anymore

TCGAbiolinks not working anymore 0 The script in this tutorial does not work anymore https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html I get to GDCprepare stage and get error: Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix paper_ brca…

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gladiaio-torchaudio 2.1.0a0 on PyPI – Libraries.io

The aim of torchaudio is to apply PyTorch to the audio domain. By supporting PyTorch, torchaudio follows the same philosophy of providing strong GPU acceleration, having a focus on trainable features through the autograd system, and having consistent style (tensor names and dimension names). Therefore, it is primarily a machine…

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Massachusetts General Hospital hiring Bioinformatics Specialist I in Boston, MA

General Summary & Overview StatementThe Iafrate Lab conducts pioneering research in the field of clinical genomics, working to develop personalized approaches to early cancer detection, diagnosis, and therapy. We are seeking a highly motivated bioinformatician with a background in statistics and/or software development to be a part of our team…

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Installing R and RStudio on Linux for Data Analysis

R is a versatile programming language and environment designed specifically for data analysis and statistical computing, making it an incredible choice for data-driven work. R has gained significant popularity across the data science, data analysis, data visualization, and statistical communities due to its extensive capabilities and active user community. In…

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How can I use vpn from command line running on a centos virtual machine

How can I use vpn from command line running on a centos virtual machine 0 I built a centos virtual machine on windows10 and connected the host network using bridge mode. Currently I use clash for windows to link to the host vpn and enable the LAN so that the…

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Rstudio can’t find CMAKE even though it is in /usr/local/bin – Package Management

I have been attempting to install a package that requires cmake. However, Rstudio can’t seem to find it for some reason: R version 4.3.1 (2023-06-16) — “Beagle Scouts” Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin22.4.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY….

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Filter gene with low count in RNA-seq using a function from edgeR

Hi all, I try to filter out gene with low count from raw count matrix I run d <- DGEList(counts=counts,group=factor(conditions)) keep <- filterByExpr(d) bcv <- 0.2 et <- exactTest(keep, dispersion=bcv^2) Error in exactTest(d, dispersion = bcv2) : Currently only supports DGEList objects as the object argument. d <- estimateTagwiseDisp(d) Error…

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“, cdfname, object ‘cdf’ not found

Hello, I would like your suggestions for this error with rma() function, for analysing microRNA-affymetrix data. I downloaded the package cdf (miRNA-4_0-st-v1_CDF) (provided below), created the package with make.cdf.package, installed it with R CMD INSTALL. library(makecdfenv) make.cdf.package(filename = “miRNA-4_0-st-v1.cdf”, packagename = “miRNA-4_0-st-v1.cdf”, cdf.path = “./miRNA_4_0_CDF/”, package.path= “/shared/home/mkondili/Tools_Packages/”, compress = FALSE,…

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Gromacs installation with cp2k – User discussions

vikas July 25, 2023, 12:40pm 1 GROMACS version: 2021.4GROMACS modification: NoBelow is the cmake command I am using:cmake … -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF -DGMX_DOUBLE=ON -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=$cp2k_install/fftw-3.3.10/lib/ -DFFTWF_INCLUDE_DIR=$cp2k_install/fftw-3.3.10/include -DGMX_BLAS_USER=$cp2k_install/openblas-0.3.20/lib/ -DGMX_LAPACK_USER=$cp2k_install/scalapack-2.1.0/lib/ -DGMX_CP2K=ON -DCP2K_DIR=$cp2k_home/lib/local/psmp/ -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_cp2k -DGMX_LIBS_SUFFIX=_cp2k -DCMAKE_INSTALL_PREFIX=/home/chemistry/phd/cyz208667/Softwares/new_cp2k/gmx_install -DCP2K_LINKER_FLAGS=“-Wl,–enable-new-dtags -L/home/soft/centOS/compilers/gcc/openmpi/4.1.4/lib -Wl,-rpath -Wl,/home/soft/centOS/compilers/gcc/openmpi/4.1.4/lib -Wl,–enable-new-dtags -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/openblas-0.3.20/lib’ -Wl,-rpath=‘/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/openblas-0.3.20/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/fftw-3.3.10/lib’ -Wl,-rpath=‘/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/fftw-3.3.10/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libxc-5.2.3/lib’ -Wl,-rpath=‘/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libxc-5.2.3/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libxsmm-1.17/lib’ -Wl,-rpath=‘/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libxsmm-1.17/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/scalapack-2.1.0/lib’ LIBS=…

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Pytorch installed via pip does not pick up CUDA – Help

I have a simple shell.nix that picks up python3.9 from nix store and immediately enters Pythons virtualenv where I installed pytorch with CUDA support from pip (using Pytorch’s official instructions). with import <nixpkgs> {}; mkShell { buildInputs = [ stdenv.cc.cc.lib python39 python39Packages.pip ]; shellHook = ” # Add the library…

