Tag: HPC

Professor of Medical Bioinformatics and Statistical Genetics job with Aarhus University (AU)

The Department of Biomedicine at Faculty of Health at Aarhus University invites applications for a position as Professor in the field of Medical Bioinformatics and Statistical Genetics as per 1 July 2024 or as soon as possible thereafter. The position is a time-limited full-time position for 5 years with extension…

Continue Reading Professor of Medical Bioinformatics and Statistical Genetics job with Aarhus University (AU)

NYU High Performance Computing – HPC Projects

Depending on your role, you will see the corresponding interface at the Portal. HPC Project Owner You can register an HPC project if you are a full-time faculty and sponsoring a currently active HPC account for research or instruction. If you are a part-time faculty teaching a course, please get…

Continue Reading NYU High Performance Computing – HPC Projects

Sperm-specific histone H1 in highly condensed sperm nucleus of Sargassum horneri

Cho, C. et al. Haploinsufficiency of protamine-1 or-2 causes infertility in mice. Nat. Genet. 28, 82–86 (2001). Article  CAS  PubMed  Google Scholar  Oliva, R. Protamines and male infertility. Hum. Reprod. Update 12, 417–435 (2006). Article  CAS  PubMed  Google Scholar  Balhorn, R. The protamine family of sperm nuclear proteins. Genome Biol….

Continue Reading Sperm-specific histone H1 in highly condensed sperm nucleus of Sargassum horneri

mtDNA Cyclic Sequence Alignment CSAtool

mtDNA Cyclic Sequence Alignment CSAtool 1 Hi everyone, I encountered an issue while running CSAtool. This is my command and report: What’s free(): invalid next size (fast)? Maybe it’s due to the way I formatted the sequences? I hope you can help me. Thanks! mtDNA alignment CSA • 268 views…

Continue Reading mtDNA Cyclic Sequence Alignment CSAtool

Memorial Sloan Kettering Cancer Center hiring Bioinformatics Software Engineer III – Chan Lab in New York, NY

 The people of Memorial Sloan Kettering Cancer Center (MSK) are united by a singular mission: ending cancer for life. Our specialized care teams provide personalized, compassionate, expert care to patients of all ages. Informed by basic research done at our Sloan Kettering Institute, scientists across MSK collaborate to conduct innovative…

Continue Reading Memorial Sloan Kettering Cancer Center hiring Bioinformatics Software Engineer III – Chan Lab in New York, NY

hpc – For SLURM clusters why do we need to specify memory allocation for jobs?

It’s not so much a problem of allocating memory, but of knowing the shape of the workload to place it optimally (or at least non-problematically) in the cluster. The point is so that jobs can be placed on nodes with sufficient memory to handle the task. This avoids problems that…

Continue Reading hpc – For SLURM clusters why do we need to specify memory allocation for jobs?

Problem getting GPU solving to work with our Azure CycleCloud / Slurm HPC cluster System

I am using the Azure CycleCloud 8.4 Marketplace image and it is fully updated, along with Slurm version 22.05.8-1. I have configured a GPU Enabled Slurm Partition consisting of some NC24sv3 VMs (which have 4x Nvidia Tesla V100 GPUS in each), but the Slurm Scheduler is showing the Partition as…

Continue Reading Problem getting GPU solving to work with our Azure CycleCloud / Slurm HPC cluster System

Sr. Software Engineer in Test (Bioinformatics or Data Sciences) / SDET – Key Infotek LLC

Job Title: Sr. Software Engineer in Test (Bioinformatics or Data Sciences) Location: Mississauga, CAD Pay Rate: DOE   Requirements: B.S. or M.S. in Computer Science, Data Sciences, Bioinformatics, Biomedical engineering or equivalent field 5+ years of experience in software development or software test engineering or data engineering Proficiency in Python,…

Continue Reading Sr. Software Engineer in Test (Bioinformatics or Data Sciences) / SDET – Key Infotek LLC

Vimerse InfoTech Inc hiring Sr. Software Engineer (Bioinformatics) in Mississauga, Ontario, Canada

Job Title: Sr. Software Engineer in Test (Bioinformatics or Data Sciences) Location: Mississauga, CAD Impact Healthcare Roche Sequencing is not only changing science, but we are changing lives. Our software teams are laying the groundwork for the future by developing powerful bioinformatics algorithms, data analysis tools, and software/systems infrastructures so…

Continue Reading Vimerse InfoTech Inc hiring Sr. Software Engineer (Bioinformatics) in Mississauga, Ontario, Canada

KeyInfo hiring SDET must have (Bioinformatics or Data Sciences) in Canada

Job Title: Sr. Software Engineer in Test (Bioinformatics or Data Sciences) Remote Description: Responsibilities: •         Implement and maintain an end-to-end automation test framework for running UI integration tests and quality dashboards using various tools: Java, JavaScript/TypeScript, Cypress, Selenium WebDriver, Cucumber, TestNG, Junit •         Design and develop requirements based test cases •         Implement automated…

Continue Reading KeyInfo hiring SDET must have (Bioinformatics or Data Sciences) in Canada

CVE-2023-41914 | SUSE

SchedMD Slurm 23.02.x before 23.02.6 and 22.05.x before 22.05.10 allows filesystem race conditions for gaining ownership of a file, overwriting a file, or deleting files. Please note that this evaluation state might be work in progress, incomplete or outdated. Also information for service packs in the LTSS phase is only…

