Tag: usr

RStudio Guide | The GitLab Handbook

RStudio Guide {:toc .toc-list-icons .hidden-md .hidden-lg} {::options parse_block_html=“true” /} What is R? Similar to Python, R is an open-source statistical software that is used to clean and analyze data. It is popular within the data science community and has many packages that make statistical modeling easier for statisticians and data…

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Snakemake issue with wrappers

I have issues when running a wrapper of BWA mem with Snakemake. The error message “No module named ‘snakemake_wrapper_utils’” appear (see below). However, when checking if the package is installed in Python, I found the following: import snakemake_wrapper_utils print(snakemake_wrapper_utils.__version__) 0.1.0 Did anyone have this problem? Would you know why there…

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minimap2 error while running TrinityFusion

I have followed the steps you outlined previously, but I’m encountering errors with both methods, whether I’m using Singularity or running it locally. COMMAND USED FOR MOUNTING: singularity exec -e -B /home/sklab/simran/star_run/library/ctat_genome_lib_build_dir/:/ctat_genome_lib trinityfusion.v0.4.0.simg /usr/local/src/TrinityFusion/CTAT-LR-fusion/ctat-LR-fusion –prep_reference_only -T long_read.fastq(fake)–genome_lib_dir /home/sklab/simran/star_run/library/ctat_genome_lib_build_dir/ COMMAND USED FOR RUNNING SAMPLE: singularity exec -e -B ~/simran/star_run/library/ctat_genome_lib_build_dir/:/ctat_genome_lib_build_dir…

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Wrong with code_coverage – C++

When I run python oss_coverage.py –run-only=test_complex.py, I get a Warning pytorch/tools/code_coverage/package/util/../../profile/raw/test_complex.py.profraw: unsupported instrumentation profile format version and a Error error: no profile can be merged The results as follows: (pytorchcov) myconda@.. code_coverage % python oss_coverage.py –run-only=test_complex.py …. ———————————————————————- Ran 4 tests in 0.002s OK …. ———————————————————————- Ran 4 tests in…

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Jupyterhub with AzureAD – JupyterHub

Hello, I’m trying to create docker image with azure ad login im able to login with my account after login in webpage i get Unhandled error starting server Username You can try restarting your server from the [home page]( Log D 2023-11-01 14:34:46.657 JupyterHub base:961] Initiating spawn for USER.Ext [D…

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Issues while installing VG

Issues while installing VG 1 Hi, I am trying to install vg on my Mac (M1 Pro) and during the ‘make’ command I am getting the following error: LDFLAGS are -L/usr/local/lib -L/opt/homebrew/lib -L/opt/homebrew/opt/libomp/lib make: *** No rule to make target `lib/libsdsl.a’, needed by `obj/aligner.o’. Stop. I also had the same…

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Passing parameters to Llama 2 deployed in Vertex AI

I deployed Llama 2 Chat 13B in Vertex AI from model garden. I can also run inference, however, I can not pass any parameter other than prompt and temperature such as max_output_token, top_p, top_k. from typing import Dict, List, Union from google.cloud import aiplatform from google.protobuf import json_format from google.protobuf.struct_pb2…

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GPU problems with gromacs 2023 – User discussions

GROMACS version: 2023.2 / 2023.3GROMACS modification: No Hi, im having issues on using the GPU for running simulations with GROMACS 2023.2. whenever i try to use the ¨mdrun” command, the following error appears: Program: gmx mdrun, version 2023.2Source file: src/gromacs/gpu_utils/devicebuffer.cuh (line 91)Function: freeDeviceBuffer<float>(float*)::<lambda()>** Assertion failed:Condition: stat == cudaSuccessFreeing of the…

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How to Crack Windows Passwords with John the Ripper | by Frost | Oct, 2023

In this tutorial, l will show you how to use John the Ripper to crack Windows 10, 8 and 7 passwords on your own PC. John the Ripper is an offline password-cracking tool designed to test password strength, brute-force encrypted (hashed) passwords, and crack passwords via dictionary attacks. Simply put,…

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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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Different number of reads when converting data from FASTQ to BAM and CRAM to FASTQ

Different number of reads when converting data from FASTQ to BAM and CRAM to FASTQ 1 This post is following up on this other question FASTQ to BAM to CRAM to FASTQ. I have developed an NGS pipeline for calling variants from amplicon data. Regarding the backup, we want to…

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Pytorch torch.distributed.launch v. torchrun | Wyzant Ask An Expert

I found this GitHub Repo, github.com/hbzju/pico, which trains a pytorch model to identify mislabeled data in a dataset. I don’t have much experience with torch and am trying to modify the repo’s code to train the model on my dataset. Running this command: python3 -m torch.distributed.launch –nproc_per_node 2 train.py \…

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Bug#1054792: lammps: FTBFS: dh_install: error: missing files, aborting

Source: lammps Version: 20220106.git7586adbb6a+ds1-2 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu…@debian.org Usertags: ftbfs-20231027 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[2]: Entering directory ‘/<<PKGBUILDDIR>>/debian/build’ > make[2]: Nothing to be done for ‘preinstall’. >…

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Gromacs 2023 installation issue, slower run with gmx_mpi on multiple nodes – User discussions

GROMACS version: 2023GROMACS modification: NoHere post your question I am trying to install Gromacs 2023 on an HPC and hoping to do it correctly to get highest performance possible. HPC has Dual Intel Xeon Gold Skylake 6154 (3.0 GHz, 18-core) processors and Dual NVIDIA Tesla V100 PCIe 16 GB Computational…

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python – Error in snakemake when running conda envs in container