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Tljh compatibility with AWS Linux2 – The Littlest JupyterHub

A98 July 20, 2023, 9:52am 1 I have an “Amazon Linux2” server is it compatible to install jupyterhub? Do i follow the same steps as in Installing on your own server — The Littlest JupyterHub documentation to install jupyterhub on an existing ec2 instance? The needs are spelled out in…

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How can I install R packages in newest version of R 4.2.3 image while building the image through docker file

I am trying to update and rebuild my RStudio image on centos with the docker file. Initially I was using R-3.6.0 which I am planning to update to R-4.3.1 Updated code snippet RUN yum install -y java-1.8.0-openjdk-devel \ R-4.3.1 \ # Updated this line from R-3.6.0 devtoolset-8 –nogpgcheck && \…

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python – Could not install tensorflow in RStudio

I am trying to install tensorflow in R Studio through Linux terminal, by following the three methods mentioned in this link https://tensorflow.rstudio.com/install/, namely “auto”, “virtualenv” and “conda”. However, none of them worked. Following the method “auto”, we tried with the command tensorflow::install_tensorflow() However, it gave an error related to the…

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Programmer Analyst II (Bioinformatics) – Frederick National Laboratory for Cancer Research

Programmer Analyst II (Bioinformatics) Job ID: req3577Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: Frederick: Ft DetrickLocation: PO Box B, Frederick, MD 21702 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc.  The lab addresses…

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RStudio Server Professional Edition 1.3.952-1

Logging In By default RStudio Server runs on port 8787 and accepts connections from all remote clients. After installation you should therefore be able to navigate a web browser to the following address to access the server: http://<server-ip>:8787 RStudio will prompt for a username and password and will authenticate access…

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CIQ Completes Testing of Popular Machine Learning Frameworks, Utilities and Libraries for Artificial Intelligence for Mountain Subscribers

Powering the next generation of software infrastructure We are demonstrating that the HPC software infrastructure fits the range of workloads from classic HPC simulations to the newer AI use cases. RENO, Nev. (PRWEB) July 06, 2023 CIQ, the company building innovation with Rocky Linux, today unveiled new capabilities of…

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FastQC command line usage

FastQC command line usage 2 Hi, I am supposed to run FastQC in linux server (I don’t have chance to use graphical user interface) how can I use command line for running fastqc for my sequences? Thanks in advance. command-line FastQC linux CentOS • 7.8k views After installing FastQC, you…

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Failing to publish/deploy a shiny app to an Posit Connect because of Bioconductor – Posit Connect

I have a shiny app the I’ve been publishing to a Posit Connect server hosted by the HPC at my institution. The app is from my RStudio on my laptop . The Cluster has configured Posit Connect to use Package Manager to host and vet packages for security and stability….

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Cannot access RStudio IDE instance using Conda Environment – RStudio IDE

Hello Experts. I am getting the following error when I try to load the reticulatepackage I built in a local conda environment: Error: package or namespace load failed for ‘reticulate’ in dyn.load(file, DLLpath = DLLpath, …): unable to load shared object ‘~/Gits/nlp_r_in_python_testing/nlp_py_env/lib/R/library/reticulate/libs/reticulate.so’: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20′ not found (required by ~/Gits/nlp_r_in_python_testing/nlp_py_env/lib/R/library/reticulate/libs/reticulate.so)…

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Installation error: undefined symbol: PyFPE_jbuf

On an up to date Centos 7 installation, I can’t do anything to make this error go away. I understand that it shouldn’t effect our ability to run the software, but the error remains. [root@slurm-01 cutadapt-1.9.1]# find . -name “*.pyc” -exec rm -rf {} \; [root@slurm-01 cutadapt-1.9.1]# [root@slurm-01 cutadapt-1.9.1]# /usr/bin/python2.7…

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How to install sagemath 10.0 in centos 8

My school server only provides the CentOS 8 system (CentOS Linux release 8.0.1905 (Core)), and I want to compile Sage from source, but I failed. It shows that some dependencies are missing, and when building, it suggests installing the following dependencies. sudo yum install 4ti2 coin-or-Cbc coin-or-Cbc-devel coxeter coxeter-devel coxeter-tools…

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Understanding performance metrics – LAMMPS Beginners

BKFCAW June 16, 2023, 2:49pm 1 I’m running a 3 Nov 2022 build on an AMD 8-core (16-thread) machine at home, as well as on the SDSC Expanse supercomputer with more cores available. At SDSC, I’ve run with 16, 32 and 64 cores. The efficiency in each run is about…

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Deploy LAMMPS on an Azure virtual machine – Azure Architecture Center