Continue Reading CVE-2023-41914 | SUSE

insideBIGDATA AI News Briefs Bulletin Board

Welcome insideBIGDATA AI News Briefs Bulletin Board, our timely new feature bringing you the latest industry insights and perspectives surrounding the field of AI including deep learning, large language models, generative AI, and transformers. We’re working tirelessly to dig up the most timely and curious tidbits underlying the day’s most…

Continue Reading insideBIGDATA AI News Briefs Bulletin Board

Supports Instinct MI300, Radeon 7000 GPUs, AI Additions

AMD’s ROCm 6.0 software stack and the full source code are now available to download & come with Instinct MI300 & Radeon 7000 GPU support. AMD’s ROCm 6.0 Software Stack Now Brings Support For Additional AI Libraries, Unlocks FP8 Performance At PyTorch, Adds Instinct MI300 & Radeon 7000 GPU Support…

Continue Reading Supports Instinct MI300, Radeon 7000 GPUs, AI Additions

Senior Bioinformatics Engineer / Software Developer| Science, Engineering & Life Science Recruitment, Jobs & Staffing | SRG

A Bioinformatics Engineer is required to join a small but rapidly expanding company – by joining early in the journey you will gain exposure to the various facets of start-up life and have a unique chance to contribute to the technology and influence company culture. As the company expands this…

Continue Reading Senior Bioinformatics Engineer / Software Developer| Science, Engineering & Life Science Recruitment, Jobs & Staffing | SRG

Senior R Studio Administrator – Remote – EPAM Systems

If you are looking for a high-impact Senior R Studio Administrator with a global leader in digital transformation, EPAM is the perfect next step in your career! As an EPAMer, you’ll have the opportunity to work with a supportive team, on a variety of interesting projects for some of the…

Continue Reading Senior R Studio Administrator – Remote – EPAM Systems

Cloud Deep Learning: 3 Focus Areas & Key Things to Know

Cloud deep learning is the integration of cloud computing and deep learning models that can process inputs through different layers. By developing deep learning, businesses can perform more complex tasks compared to classical algorithms. There are various facets of the process to achieve this goal. Choosing classical models can require…

Continue Reading Cloud Deep Learning: 3 Focus Areas & Key Things to Know

[slurm-users] How to check the bench mark capacity of the SLURM setup

On 12/13/23 10:44, John Joseph wrote: > Thanks for the mail, and sorry for not properly explaining what info I was > requesting, what actually I meant was that how could we could  do a check > how the HPC system I set is working. > > Eg a program…

Continue Reading [slurm-users] How to check the bench mark capacity of the SLURM setup

SRA Staffing – SRA Group hiring QA Analyst with Bioinformatics in Mississauga, Ontario, Canada

Title: QA Analyst with Bioinformatics Work location: Mississauga, Canada (Hybrid) Duration: 1 Year Plus Contract Job Description: B.S. or M.S. in Computer Science, Data Sciences, Bioinformatics, Biomedical engineering or equivalent field • Min 5 years of experience in software development or software test engineering or data engineering • Proficiency in…

Continue Reading SRA Staffing – SRA Group hiring QA Analyst with Bioinformatics in Mississauga, Ontario, Canada

CEDARS-SINAI Research Bioinformatician II – Human Microbiome Research Institute in Beverly Hills, CA | 889550076

Cedars-Sinai has established a new Human Microbiome Research Institute that will support investigators studying how the microbiome plays a role in human health and disease with key focus areas in: Cancer, Metabolism, Early Life, GI & Liver, and Autoimmunity. The Human Microbiome Research Institute (HMRI) is an innovation hub and…

Continue Reading CEDARS-SINAI Research Bioinformatician II – Human Microbiome Research Institute in Beverly Hills, CA | 889550076

Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015). Article  PubMed  Google Scholar  Kanter, D. R. et al. Nitrogen pollution policy beyond the farm. Nat. Food 1, 27–32 (2020). Article  ADS  Google Scholar  Tian, H. et al. A comprehensive quantification of global…

Continue Reading Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

Command to run gromacs in parallel – User discussions

cjbraz December 11, 2023, 5:06pm 1 GROMACS version: 2023.2GROMACS modification: Yes/NoHere post your question Hello all. I have used CHARMM-GUI solvent builder to print out a script I can use in a protein simulation. I am able to run the script successfully, but would like to run the full script…

Continue Reading Command to run gromacs in parallel – User discussions

AstraZeneca Bioinformatics Job – Bioinformatics Consultant Post

“Unlock Your Potential: Join AstraZeneca as a Bioinformatics Consultant and Revolutionize Drug Discovery!” –Must See– AstraZeneca Bioinformatics Job Job Post: Consultant – Bio Informatician At AstraZeneca, our mission is to improve the quality of healthcare and make a positive impact on the lives of millions of patients. We are seeking…

Continue Reading AstraZeneca Bioinformatics Job – Bioinformatics Consultant Post

How to push PaaS usage beyond 12-factor apps

Sylvain Kalache Contributor Sylvain Kalache is the co-founder of Holberton, an edtech company training digital talent in more than 10 countries. An entrepreneur and software engineer, he has worked in the tech industry for more than a decade. Part of the team that led SlideShare to be acquired by LinkedIn,…