I am facing an issue when running snakemake with a container and conda. Let me explain better. I am developing a workflow (locally) in snakemake, where some rules use a conda env (defined in /envs/env.yaml) and other rules use wrappers (so they also are based on conda envs). An example…

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python – PyTorch Gradient Calculation Error in a Function

I need to calculate some partial derivatives for my specific loss function that I defined below. When I run the code, I get the following error for it. I think it stems from two different v_input values generated, one of which used in u_res is unconnected with the computational graph…

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Rstudio does not found R, but R is install – RStudio IDE

Hi,Here is my PC configuration : Ubuntu 22.04.3 I am trying to install Rstudio on my computer (version rstudio-2023.09.1-494-amd64)The install goes at the end but when i am trying to open Rstudio , there is a prompt with the messqge : R dos not appear to be installed.please install R…

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Could connect to the R session on RStudio Server – R Admins

I ran a RStudio Server on a cent-os7 server and it used to work fine for a long time.Recently I got the error when login remotely from the web browser,Could connect to the R session on RStudio Server. Error occurred during transmission (6).I have tried several solutions such as 1)…

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Precompiling IJulia times out – Kernels

I’m having an issue starting Julia kernels and the Pluto interface when using the jupyter/datascience-notebook image as a base to build my own image. The issues occur when running locally on my Macbook (M1) and when used on a JupyterHub hosted on GCP. When using the jupyter/datascience-notebook image “as is”,…

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Solved Now write an R script with the contents shown below

Now write an R script with the contents shown below to import the Salmon alignments into `DESeq2` and perform differential expression analysis. As with the previous script, since I provide the complete script, look up each of the functions used and make sure you understand how they are used here….

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gnu parallel – How to get reliable results on SLURM for performance tests?

I want to benchmark two algorithms ALG1 and ALG2 against each other using SLURM. Both binaries ALG1.o and ALG2.o contain serial implementations of the algorithms. In now, that ALG1.o is always faster than ALG2.o. Since I have thousands of experiments I want to use our cluster to run them. Each…

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main-powerpc64le-default][misc/pytorch] Failed for pytorch-1.13.1_1 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/main-powerpc64le-default/pbc0e38d0f08e_s0afcac3e37/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=pbc0e38d0f08e_s0afcac3e37 Log: =>> Building misc/pytorch build started at Tue Oct 24…

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Issues while running abundance_estimates_to_matrix.pl

Issues while running abundance_estimates_to_matrix.pl 0 Hello,I am trying to generate a count matrix using abundance_estimates_to_matrix.pl script in Trinity, but I keep running into the same error. /usr/lib/trinityrnaseq/util/abundance_estimates_to_matrix.pl –est_method RSEM –gene_trans_map –name_sample_by_basedir GSNO_rep1/RSEM.isoforms.results GSNO_rep2/RSEM.isoforms.results GSNO_rep3/RSEM.isoforms.results wt_rep1/RSEM.isoforms.results wt_rep2/RSEM.isoforms.results wt_rep3/RSEM.isoforms.results -reading file: GSNO_rep1/RSEM.isoforms.results -reading file: GSNO_rep2/RSEM.isoforms.results -reading file: GSNO_rep3/RSEM.isoforms.results -reading file: wt_rep1/RSEM.isoforms.results -reading…

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What does a Slurm job have to do with ssh?

I am trying to run my first Slurm job. It is hanging right after the executable begins running. I get the error Could not create directory ‘/p/home/mydir/.ssh’. Could not create directory ‘/p/home/mydir/.ssh’. Could not create directory ‘/p/home/mydir/.ssh’. ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Host key verification failed. ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass):…

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r – Problems with Rprofile, dont load at startup

I have a R (4.2.2) and RStudio (2023.06.2) installed on a MacOS system, before I update Rstudio I have no problem, but with those version I don’t how to load .Rprofile at startup RStudio. The defaul working directory for RStudio is in ~/R and my ~/.Rprofile is at home file.path(Sys.getenv(“HOME”),…

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OrthoMCL installation on Ubuntu Linux

About OrthoMCL OrthoMCL is a software used for assigning proteomes to ortholog groups. About this tutorial These are the steps I followed to install OrthoMCL on an Ubuntu 14.04 Linux server using MySQL as the database system. Requirements Ubuntu 14.04 (tested). Might work on other versions. All these steps are…

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r – Kaggle scatterplot showing a unique error

I’m using kaggle and today I received an error which I’ve never seen before. library(“tidyverse”) #everything you need for data manipulation library(“ggplot2”) #everything you need for visualization remove.packages(“ggmap”) #stamen is migrating to stadia install.packages(“devtools”) #cran install devtools devtools::install_github(“stadiamaps/ggmap”) #stadia is used for stamen maps stations <- read.csv(“/…/Divvy_Stations_2017_Q3Q4.csv”, na = “”)…

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Question on samtools view with –fast option

Question on samtools view with –fast option 0 Hi I had a question on samtools view with –fast option. I was trying to find any relevant docs and/or blogs detailing its usage and how best to use it. I could not find any and I thought I will ask the…

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Installing Tensorflow and Pytorch with GPU/CUDA access: Question

This question does not appear to be about programming within the scope defined in the help center. Pytorch Installed the following versions in Ubuntu Nvidia Driver >=535 Cuda 12.2 ( Global Initialization) 1st Method: Tensorflow (Problem Starts when installing Tensorflow) Above mentioned nvidia drivers Above…

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[slurm-users] problem with slurm configuration and pmix