This article briefly describes the steps for installing and running LAMMPS on a virtual machine (VM) that’s deployed on Azure. It also presents the performance results of running LAMMPS on single-node and multi-node VM configurations. LAMMPS is a classical molecular dynamics simulator that’s used for materials modeling. It can model…

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Massachusetts General Hospital hiring Bioinformatics Specialist I in Boston, Massachusetts, United States

General Summary & Overview StatementThe Iafrate Lab conducts pioneering research in the field of clinical genomics, working to develop personalized approaches to early cancer detection, diagnosis, and therapy. We are seeking a highly motivated bioinformatician with a background in statistics and/or software development to be a part of our team…

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Bioinformatics Specialist I – Massachusetts General Hospital(MGH)

GENERAL SUMMARY & OVERVIEW STATEMENT: The Iafrate Lab conducts pioneering research in the field of clinical genomics, working to develop personalized approaches to early cancer detection, diagnosis, and therapy. We are seeking a highly motivated bioinformatician with a background in statistics and/or software development to be a part of our…

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Conda environment fails to solve. qiime2-2023.5 – Technical Support

rgas20 (rgas20) June 10, 2023, 4:34am 1 Hello, We are experiencing this problem with qiime2-2023.5. We are attempting to install on a CentOS 7 machine using a Conda environment. We are using the instructions below: wget https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.ymlconda env create -n qiime2-2023.5 –file qiime2-2023.5-py38-linux-conda.yml When we follow these exact instructions, the…

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Frederick National Laboratory Programmer Analyst II (Bioinformatics) in Frederick, MD | 845321518

Programmer Analyst II (Bioinformatics) Job ID: req3577Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: Frederick: Ft DetrickLocation: PO Box B, Frederick, MD 21702 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…

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We do Data Science, Big Data, Statistics, RStudio, Python, SPSS | Classes & Lessons | City of Toronto

We are a team of experts offering top-quality assignment writing services in the fields of Artificial Intelligence, Machine Learning, Data Science, Big Data, and Statistics. We have in-depth knowledge and experience in the following areas: AI: ✅ Natural Language Processing ✅ Computer Vision ✅ Robotics ✅ Deep Learning ✅ Neural…

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PyTorch to Fedora Introduction – Fedora Discussion

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…

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Slurm Cluster Not working – Nvidia Bright Cluster Manager

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…

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Microsoft Azure Marketplace

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…

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Is it normal to get truncated identifiers after applying SQL scema of RegaDB?

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…

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Potential segfault bug in featureCounts using long read data

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…

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LAMMPS produce memory error with ReaxFF and OpenMP – LAMMPS Development

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…

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Nsys and RUNPATH loading – Profiling Linux Targets

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…

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How to use pvserver in Slurm with singularity? – ParaView Support

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…

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New terminal failed – JupyterHub

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…

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Gromacs Installation Issue – AMD Community

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…

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Problem with fatsq-dump

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…

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Can’t get multiple R installation in RStudio Server – General

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…

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Missing mdrun_mpi binary after compile – User discussions

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…

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2 Server Management | RStudio Server Professional Edition 1.4.1103-3

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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Unlocking generative AI with ubiquitous hardware and open software

Presented by Intel Generative Artificial Intelligence (AI) is the ability of AI to generate novel outputs including text, images and computer programs when provided with a text prompt. It unlocks new forms of creativity and expression by using deep learning techniques such as diffusion models and Generative Pre-Trained Transformers (GPTs)….

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Fix nve/asphere requires extended particles (../fix_nve_asphere.cpp:54) – LAMMPS General Discussion

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: https://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…

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5 Best R Programming IDE 2023

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…

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Hub Error about SQLite3 Version – Zero to JupyterHub on Kubernetes

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…

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Anomalous behaviour of PF6- with ECHEMDID – LAMMPS Beginners

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…

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Problem with PyTorch – Install, Configure and Update

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…

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2 BIGQUERY | RStudio Professional Drivers

============================================================================== 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…

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[slurm] wandb hangs at the end of jobs in dryrun mode

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…

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Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment

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…

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parallel downloads from SRA with SRA toolkit or other ways to speed up downloads

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…

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AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required

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….

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Git/SVN Repository and Slurm based Job Management – Freelance Job in Network & System Administration – $100 Fixed Price, posted March 20, 2022

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…

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Error in creating cyclecloud cluster (No nodes found for nodearray hpc)

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:…

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[lammps-users] installing lammps with cmake – LAMMPS Mailing List Mirror

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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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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traviz 1.0.0 installation fails: ERROR: lazy loading failed

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…

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deepmind alphafold github

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…

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weird MAplot or volcano plot of DESeq2 diff result

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…

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