Continue Reading How to push PaaS usage beyond 12-factor apps

Rstudio cloud

Rstudio cloud 1 Dear fellows, a bit off topic today. I am just starting to use R studio cloud from a supercomputer to analyze my single cell and have recently experienced issue with installing packages. Not sure whether anyone have any experience installing packages in R studio cloud and could…

Continue Reading Rstudio cloud

Revolutionizing Machine Learning with Large Model Training on AWS & PyTorch

🌐 Large models are reshaping our digital and physical existence, revolutionizing technology and solving more interesting use cases. 🛡️ AWS takes security seriously, scanning daily for vulnerabilities and patching critical issues regularly to ensure the lowest possible TCU for running distributed training jobs. 💡 Model training for recommendation use cases…

Continue Reading Revolutionizing Machine Learning with Large Model Training on AWS & PyTorch

Senior Bioinformatics Scientist – 127022

UCSD Layoff from Career Appointment: Apply by 12/08/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 12/20/2023. Eligible Special Selection clients should contact their Disability Counselor for assistance. This position will work a hybrid schedule which includes a combination…

Continue Reading Senior Bioinformatics Scientist – 127022

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…

Continue Reading Slurm REST API in AWS ParallelCluster

Genomics England hiring PhD Bioinformatics Intern in London, England, United Kingdom

Company DescriptionGenomics England partners with the NHS to provide whole genome sequencing diagnostics. We also equip researchers to find the causes of disease and develop new treatments – with patients and participants at the heart of it all. Our mission is to continue refining, scaling, and evolving our ability to…

Continue Reading Genomics England hiring PhD Bioinformatics Intern in London, England, United Kingdom

When is RESUME an invalid node state?

Hi Xaver, Your version of Slurm may matter for your power saving experience. Do you run an updated version? /Ole On 12/6/23 10:54, Xaver Stiensmeier wrote: > Hi Ole, > > I will double check, but I am very sure that giving a reason is possible > as it has been done at…

Continue Reading When is RESUME an invalid node state?

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

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

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

Execute R command on specific termimal

Execute R command on specific termimal 1 Hi all, I am running R vscode on linux HPC node. I ran command in a R script (using ctrl + enter), but it was executed on a login node. I would like to execute the command in a specific terminal, where I…

Continue Reading Execute R command on specific termimal

JupyterHub server spawning never completes; new JupyerHub admin – JupyterHub

Hello, I’ve recently started a position responsible for a JupyterHub installation as part of an HPC environment; the old team left without leaving much in the way of documentation, and I’ve never worked on JupyterHub before, so please bear with me. When launching JupyterHub, the system will stay on the…

Continue Reading JupyterHub server spawning never completes; new JupyerHub admin – JupyterHub

Kill Slurm Job when browser tab closes – JupyterHub

pgierz December 4, 2023, 9:22am 1 Hello, I’m deploying an HPC-enabled Jupyterhub which will use a SLURM spawner. I would like to communicate to SLURM to cancel the scheduler jobs when the browser tab is closed. Is it possible to send signals to the system on a browser-tab-close action? (sorry…

Continue Reading Kill Slurm Job when browser tab closes – JupyterHub

HPC Kubernetes: AI Training on 3,500 GPUs

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

Continue Reading HPC Kubernetes: AI Training on 3,500 GPUs

PhD Bioinformatics Intern Job in Greater London, Pharmaceuticals & Life Sciences Career, Intern/Graduate Jobs in Genomics England

Company Description Genomics England partners with the NHS to provide whole genome sequencing diagnostics. We also equip researchers to find the causes of disease and develop new treatments – with patients and participants at the heart of it all. Our mission is to continue refining, scaling, and evolving our…

Continue Reading PhD Bioinformatics Intern Job in Greater London, Pharmaceuticals & Life Sciences Career, Intern/Graduate Jobs in Genomics England

Postdoctoral Fellowship in bioinformatics and genetic epidemiology – University of Copenhagen – job portal

Job Portal                                                                                         Postdoctoral Fellowship in bioinformatics and genetic epidemiology   A two-year postdoctoral fellowship is available at the Section for Computational and RNA Biology, Department of Biology, University of Copenhagen. The position will be available from April 1st, 2024 or thereafter. The specific projects involve analyzing…

Continue Reading Postdoctoral Fellowship in bioinformatics and genetic epidemiology – University of Copenhagen – job portal

King’s College London hiring Research Associate (Bioinformatician) in London, England, United Kingdom

Job DescriptionThis is an exciting opportunity to join an internationally leading interdisciplinary team of King’s College London, Oxford University and Surrey University scientists working on the ‘Mind & Skin’ research programme. Funded by the UK Medical Research Foundation, we are generating complex sleep monitoring, brain imaging and skin phenotyping data…

Continue Reading King’s College London hiring Research Associate (Bioinformatician) in London, England, United Kingdom

qiime2 illegal instruction – Technical Support

Andrea_G (Andrea Gatti) November 28, 2023, 2:19pm 1 Hello, I have to start working on a cluster and I tired to install Qiime2 in a conda environment, but I was reported with an error during Qiime2 installation, specifying: Preparing transaction: done Verifying transaction: – SafetyError: The package for r-base located…

Continue Reading qiime2 illegal instruction – Technical Support

Vacature Postdoc position in Bioinformatics

In this TKI-PPP funded project, our objective is to construct a comprehensive landscape of the tumor microenvironment in cervical cancer patients and investigate its potential clinical applications using cutting-edge bioinformatic and molecular profili… Cervical cancer ranks fourth leading causes of cancer death in women globally, with approximately 800-900 diagnosis annually…