Hi I clone the slurm repository from github (version 23.11), and tried to configure it as follows: configure –config-cache –prefix=/usr/slurm_vm_23.11 –sysconfdir=/etc/slurm_vm_23 –with-http-parser=/usr/ –with-yaml=/usr/ –with-jwt=/usr/ –with-mysql_config=/usr/bin –enable-debug –with-pmix=/usr/lib/x86_64-linux-gnu/pmix2 But I receive the following error message: configure: error: unable to locate pmix installation I checked the pmix installation location, and it exists. I…

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linux – SLURM able to send CPU, but not GPU jobs

I’ve built out a slurm “cluster” (just a job server and single compute server at the moment) and am trying to run jobs on it. I can run CPU jobs just fine, it sends them to the machine and runs them. However, when I try to run a GPU job,…

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error running gmx_MMPBSA HPC

Hello, I’m trying to run gmx_MMPBSA on the university cluster. The following error is occurring: [INFO ] Building AMBER topologies from GROMACS files… [INFO ] Get PDB files from GROMACS structures files… [INFO ] Making gmx_MMPBSA index for complex… [DEBUG ] Running command: echo -e “name 1 GMXMMPBSA_REC\n name 13…

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Object has no attribute ‘cancel’

From this forum post by @yambottle, I saw that we have a bug that shows during another erroring situation. [E 2023-10-18 19:00:12.626 JupyterHub user:884] Unhandled error starting test’s server: ‘coroutine’ object has no attribute ‘cancel’ Traceback (most recent call last): File “/usr/local/lib/python3.11/site-packages/jupyterhub/user.py”, line 798, in spawn url = await gen.with_timeout(timedelta(seconds=spawner.start_timeout),…

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Jupyterhub helm chart 3.1.0+k8s 1.27.6: User pods not spawning got TimeoutError – Zero to JupyterHub on Kubernetes

Context k8s: v1.27.6helm: v3.13.0jupyterhub helm chart: 3.1.0 # configs.yaml proxy: service: type: NodePort ingress: enabled: true annotations: kubernetes.io/ingress.class: nginx nginx.ingress.kubernetes.io/proxy-body-size: 512m cert-manager.io/cluster-issuer: letsencrypt-prod hosts: – xxxxxxxxxxxxxxxxxxxxxxxx tls: – hosts: – xxxxxxxxxxxxxxxxxxxxxxxx secretName: codebook-tls singleuser: startTimeout: 300 debug: enabled: true Deployment seems to work fine: NAME READY STATUS RESTARTS AGE continuous-image-puller-2v74w…

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Palmitoylation – User discussions – GROMACS forums

GROMACS version: 2020.1-Ubuntu-2020.1-1 How to N-terminally palmitoylate without errors? gmx pdb2gmx -f PAMYKK.pdb -o micoa.gro -p micoa.top -water spc -ignh -ter Select the Force Field:From ‘/usr/share/gromacs/top’:1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)3: AMBER96…

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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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python – BioPython: KEGG REST keeps reporting HTTP Error 403: Forbidden – Stack Overflow

I’m attempting to use BioPython’s REST module from Bio.KEGG to query the KEGG database to get the names and formulas of some compounds, using the compounds chemical identification number (CID), e.g. C0001 is water, C00123 is leucine, etc: from Bio.KEGG import REST from Bio.KEGG import Compound def cpd_decoder(cid): #gets the…

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Deploying text-generation-webui – Build debugging

Hello everybody, I would be really thankful if you help.I am trying to deploy GitHub – oobabooga/text-generation-webui: A Gradio web UI for Large Language Models. Supports transformers, GPTQ, AWQ, llama.cpp (GGUF), Llama models. .Unfortunately I always get email that free-builder crashed due to insufficient RAM and get this error =>…

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Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb?

Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb? 1 I want to run diamond and also get taxon identifiers for each hit. Is the only way to do this by incorporating it during the makedb step? Is there any other option? The reason…

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[Question]: What does htvc stand for in haplotypecaller – Parabricks 4.2.0-1 – Parabricks

Hi This is with reference to Parabricks 4.2.0-1 – nvcr.io/nvidia/clara/clara-parabricks:4.2.0-1 I want to know what htvc means in haplotypecaller and what does the associated binary at /usr/local/parabricks/binaries//bin/htvc do within the program. I tried searching for documentation around this but could not find any useful information /usr/local/parabricks/run_pb.py haplotypecaller <…..snipped…..> –verbose –x3…

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Gromacs-2023.2 fails to build properly but 2023.1 and 2023 builds do – User discussions

GROMACS version: 2023 & 2023.1 & 2023.2GROMACS modification: NoSystem: Apple m2 mac Hello, I was trying to install Gromacs using the most recent 2023.2 build with GPU (OpenCL) support, and after a lot of testing I was unable to succeed. I tried different compilers, different cmake options, and every option…

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main-armv7-default][biology/viennarna] Failed for viennarna-2.6.3 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-armv7-default/p08943441f26e_s6e92fc9309/logs/viennarna-2.6.3.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p08943441f26e_s6e92fc9309 Log: =>> Building biology/viennarna build started at Mon Oct 16…

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How to properly run prokka on Ubuntu 22?

How to properly run prokka on Ubuntu 22? 0 Hello I have installed prokka on Ubuntu 22 with the command sudo apt -y install prokka. The installation seems complete but when I try to set the database I get the error: $ prokka –setupdb [19:13:28] Appending to PATH: /usr/bin [19:13:28]…

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How to properly run prokka on Unbuntu 22?

