Tag: CentOS 7

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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[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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[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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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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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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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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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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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 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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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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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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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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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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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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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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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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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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