Continue Reading Vacature Postdoc position in Bioinformatics

Jensen Huang Brings re:Invent to Life

Jensen Huang is everywhere, and so is NVIDIA. The company seems to be stealing the spotlight at all the major events – be it Google Cloud Next, AWS re:Invent or Microsoft Ignite, bringing the party to life at each one of them.  During the recent re:Invent keynote, AWS and NVIDIA…

Continue Reading Jensen Huang Brings re:Invent to Life

Puzzling error with ‘importnk2()’ function using SLURM job manager

I have a very specific problem that only occurs when using the SLURM job manager on the high-performance cluster (HPC) of my university. It does not happen when I run the code on the login node of the HPC or on my own computer. When I call FDTD via Python,…

Continue Reading Puzzling error with ‘importnk2()’ function using SLURM job manager

bwa mem hangs after a few thousand reads

I am trying to align a bunch of paired sample fastq files using bwa mem. My original command was: bwa mem -t 8 hg38.fa sample_read1.fq.gz sample_read2.fq.gz > sample_paired.sam I am running this on a HPC cluster. These files have approx. 25 million reads, so I initially anticipated that they might…

Continue Reading bwa mem hangs after a few thousand reads

Senior Bioinformatics Software Engineer – Land A Remote Job From Top Employers

The Center for Applied Bioinformatics (CAB) at the St. Jude Children’s Research Hospital (SJCRH) is seeking a creative Software Engineer with a strong background in bioinformatics to join our development team to create and maintain our vital analytical infrastructure. The new hire will work closely with a team of computer…

Continue Reading Senior Bioinformatics Software Engineer – Land A Remote Job From Top Employers

Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M. & Cunningham, P. Evidence for two independent domestications of cattle. Proc. Natl Acad. Sci. USA 91, 2757–2761 (1994). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Verdugo Marta, P. et al. Ancient cattle genomics, origins, and rapid turnover…

Continue Reading Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

Cineca-ai – HPC Cineca

Version: 2.02 (G100) Availability: GALILEO100 Target: all Official web site: gitlab.www.hpc.cineca.it/sorland2/cineca-ai Related Commands: If you wish to activate the default environment:        $ conda activate $CINECA_AI_ENV   – If you wish to create a personal conda env with your installations, you can use the local conda channel to access…

Continue Reading Cineca-ai – HPC Cineca

Security update for slurm SUSE-SU-2023:4578-1 | SUSE Support

Announcement ID: SUSE-SU-2023:4578-1 Rating: important References: bsc#1216207 bsc#1216869 Cross-References: CVE-2023-41914 CVSS scores: CVE-2023-41914 ( SUSE ): 8.8 CVSS:3.1/AV:N/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H CVE-2023-41914 ( NVD ): 7.0 CVSS:3.1/AV:L/AC:H/PR:L/UI:N/S:U/C:H/I:H/A:H Affected Products: HPC Module 15-SP5 openSUSE Leap 15.5 SUSE Linux Enterprise Desktop 15 SP5 SUSE Linux Enterprise High Performance Computing 15 SP5 SUSE Linux Enterprise Micro…

Continue Reading Security update for slurm SUSE-SU-2023:4578-1 | SUSE Support

SUSE alert SUSE-SU-2023:4581-1 (slurm_22_05) [LWN.net]

From:   sle-security-updates@lists.suse.com To:   sle-security-updates@lists.suse.com Subject:   SUSE-SU-2023:4581-1: important: Security update for slurm_22_05 Date:   Mon, 27 Nov 2023 12:30:18 -0000 Message-ID:   <170108821854.634.5846566020364917363@smelt2.prg2.suse.org> # Security update for slurm_22_05 Announcement ID: SUSE-SU-2023:4581-1 Rating: important References: * bsc#1208810 * bsc#1216207 * bsc#1216869 Cross-References: * CVE-2023-41914 CVSS scores: * CVE-2023-41914 (…

Continue Reading SUSE alert SUSE-SU-2023:4581-1 (slurm_22_05) [LWN.net]

How to run python experiments with Slurm and Conda? | by Hitesh Vaidya | Nov, 2023

source: getyarn.io/yarn-clip/368e3529-f540-4cfa-af28-d40a2ca2b99d As data scientists and researchers, efficiently managing multiple machine learning experiments is fundamental to our work. Tools like Slurm and Conda offer powerful capabilities that streamline the execution of experiments on high-performance computing clusters while ensuring environment consistency and reproducibility. In this blog, we will take a look…

Continue Reading How to run python experiments with Slurm and Conda? | by Hitesh Vaidya | Nov, 2023

LAMMPS – HPC Cineca

LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state…

Continue Reading LAMMPS – HPC Cineca

AMD Empowers AI Developers With Expanded GPU Support

Explore the features, including HIPTensor and MIGraphX, that make AMD’s ecosystem a robust choice for the AI community, providing flexibility, efficiency, and accessibility in machine learning. AMD has expanded its support for machine learning (ML) development workflows with the release of AMD ROC 5.7, targeting the Radeon RX 7900 XT…