How to properly run prokka on Unbuntu 22? 0 Hello I have installe prokka on Ubuntu 22 with the command sudo apt -y install prokka. The installation seems complete but when I try to set the database I get the error: $ prokka –setupdb [19:13:28] Appending to PATH: /usr/bin [19:13:28]…

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Custom Domain – Inmatura AWS Docs

By default JupyterHub will be available at the public IP address of the instance. You can easily set a a custom domain, e.g. jupyterhub.domain.com, that the Load Balancer and JupyterHub will use. Optional but recommended: Configure a Elastic IP address to the EC2 instance Add a DNS A record to…

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System-wide installed version of Boost gets picked up during build instead of GROMACS bundled one and results in build failure with GMX_GPU=OpenCL

Our usage of Boost is not compatible with arbitrary Boost versions, which is why we ship the files we require at the exact version we support. However, under certain occasions system Boost can be picked up with higher priority than the bundled one. For some reason, this seems to affect…

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Pytorch does not support NCCL – Jetson AGX Orin

whoops October 15, 2023, 5:55am 1 machine: 2 *Jetson AGX Orin 64GB environment: Jetpack 5.1.1 Python 3.8.10 NCCL 2.11.4+cuda11.4 Pytorch v1.11.0 The pytorch i used is provided by NVIDIA;PyTorch for JetsonI try to build a distributed development environment based on AGX Orin, and communicate using nccl.I’ve tried version 2.1 of…

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Unable to install Kmergenie

Unable to install Kmergenie 3 Hello there, I’m trying to install KmerGenie following the README file. I downloaded the kmergeni-1.6892.tar.gz, unzipped it and did make under the folder, but it didn’t work. It shows like the following julibio@DESKTOP-OTF949V ~/curso-bio/kmergenie/kmergenie-1.7051/kmergenie-1.7051 $ make cd ntCard && ./configure && make checking for a…

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incompatible with python3-biopython > 1.79

Source: prody Version: 2.3.1+dfsg-3 Severity: serious Justification: FTBFS Tags: sid ftbfs Forwarded: github.com/prody/ProDy/issues/1723 Hello, prody FTBFS with python3-biopython > 1.79: ====================================================================== FAIL: testBuildMSAlocal (prody.tests.sequence.test_analysis.TestBuildMSA.testBuildMSAlocal) ———————————————————————- Traceback (most recent call last): File “/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence/test_analysis.py”, line 1210, in testBuildMSAlocal assert_array_equal(expect, result) File “/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py”, line 985, in assert_array_equal assert_array_compare(operator.__eq__, x, y, err_msg=err_msg, File “/usr/lib/python3.11/contextlib.py”,…

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Docker image to use Rscript

Hi! I am having some issues combining docker with snakemake workflows. I have some rules that involve running an R script on the input(s) and producing some output(s). Until now, I’ve also been able to solve the environments for these R scripts with conda environments , however, I’m now at…

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Failure to Verify when reinstalling updated version of QIIME2 – Technical Support

I am trying to install an updated version of QIIME2 on a departmental computer. I first ran into some problems with permissions, but once an override code was identified I am now getting an unfamiliar error response during the final stage of installation. Wget is working find from what I…

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Quickstart your Hugo website with this Hugo tutorial

We recommend the easy one-minute website creation with GitHub before considering following the steps on this page to download and edit your site locally 🧙‍♂️ Did you know that editing or updating a site can be more easily performed online using the GitHub Editor and the open source Wowchemy CMS?…

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Fatal Error: Too many warnings (1) Use -maxwarn option in gromacs 2023.2 – User discussions

Respected Sir/Ma’am,I am getting an error as shown below.🙂 GROMACS – gmx grompp, 2023.2 (-: Executable: /usr/local/gromacs/bin/gmxData prefix: /usr/local/gromacsWorking dir: /home/drr-18/Complex_02_EMinimizedCommand line:gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr Ignoring obsolete mdp entry ‘title’Ignoring obsolete mdp entry ‘ns_type’ WARNING 1 [file npt.mdp]:The…

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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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python – Encountering ImportError: Using the `Trainer` with `PyTorch` requires `accelerate>=0.20.1`: when accelerate 0.23.0 already installed

I am creating a text classification model using IndoBERT. Below is some of my code : from transformers import AutoModelForSequenceClassification, AutoModel, TrainingArguments, Trainer model = AutoModelForSequenceClassification.from_pretrained( “indolem/indobert-base-uncased”, num_labels=2, id2label=id2label, label2id=label2id ) but when I will run training args. : training_args = TrainingArguments( output_dir=”IndobertTypeNewsclassification”, learning_rate=2e-5, per_device_train_batch_size=32, per_device_eval_batch_size=32, num_train_epochs=3, weight_decay=0.01, evaluation_strategy=”epoch”, save_strategy=”epoch”,…

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Bug#1053533: mbedtls: enable MBEDTLS_NIST_KW_C

Source: mbedtls Severity: wishlist X-Debbugs-Cc: phc…@silabs.com, jerome….@gmail.com Hello, I have just noticed MBEDTLS_NIST_KW_C was not enabled (and obviously my project[1] depends on it). I usually use the default config provided by mbedtls (which I believe enable all the possible options). Do you know if there is any reason to strip down this configuration? …

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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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Getting error when trying to use pytorch 1.12.1 with jetpack version 5.1.1 – Jetson AGX Orin

When I am using Cuda 11.4 with the PyTorch 1.12 model on jetpack 5.1.1, I am getting error …torch::Device device_ = torch::kCUDAif (device_.is_cuda()) {c10::cuda::getCurrentCUDAStream().synchronize();}This runs fine but,const auto inputs =torch::from_blob(working_img.data,{working_img.rows, working_img.cols, 3}, torch::kUInt8).to(device_, torch::kFloat).permute({2, 0, 1}).contiguous();throws error[ERROR] [1696585409.990943029]: Segmentation error: CUDA error: no kernel image is available for execution on…

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Bugs : systemd package : Ubuntu

tests-in-lxd seems to fail to download the lxd image used for the test (or something similar), looking at the log:…Publishing instance: Image pack: 85% (5.51MB/s) Instance published with fingerprint: 83b511be44395f2afc7d4d1ee0708cb18834c8b15cb208c9d218964ed84791146845s autopkgtest [09:11:14]: starting date and time: 2023-10-03 09:11:14+00006845s autopkgtest [09:11:14]: version 5.28ubuntu16845s autopkgtest [09:11:14]: host autopkgtest; command line: /usr/bin/autopkgtest -U…

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Help Compiling STAR

It seems like you are facing issues with compiling STAR on your Ubuntu 20.04 LTS system. The error message indicates that the ‘cc’ command (which is the C compiler) is not found. This typically happens when the build environment is not set up correctly. Let’s try to troubleshoot this step…

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How to Handle “IndexError: index out of range in self” in PyTorch

The popular deep learning and natural language processing framework PyTorch is renowned for being user-friendly and adaptable, so what’s the deal with the IndexError: index out of range in self error? This happens when a PyTorch embedding tensor attempts to access an index that is out of bounds. A lookup…

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Unable to spawn server after login JupyterHub on EKS cluster – Zero to JupyterHub on Kubernetes

HiI have installed jupyterhub with my newly created EKS Cluster with helm install, Installation was success and able to get the login page, while login with admin userI’m getting error message like below Your server is starting up. You will be redirected automatically when it’s ready for you. 100% Complete…

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How Do I Convert From Bed Format To Gff Format?

How Do I Convert From Bed Format To Gff Format? 4 I have a file in GFF format and I need to convert it to BED format. What do I do? bed gff galaxy • 29k views Both formats are tab delimited text files used to represent DNA features in…

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Reinstalling GROMACS with CUDA GPU – User discussions

GROMACS version: 2023.2GROMACS modification: Yes/NoHere post your question $ nvcc –versionnvcc: NVIDIA (R) Cuda compiler driverCopyright (c) 2005-2021 NVIDIA CorporationBuilt on Thu_Nov_18_09:45:30_PST_2021Cuda compilation tools, release 11.5, V11.5.119Build cuda_11.5.r11.5/compiler.30672275_0 $ nvidia-smiTue Oct 3 13:42:40 2023±————————————————————————————–+| NVIDIA-SMI 535.103 Driver Version: 537.13 CUDA Version: 12.2 ||—————————————–±———————±———————+| GPU Name Persistence-M | Bus-Id Disp.A |…

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Mdrun : An error occurred in MPI_Allreduce – User discussions

AKA October 1, 2023, 9:58pm 1 GROMACS version: 2022.6GROMACS modification: No I am running gromacs-cp2k and I get the following error when running mdrun on qmmm system. 🙂 GROMACS – gmx mdrun, 2022.6 (-: Executable: /usr/local/gromacs-cp2k-gpu/bin/gmx_mpi Data prefix: /usr/local/gromacs-cp2k-gpu Working dir: /home/vivek/Desktop/cp2k_test/tutorial/egfp Command line: gmx_mpi mdrun -s egfp-qmmm-nvt.tpr -deffnm egfp-qmmm-nvt…

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CUDA error: CUBLAS_STATUS_EXECUTION_FAILED when using roberta – nlp

Hi everyone, I’m training a model that uses roberta to encoder sentence. I got an error that is:RuntimeError: CUDA error: CUBLAS_STATUS_EXECUTION_FAILED when calling cublasGemmStridedBatchedExFix( handle, opa, opb, m, n, k, (void*)(&falpha), a, CUDA_R_16F, lda, stridea, b, CUDA_R_16F, ldb, strideb, (void*)(&fbeta), c, CUDA_R_16F, ldc, stridec, num_batches, CUDA_R_32F, CUBLAS_GEMM_DEFAULT_TENSOR_OP) My problem is…

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“Installing PyTorch for Jetson Platform”: Error in pytorch install instructions? (Missing semicolon?) – Jetson Nano

Tried to install PyTorch for Jetson Platform using the command shown on Installing PyTorch for Jetson Platform – NVIDIA Docs and got errors about LD_LIBRARY_PATH . I’m not a PIP expert, but it looks to me like that export was intended to be a separate command and a semicolon was…

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Issues Installing pytorch through jetson inference install script – Jetson Nano

More debug info: Command “/usr/bin/python3 -u -c “import setuptools, tokenize;file=‘/tmp/pip-build-yfzvgbyx/grpcio/setup.py’;f=getattr(tokenize, ‘open’, open)(file);code=f.read().replace(‘\r\n’, ‘\n’);f.close();exec(compile(code, file, ‘exec’))” install –record /tmp/pip-b0li_63y-record/install-record.txt –single-version-externally-managed –compile –user –prefix=” failed with error code 1 in /tmp/pip-build-yfzvgbyx/grpcio/Exception information:Traceback (most recent call last):File “/usr/lib/python3/dist-packages/pip/basecommand.py”, line 215, in mainstatus = self.run(options, args)File “/usr/lib/python3/dist-packages/pip/commands/install.py”, line 360, in runprefix=options.prefix_path,File “/usr/lib/python3/dist-packages/pip/req/req_set.py”, line 784,…

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Error finetuning wav2vec2-xls-r-300m on kaggle TPU – Models