Continue Reading AMD Empowers AI Developers With Expanded GPU Support

7 Protein Folding Updates From 2023

For over 50 years, scientists were stuck on the protein-folding problem. It’s like trying to figure out how a complex origami structure folds up. But then, in 2020, DeepMind’s AlphaFold cracked the code. It aced a big contest by predicting how proteins fold with an amazing 90% accuracy. Jump ahead…

Continue Reading 7 Protein Folding Updates From 2023

r-studio: “warning in install.packages: installation of package “spant” had non-zero exit status” problem

running R (version 4.2.2) and R Studio (version 1.4.1717), with 10GB of memory. trying to install the toolbox “spant” on HPC (high performance computer) cluster, and i get this error > Warning in install.packages: installation of package “spant” had non-zero exit status what am i missing to fix this? i…

Continue Reading r-studio: “warning in install.packages: installation of package “spant” had non-zero exit status” problem

Which Cloud Stocks are Benefitting from the AI Boom?

WisdomTree’s Cloud Computing Fund appears not to have capitalised on the AI rally this year, despite cloud models being fundamental to AI programs. However, two-thirds of the global cloud infrastructure market is accounted for by three Magnificent Seven companies: Google, Microsoft and Amazon. These companies are already shaping themselves for…

Continue Reading Which Cloud Stocks are Benefitting from the AI Boom?

2024 Summer Intern – Oncology Bioinformatics – GRED Job In California – Genentech

The Position 2024 Summer Intern – Oncology Bioinformatics – gRED Oncology Bioinformatics supports and expands oncology research within the larger gRED organization, with our team focusing on cancer immunogenomics and cell therapies. One aspect of these efforts is genomic sequence analysis and optimization, especially in the context of regulatory…

Continue Reading 2024 Summer Intern – Oncology Bioinformatics – GRED Job In California – Genentech

AMD enables AI development with PyTorch and ROCm on Radeon RX 7900 XT GPUs

AMD has recently released AMD ROCm 5.7 for the AMD Radeon RX 7900 XTX and Radeon PRO W7900 GPUs, which are specifically designed for Machine Learning (ML) development workflows using PyTorch. This platform has now been extended to include the Radeon RX 7900 XT GPU, which provides more options for…

Continue Reading AMD enables AI development with PyTorch and ROCm on Radeon RX 7900 XT GPUs

Is there a way to query Ensembl to get all 3’UTRs from all species?

Is there a way to query Ensembl to get all 3’UTRs from all species? 1 I am trying to obtain stats on how many 3’UTRs are annotated in Ensembl. I would really like to download the as many annotated 3’UTRs as possible from as many species as possible and find…

Continue Reading Is there a way to query Ensembl to get all 3’UTRs from all species?

AMD Ryzen Threadripper 7980X & 7970X Linux Performance Benchmarks Review

Page 1 – IntroductionPage 2 – Ryzen Threadripper 7000 SeriesPage 3 – Linux Test ConfigurationPage 4 – HPC Benchmarks, NAMD, OpenFOAM CFDPage 5 – Altair OpenRadioss Benchmarks, Xmrig Miner, easyWave, GROMACSPage 6 – LuxCore Render, Embree BenchmarksPage 7 – Video Encoding BenchmarksPage 8 – Intel oneAPI: OIDn, OSPRay BenchmarksPage 9…

Continue Reading AMD Ryzen Threadripper 7980X & 7970X Linux Performance Benchmarks Review

Optimizing Language Model Training: A Practical Guide to SLURM | by Viktorciroski | Nov, 2023

In the dynamic world of deep learning, pushing the boundaries of language models often bumps into the memory limits of individual GPUs, like the NVIDIA GeForce RTX 3090. With 24 GB of GDDR6X memory, it’s a powerhouse, but models such as Llama 2 can still stress these resources, causing headaches…

Continue Reading Optimizing Language Model Training: A Practical Guide to SLURM | by Viktorciroski | Nov, 2023

[slurm-users] slurm job_container/tmpfs

Dear slurm community,   I run slurm 21.08.1 under Rocky Linux 8.5 on my small HPC cluster and am trying to configure job_container/tmpfs to manage the temporary directories.   I have a shared nfs drive “/home” and a local “/scratch” (with permissions 1777) on each node.   For each submitted…

Continue Reading [slurm-users] slurm job_container/tmpfs

Sr Scientist I, Bioinformatics Engineer job with AbbVie

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…

Continue Reading Sr Scientist I, Bioinformatics Engineer job with AbbVie

MAJOR Computational Biology Research Lab

MAJOR Computational Biology Research Lab (MCBRL) uses computer science algorithms to solve biology related problems, bioinformatics software development and develop bioinformatics cloud computing platforms or services for handling and analyzing large-scale biological data.. The workflow of hdWGCNA analysis for Single-cell Spatial Transcriptomics data RNA-seq Schematicsc/nRNA-seq Schematic ” RNA-seq Schematic 空间转录共表达网络分析流程…

Continue Reading MAJOR Computational Biology Research Lab

University Positions – Postdoc in GPU algorithms for molecular dynamics with GROMACS

Job description We are looking for an HPC expert to contribute to one or multiple projects related to the GROMACS molecular simulation software. GROMACS is one of the most important HPC applications in the world and runs on all modern CPU and GPU architectures. GROMACS uses a hierarchical parallelization with…

Continue Reading University Positions – Postdoc in GPU algorithms for molecular dynamics with GROMACS