Here is my current code:from transformers import Wav2Vec2ForCTC`model = Wav2Vec2ForCTC.from_pretrained(“facebook/wav2vec2-xls-r-300m”,attention_dropout=0.1,hidden_dropout=0.1,feat_proj_dropout=0.0,mask_time_prob=0.0,layerdrop=0.1,ctc_loss_reduction=“mean”,pad_token_id=processor.tokenizer.pad_token_id,vocab_size=len(processor.tokenizer),) from transformers import TrainingArguments training_args = TrainingArguments(output_dir=run_config[“hub_repo”],per_device_train_batch_size=64,per_device_eval_batch_size=64,gradient_accumulation_steps=1,evaluation_strategy=“steps”,num_train_epochs=30,gradient_checkpointing=True,torch_compile=True,bf16=True,save_steps=400,eval_steps=400,logging_steps=400,learning_rate=3e-4,warmup_steps=500,save_total_limit=2,push_to_hub=True,dataloader_num_workers=2,tpu_num_cores=8,)trainer.train()` Error `KeyError Traceback (most recent call last)Cell In[67], line 1—-> 1 trainer.train() File /usr/local/lib/python3.8/site-packages/transformers/trainer.py:1547, in Trainer.train(self, resume_from_checkpoint, trial, ignore_keys_for_eval, **kwargs)1544 try:1545 # Disable progress bars when uploading models during checkpoints to avoid polluting…

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SLURM and Docker, accessing reserved GPUs not working with zsh

I’m running docker containers on a server using SLURM. Generally, I connect to a manager node, and run my jobs on one of the other nodes by using: srun -w gpu02 –gres=”gpu:xxx:1″ –cpus-per-task=16 –pty /bin/bash Once I’m connected to the required node, I can see only the reserved GPU by…

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Error in running pdb2gmx for protein with modified residue – User discussions

GROMACS version: 2021.4-Ubuntu-2021.4-2GROMACS modification: NoHere post your questionI am trying to run pdb2gmx for a pdb with a modified residue with Amber96 forcefield and TIP3P water. I have modified aminoacids.rtp and aminoacids.hdb files to include the modified residue (chromophore in 1bfp). When I am running, the following error comes: Fatal…

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Snakemake alignment script

I have been trying to write a simple alignment pipeline with Snakemake. Unfortunately, I have a hard time understanding the error messages. In the example below, the message ” ‘str’ object has no attribute ‘name’ ” is a bit cryptic. Does it means that the expression {input.r1} is incorrect? import…

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CUDA enabled Gromacs Cp2k installation error – User discussions

AKA September 27, 2023, 2:02pm 1 GROMACS version:2023.2GROMACS modification: NoCP2K version: 2023.2Hello all,I was trying to install gromacs with cp2k on nvidia GPU. I installed the psmp version of “local_cuda” cp2k. The cmake command I used is present is: cmake .. -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF -DGMX_GPU=CUDA -DGMX_CP2K=ON -DCP2K_DIR=/home/aka/Documents/cp2k-2023.2/lib/local_cuda/psmp -DCMAKE_PREFIX_PATH=’/home/aka/Documents/cp2k-2023.2/tools/toolchain/install/openblas-0.3.23;/home/aka/Documents/cp2k-2023.2/tools/toolchain/install/scalapack-2.2.1′ -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-cp2k-gpu/…

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ncbi error report log for validate fastq issue

ncbi error report log for validate fastq issue 0 Im trying to fetch a list of GSM id which could be seen that it is present in the project folder which I checked through sra explorer tool but when I try to download through a script it fails even after…

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Debian — File list of package clustalw/bookworm/armel

/usr/bin/clustalw /usr/share/clustalw/clustalw_help /usr/share/doc/clustalw/README /usr/share/doc/clustalw/README.Debian /usr/share/doc/clustalw/changelog.Debian.gz /usr/share/doc/clustalw/changelog.gz /usr/share/doc/clustalw/copyright /usr/share/doc/clustalw/examples/tests.clustalw/Makefile /usr/share/doc/clustalw/examples/tests.clustalw/nuc.data /usr/share/doc/clustalw/examples/tests.clustalw/nuc2.data /usr/share/doc/clustalw/examples/tests.clustalw/seq /usr/share/man/man1/clustalw.1.gz /usr/share/menu/clustalw Read more here: Source link

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RPM Search opensuse slurm-plugins-18.08.9-lp152.2.1.x86_64.rpm

Content of RPM slurm-plugins-18.08.9-lp152.2.1.x86_64.rpm : /etc/ld.so.conf.d/slurm.conf /usr/lib64/slurm /usr/lib64/slurm/accounting_storage_filetxt.so /usr/lib64/slurm/accounting_storage_none.so /usr/lib64/slurm/accounting_storage_slurmdbd.so /usr/lib64/slurm/acct_gather_energy_ibmaem.so /usr/lib64/slurm/acct_gather_energy_ipmi.so /usr/lib64/slurm/acct_gather_energy_none.so /usr/lib64/slurm/acct_gather_energy_rapl.so /usr/lib64/slurm/acct_gather_energy_xcc.so /usr/lib64/slurm/acct_gather_filesystem_lustre.so /usr/lib64/slurm/acct_gather_filesystem_none.so /usr/lib64/slurm/acct_gather_interconnect_none.so /usr/lib64/slurm/acct_gather_interconnect_ofed.so /usr/lib64/slurm/acct_gather_profile_influxdb.so /usr/lib64/slurm/acct_gather_profile_none.so /usr/lib64/slurm/burst_buffer_generic.so /usr/lib64/slurm/checkpoint_none.so /usr/lib64/slurm/checkpoint_ompi.so /usr/lib64/slurm/core_spec_none.so /usr/lib64/slurm/crypto_openssl.so /usr/lib64/slurm/ext_sensors_none.so /usr/lib64/slurm/ext_sensors_rrd.so /usr/lib64/slurm/gres_gpu.so /usr/lib64/slurm/gres_mic.so /usr/lib64/slurm/gres_nic.so /usr/lib64/slurm/job_container_cncu.so /usr/lib64/slurm/job_container_none.so /usr/lib64/slurm/job_submit_all_partitions.so /usr/lib64/slurm/job_submit_defaults.so /usr/lib64/slurm/job_submit_logging.so /usr/lib64/slurm/job_submit_partition.so /usr/lib64/slurm/job_submit_require_timelimit.so /usr/lib64/slurm/job_submit_throttle.so /usr/lib64/slurm/jobacct_gather_cgroup.so /usr/lib64/slurm/jobacct_gather_linux.so /usr/lib64/slurm/jobacct_gather_none.so /usr/lib64/slurm/jobcomp_elasticsearch.so /usr/lib64/slurm/jobcomp_filetxt.so /usr/lib64/slurm/jobcomp_none.so /usr/lib64/slurm/jobcomp_script.so /usr/lib64/slurm/launch_slurm.so /usr/lib64/slurm/layouts_power_cpufreq.so /usr/lib64/slurm/layouts_power_default.so /usr/lib64/slurm/layouts_unit_default.so…

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Detected that PyTorch and torchvision were compiled with different CUDA versions – CUDA Setup and Installation

AK51 September 25, 2023, 6:56pm 1 Hi, There are many version issue in cuda and pytorch. RuntimeError: Detected that PyTorch and torchvision were compiled with different CUDA versions. PyTorch has CUDA Version=11.7 and torchvision has CUDA Version=11.8. Please reinstall the torchvision that matches your PyTorch install. How can I find…

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132releng-armv7-quarterly][misc/pytorch] Failed for pytorch-1.13.1_1 in configure

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere1/data/132releng-armv7-quarterly/2be22e0743b5/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/ampere1/build.html?mastername=132releng-armv7-quarterly&build=2be22e0743b5 Log: =>> Building misc/pytorch build started at Mon Sep 25…

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error when running local chlorop1.1

error when running local chlorop1.1 0 Hi everyone, I’ve installed the chlorop1.1, following the readme file. But when testing with the file in the test fold, it came to the error message below: ./chlorop test/test1.fsa open: can’t stat file apparent state: unit 3 named tmp/res.3180/infile.how lately reading sequential formatted external…

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main-arm64-default][biology/viennarna] Failed for viennarna-2.6.3 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-arm64-default/p85ccf094713a_sc584bb9cac1/logs/viennarna-2.6.3.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p85ccf094713a_sc584bb9cac1 Log: =>> Building biology/viennarna build started at Sat Sep 23…

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Just adding the full trace that sage produces

Package: sagemath Version: 9.5-6 Followup-For: Bug #1052051 X-Debbugs-Cc: jordi.burguet.cast…@gmail.com Dear Maintainer, When running sage, there is an ImportError related to libsingular- Singular-4.3.1.so (full trace below). From what I can see, python3-sage depends on libsingular4m3n0: $ apt depends python3-sage | grep libsingular Depends: libsingular4m3n0 (>= 1:4.3.1-p3+ds) Depends: libsingular4-dev (>= 1:4.2.1-p2+ds-3) but…

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Modify the code to take most abundant reads from a cluster and process it.

I have a code that processes the cd-hit-est cluster file. The code looks like this: #!/usr/bin/awk -f />Cluster/{ getline a=$3 b=$3 gsub(/[.]/,””,a) gsub(/[>0-9_.]/,””,b) print a “\n” b } One of the clusters in cluster file looks like this >Cluster 9 0 22nt, >35067_10_CCAATTCACTTGTCCCGCCCCC… * 1 21nt, >2636_236_CCACCACTTGTCCCGCCCCCC… at +/85.71% 2…

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CP2K version 2023.2 compile error

Thank you for helping me, Mishra. However, I still got problems. I modified the script according to my architecture, as below:“spack -d install cp2k@2023.1+elpa %g…@8.3.1 target=icelake ^elpa+openmp ^ope…@4.1.4 fabrics=auto”Then I got very, very long error message below and I dont’ know what is the reason. ———————————————————————————————————————————————————————————– ==> [2023-09-22-11:22:05.969419] Error: ProcessError:…

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How to find Hashicorp vault API endpoints that require sudo capability

Short solution found in September 2023 sudo paths list can be found in the vault API source code at github.com/hashicorp/vault/blob/main/api/sudo_paths.go. Step by step guide Step 1 – Login to your vault instance $ vault login … Step 2 – Get the OpenAPI spec $ vault read -format=json sys/internal/specs/openapi > vault-openapi-spec.json…

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How to use lift_x in python?