Hybrid quantum computing collaboration from NVIDIA

Terra Quantum, a quantum technology company, announced it is collaborating with NVIDIA to enhance the world of data analytics powered by hybrid quantum computing, with the goal of empowering businesses to achieve unparalleled performance and insights. Jointly, Terra Quantum and NVIDIA established a technical collaboration accelerating the integration of hybrid quantum…

Continue Reading Hybrid quantum computing collaboration from NVIDIA

Intel updates HPC processor roadmap

Intel kicked off the Supercomputing 2023 conference with a series of high performance computing (HPC) announcements, including a new Xeon line and Gaudi AI processor. Intel will ship its fifth-generation Xeon Scalable Processor, codenamed Emerald Rapids, to OEM partners on December 14. Emerald Rapids features a maximum core count of…

Continue Reading Intel updates HPC processor roadmap

Optimizing PyTorch for Efficient AI Model Training and Inferencing

Optimizing PyTorch for Efficient AI Model Training and Inferencing Introduction Scaling Neural Networks Adding More Layers Capturing More Nuance in Data Performing Complex Tasks Increased Memory and Compute Requirements Distributed Data Parallel (DDP) Three Steps of DDP Training Computation and Communication Overlap Bucket Division and Gradients Synchronization Full Utilization of…

Continue Reading Optimizing PyTorch for Efficient AI Model Training and Inferencing

Nvidia announces H200, designed to handle AI work better, How better is it than the H100? Know here

Nvidia H200: Leading chip manufacturer Nvidia has released the H200, a top-of-the-line chipset designed for AI applications. With numerous large firms, including Amazon Web Services, Google Cloud, Microsoft Azure, and Oracle Cloud Infrastructure, already pledging to utilise the chipset next year, the upgrade to the already well-liked H100 chipset will begin…

Continue Reading Nvidia announces H200, designed to handle AI work better, How better is it than the H100? Know here

Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses

INTRODUCTION Microbiome research, especially the detection of microorganisms by molecular techniques, has become a fundamental tool for investigating host-associated bacteria, such as those harbored by veterinary or human clinical samples[1,2]. Next-generation sequencing (NGS) approaches now enable the identification of slow-growing, non-cultivable, or non-viable bacteria contained in clinical specimens without relying…

Continue Reading Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses

Are these timings fine? – User discussions

lutek14 November 14, 2023, 7:02am 1 GROMACS version: gromacs/2021.4_mpi_plumedGROMACS modification: No Hello,I am running Gromacs on HPC for the first time, and I am unsure if the timings are fine. I am not sure whether I have allocated too many or too few resources. The system consists of 57,810 atoms.The…

Continue Reading Are these timings fine? – User discussions

Online metagenomics training (free) in April

Free Cloud-SPAN course on METAGENOMICS 11-21 April 2023  Join our experts for this free online module! We welcome environmental scientists who would like to use high performance computing for metagenomics analysis, or anyone with an interest in metagenomics to register. No previous experience of the command line or HPC is…

Continue Reading Online metagenomics training (free) in April

Predoctoral Research Assistant for the Bioinformatics Unit ( AIPREBIOINF13) – National Center for Oncological Research – job portal

Referencia de la oferta: AIPREBIOINF13 Inicio de la oferta: 14/11/2023 Fin de la oferta: 13/12/2023 23:59:00 Descripción The Bioinformatics Unit (BU) within the Structural Biology Programme is seeking to recruit a highly motivated and talented student to conduct a PhD study as part of the GENCODE project to annotate the…

Continue Reading Predoctoral Research Assistant for the Bioinformatics Unit ( AIPREBIOINF13) – National Center for Oncological Research – job portal

Senior Bioinformatics Scientist @ Storm3

⚡ Senior Bioinformatics Scientist (HUMAN GENETICS) 🧪 Healthtech Start-Up 📌 Remote (US) 💰 $150K Base + Bonus + Impressive equity Are you interested in joining a revolutionary Biotech start-up that is using their ground-breaking AI platform to change the way we discover drugs? This established start-up with over $30M in…

Continue Reading Senior Bioinformatics Scientist @ Storm3

Award-Winning Tools Make Super Computers Run 40% Faster

In the fall of 2019, Rohan Basu Roy was sitting in the Goodwill Computing Laboratory on Northeastern’s Boston campus.  He had just started pursuing his doctorate in computer engineering and was working on high-performance computing (HPC) systems and applications. These systems sequence, analyze and extract large amount of data in…

Continue Reading Award-Winning Tools Make Super Computers Run 40% Faster

Nvidia’s H200 GPU To One-Up H100 With 141GB Of HBM3e As Memory Race Heats Up

Components & Peripherals News Dylan Martin November 13, 2023, 09:00 AM EST The H200 features 141GB of HBM3e and a 4.8 TB/s memory bandwidth, a substantial step up from Nvidia’s flagship H100 data center GPU. ‘The integration of faster and more extensive memory will dramatically improve…

Continue Reading Nvidia’s H200 GPU To One-Up H100 With 141GB Of HBM3e As Memory Race Heats Up

Intel Xeon Emerald Rapids-SP to Offer 40% More Performance than Sapphire Rapids in AI

Intel has unveiled additional details about its upcoming 5th Gen Xeon processors. Codenamed Emerald Rapids, these CPUs are architecturally identical to Sapphire Rapids but pack more cores and cache on the same platform. More specifically, the new Xeon Scalable chips will offer up to 448MB of L3 cache, thrice as…