I am trying to use sage library in python3, but I have the following problem when I try to find points with given x-coordinate: >>> from sage.all import * >>> E = EllipticCurve(’37a’); E Elliptic Curve defined by y^2 + y = x^3 – x over Rational Field >>> E.lift_x(1)…

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Gromacs +cp2k installation – User discussions

GROMACS version: 2023.1 Hello. I am trying to compile gromacs-2023.1 with cp2k-2023.2, but I am not being able to link the fftwf3 library. So when I run the following command: cmake … -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF -DGMX_DOUBLE=ON -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/home/edivaldo/cp2k/tools/toolchain/install/fftw-3.3.10/lib -DFFTWF_INCLUDE_DIR=/home/edivaldo/cp2k/tools/toolchain/install/fftw-3.3.10/include -DGMX_BLAS_USER=/home/edivaldo/cp2k/tools/toolchain/install/openblas-0.3.23/lib/libopenblas.a -DGMX_LAPACK_USER=/home/edivaldo/cp2k/tools/toolchain/install/scalapack-2.2.1/lib/libscalapack.a -DGMX_CP2K=ON -DCP2K_DIR=“/home/edivaldo/cp2k/lib/local/psmp” -DGMX_MPI=on I keep getting this warning:– The…

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Cluster Interactive/remote Computing with VS Code | crc.pitt.edu

This tutorial outlines how to set up VS Code for interactive/remote development/debugging on Pitt CRC computing nodes. Prerequisits: Latest version of VS Code on your local machine Latest version of the “Remote Development” extension pack (here)  Steps performed only once Add the following lines to the ssh config file on…

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gromacs23.2+Cp2k23.2 installation error – User discussions

AKA September 19, 2023, 8:04am 1 GROMACS version: 2023.2GROMACS modification: NoHello. I am trying to compile gromacs 2023.2 with cp2k 2023.2 support. I am facing the following error while running make: lto1: fatal error: multiple prevailing defs for ‘__def_init_helium_types_Density_properties_type’ compilation terminated. lto-wrapper: fatal error: /home/aka/Documents/cp2k-2023.2/tools/toolchain/install/gcc-13.1.0/bin/g++ returned 1 exit status compilation…

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r – error when installing rgdal package on ubuntu 22.04, rstudio-sever 2023.06.02

I have recently upgraded my Ubuntu version from 20.04 to 22.04 LTS and Rstudio-server to 2023.06.02. The R version is 4.3.1. After that the shiny App I am developing, which ran OK on the previous version, was giving an error of the type ‘libproj.so.15 – cannot open shared file’. After…

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Connection timing out when downloading hg19, mm10

Hi,   We are trying to setup a mirror of the UCSC browser.  The install went fine but when trying to download data we keep getting:  root@genome:/usr/install# bash browserSetup.sh mirror hg19 mm10 | | Downloading databases hg19 mm10 plus hgFixed/proteome/go from the UCSC download server | | Determining download file…

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Sagemath 9.5-6 expects libsingular-Singular-4.3.1.so but libsingular-Singular-4.3.2.so is installed

Package: sagemath Version: 9.5-6 Severity: normal Dear Maintainer, * What led up to the situation? Typing “sage” and pressing Enter * What was the outcome of this action? Sagemath did not start * What outcome did you expect instead? Sagemath should start *** End of the template – remove these template lines *** …

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Question about REDItools

Hi, I wanted to use REDItools to identify RNA editing events in my data. I had both RNA-seq and exome-seq data derived from the same sample. I download the latest version of REDItools (REDItools-1.2.1.zip, sourceforge.net/projects/reditools/files/) and test data (srv00.recas.ba.infn.it/reditools/data/testREDItools.tar.gz). When I run the scripts “REDItoolDnaRna.py” as “REDItoolDnaRna.py -i rna.bam -j…

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GROMACS SYCL for Intel GPU – User discussions

GROMACS version: 2023.2GROMACS modification: Yes/NoHi,I’ve just install GROMACS with SYCL enabled, however, it seems like GROMACS cannot detect my GPU. My GPU is Intel Iris Xe Graphics, I’m using Ubuntu 22.04, CMake 3.27.4, and Intel oneAPI DPC++/C++ Compiler with MKL library 2023.2 for SYCL. Here it says SYCL is enabled:…

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rstudio – Unable to install R packages from source

I installed R a work administered computer (I don’t have admin rights). I also installed Rtools43. When I try to install packages from source, I am consistently getting the error described below. Details about system: > sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64…

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Server Crashing: Epyc 7402P with Nvidia Tesla A100s Ubuntu 20.04 – Hardware

Swamp7 September 13, 2023, 3:35pm #1 Seeing if someone could give me some guidance on troubleshooting a new AL/DL Epyc 7402P server with Dual Nvidia Tesla A100 40GB GPUs. This is my first Epyc server (moving from Xeon E5-2680 v3s…I know very old but they work for GPU servers very…

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slurm – Submit a job to be run on several nodes on a partition that disallows it

I use LAMMPS. Usually I use the following slurm job file to submit jobs: #!/usr/bin/env bash #SBATCH –job-name=lammps #SBATCH –begin=now #SBATCH –nodes=4 #SBATCH –ntasks-per-node=32 #SBATCH –partition=medium srun -u lmp_mpi -in in.file Partition medium allows jobs up to 4-node size, partition small allows jobs that are only 1-node size. Is it…

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How to fix `Exec /usr/local/bin/jupyterhub: exec format error`? – JupyterHub

I’m trying to deploy jupyterhub with helm. When I tried the default “k8s-hub:3.0.3” image hub: image: name: jupyterhub/k8s-hub tag: “3.0.3” It shows: File “<string>”, line 4, in <module> ModuleNotFoundError: No module named ‘kubernetes’ I found a solution from this. I went on and created a custom hub based on this…

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import astropy in a sage notebook v

Hi Sagesse! I’m wondering if there’s an easy way to get a sage notebook (v8.7) to import the module astropy which is found /usr/lib/python3/dist-packages/astropy/ on my linux system. I am guessing it would require doing an export SAGE_PATH= xxx and then a launch of my notebook as sage –notebook in…

Continue Reading import astropy in a sage notebook v