Continue Reading Intel Xeon Emerald Rapids-SP to Offer 40% More Performance than Sapphire Rapids in AI

Intel 5th Gen Emerald Rapids 64-Core & Granite Rapids Xeon CPUs Performance Unveiled

Intel has unveiled the latest performance and internal projections of its upcoming 5th Gen Emerald Rapids & next-gen Granite Rapids Xeon CPUs. Intel 5th Gen Emerald Rapids Xeon 64-Core CPU Offers Up To 40% Better Performance Than 56-Core Sapphire Rapids Talking about its Xeon CPUs during SC23, Intel unveiled new…

Continue Reading Intel 5th Gen Emerald Rapids 64-Core & Granite Rapids Xeon CPUs Performance Unveiled

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…

Continue Reading Deploy CP2K on an Azure virtual machine

Sr Bioinformatics Engineer (Req IIC1440) in San Diego, California

ENGINEERING Sr. Bioinformatics Engineer (Req# IIC1440) Dvlp test infrastructure & tools to analyze large genomic datasets on-premises (DRAGEN server and HPC) & in the cloud (AWS, Azure or Google cloud). Local telecommuting permitted. MS+3orBS followed by 5 yrs prog rltd exp. $124,300-$186,500/yr Mail resumes to Illumina, Attn: SD122440, 5200 Illumina…

Continue Reading Sr Bioinformatics Engineer (Req IIC1440) in San Diego, California

Alternatives to snpflip to find ambigious and flipped snps

Alternatives to snpflip to find ambigious and flipped snps 0 Hello everyone, I having an issue with strand flips when trying to perform imputation. In the past on an old HPC I used it supported snpflip, a tool which would recognize ambigious snps as well as snps that have been…

Continue Reading Alternatives to snpflip to find ambigious and flipped snps

More Thoughts on Artificial Intelligence

I published Thoughts on Artificial Intelligence on 19 July 2023. Since then, developments in AI have continued at a breath-taking speed. In here, I want to share new thoughts on AI that I have, as well as provide updates on some of the initial discussions. Let’s start with the new thoughts, in…

Continue Reading More Thoughts on Artificial Intelligence

Advisor/Sr. Advisor – Bioinformatics – Relocation Assistance job with Lilly

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease,…

Continue Reading Advisor/Sr. Advisor – Bioinformatics – Relocation Assistance job with Lilly

Read file with the DSSAT R package – rstudio

Good evening All,I am trying to read experimental file from my system using the DSSAT R package and I get the following error below: I don’t know if there is any expert here that can help me; Here is my reprex: # Load Required Packages library(DSSAT) #> When using the…

Continue Reading Read file with the DSSAT R package – rstudio

University of Alabama at Birmingham hiring BIOINFORMATICIAN I in Birmingham, Alabama, United States

Position Summary: The primary role is to execute a variety of data management and analysis tasks, ensuring the quality, reproducibility, and efficiency of processes related to high-dimensional data. You will collaborate with study investigators and fellow bioinformatics professionals within the department to contribute to high-quality, reproducible research across various scientific…

Continue Reading University of Alabama at Birmingham hiring BIOINFORMATICIAN I in Birmingham, Alabama, United States

Use of CALYPSO in SLURM-based HPC

Dear CALYPSO community,  I am interested in using CALYPSO on a SLURM-based HPC with Intel servers. I am seeking assistance in understanding the workflow and the necessary steps for installation.  Could you kindly provide me with information on the essential prerequisites and important aspects I should be aware of before…

Continue Reading Use of CALYPSO in SLURM-based HPC

Lilly Advisor/Sr. Advisor – Bioinformatics in New York, NY | 883515845

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease,…

Continue Reading Lilly Advisor/Sr. Advisor – Bioinformatics in New York, NY | 883515845

St. Jude Children’s Research Hospital hiring Senior Bioinformatics Analyst/Bioinformatics Analyst in Memphis, Tennessee, United States

St. Jude Children’s Research Hospital is looking for a highly motivated Senior Bioinformatics Analyst/Bioinformatic Analyst to contribute to genetic research projects in the Department of Epidemiology and Cancer Control. Our research leverages comprehensive biomedical data from childhood cancer survivors participating in two world-leading cohort studies, CCSS (ccss.stjude.org/ ) and SJLIFE…

Continue Reading St. Jude Children’s Research Hospital hiring Senior Bioinformatics Analyst/Bioinformatics Analyst in Memphis, Tennessee, United States

Postdoctoral Researcher in Structural Bioinformatics, Spain

Postdoctoral Researcher in Structural Bioinformatics: The research group “Structural Bioinformatics and High-Performance Computing (BIO-HPC)” at Universidad Catolica de Murcia (UCAM) is seeking postdoctoral candidates for Fundacion Seneca 2023 postdoctoral contracts. The group is looking for individuals with expertise in the following thematic lines: Computational Drug Discovery, High-Performance Computing, and Machine…

Continue Reading Postdoctoral Researcher in Structural Bioinformatics, Spain

Post Doctoral Fellow job with University of Missouri – Columbia

Job Description Bond Lifesciences Center would like to hire up to two Post Doctoral Fellows. Duties would include: (1) Analyze diverse types of biological data, including next generation sequencing (NGS) such as RNA-seq, single cell RNA-seq, and others, multiomics data integration and microbiome data. Prepare and publish manuscripts and reports….

Continue Reading Post Doctoral Fellow job with University of Missouri – Columbia

The Singh Lab – Junior/Assistant/Associate/Full Specialist in Bioinformatics or Computational Biology job in San Francisco, California at University of California – San Francisco

The Singh Lab – Junior/Assistant/Associate/Full Specialist in Bioinformatics or Computational Biology SCHOOL OF MEDICINE – Department of Anatomy Description The lab of Dr. Param Singh at UCSF (www.singhlabucsf.org) is looking for a Junior/Assistant/Associate/Full Specialist with expertise in bioinformatics or computational biology to join our team and contribute to new and…

Continue Reading The Singh Lab – Junior/Assistant/Associate/Full Specialist in Bioinformatics or Computational Biology job in San Francisco, California at University of California – San Francisco

hpc – how start_time is calculated for slurm multi-cluster

I’m having a hard time figuring out the distribution of jobs between 2 clusters in a Slurm multi-cluster environment. The documentation says that each job is submitted to the cluster that provides the earliest start time, and once the task is submitted to a cluster, it can’t be re-distributed to…

Continue Reading hpc – how start_time is calculated for slurm multi-cluster

Job submission on HPC using pbs script – User discussions

GROMACS version:2022.1GROMACS modification: YesRespected expert, I am using our institute HPC for mdrun. I can utilise one node but cannot utilise multiple nodes. I have learnt that PBS.sh script(image attached)is used for job submission on our institute’s HPC Even though i have tried modifications like varying number of nodes, process…

Continue Reading Job submission on HPC using pbs script – User discussions

task – How to send a job to nodes of different types in SLURM

I work at a HPC centre where we use SLURM to manage queues and I’m looking for a way to force a job divided by tasks to be sent to nodes of different types. For example, let’s say we have two types of nodes called lpn and hpn, and we…

Continue Reading task – How to send a job to nodes of different types in SLURM

Security update for slurm SUSE-SU-2023:4329-1 | SUSE Support

Announcement ID: SUSE-SU-2023:4329-1 Rating: important References: bsc#1208810 bsc#1216207 Cross-References: CVE-2023-41914 CVSS scores: CVE-2023-41914 ( SUSE ): 8.8 CVSS:3.1/AV:N/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H Affected Products: openSUSE Leap 15.4 openSUSE Leap 15.5 SUSE Linux Enterprise High Performance Computing 15 SP2 SUSE Linux Enterprise High Performance Computing 15 SP2 LTSS 15-SP2 An update that solves one vulnerability…

Continue Reading Security update for slurm SUSE-SU-2023:4329-1 | SUSE Support

Large qiime2 table (107 gb) to phyloseq

Large qiime2 table (107 gb) to phyloseq 0 Hello, I’m currently engaged in a microbiome meta-analysis and have combined a dada2 table involving data from 83 different studies. The file size of this merged table is 107GB. However, I’m encountering difficulties reading this file in R to conduct statistical analyses….

Continue Reading Large qiime2 table (107 gb) to phyloseq

CEDARS-SINAI Research Bioinformatician II – Human Microbiome Research Institute in Beverly Hills, CA | 880523723

Cedars-Sinai has established a new Human Microbiome Research Institute that will support investigators studying how the microbiome plays a role in human health and disease with key focus areas in: Cancer, Metabolism, Early Life, GI & Liver, and Autoimmunity. The Human Microbiome Research Institute (HMRI) is an innovation hub and…

Continue Reading CEDARS-SINAI Research Bioinformatician II – Human Microbiome Research Institute in Beverly Hills, CA | 880523723

Issue with running LAMMPS in serial mode – LAMMPS Installation

Dear all I have question regarding running the LAMMPS successfully. I am trying to use LAMMPS in a serial way. It seems to work on the head node of the HPC but whenever I try to run it using slurm, I get the following error: lmp_nompi: error while loading shared…

Continue Reading Issue with running LAMMPS in serial mode – LAMMPS Installation

[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…

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

Keywords in command line for getting good performance in gromacs – User discussions

I am trying to run gromacs 2023.2 gpu on HPC. I am getting super slow performance in HPC. I run the calculation for the test purpose on 8 cores for 10 mins only. The projected steps of calculation is about 15,000 in 10 minuites, unfortunately couldn’t get performance upto mark….

Continue Reading Keywords in command line for getting good performance in gromacs – User discussions

NERSC Collaborations Help Illuminate Earth’s Biodiversity

Oct. 26, 2023 — How do we know who’s in our world? Genomics researchers study and map the genomes of all kinds of genetic entities, from the blue whale all the way down to mobile genetic elements (MGEs), which have genetic material but are not considered living. But many organisms…

Continue Reading NERSC Collaborations Help Illuminate Earth’s Biodiversity

Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.

News:Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions. 16 Two recent posts made it clear that we don’t have ways to directly collect feedback and suggestions regarding Biostars. As it turns out there are quite a few suggestions that make a lot of sense and are really easy…

Continue Reading Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.

Lenovo Maximizes HPC Resources via Partnership with SchedMD and Slurm Workload Manager – High-Performance Computing News Analysis

[SPONSORED GUEST ARTICLE]   In HPC, leveraging compute resources to the maximum is a constant goal and a constant source of pressure. The higher the usage rate, the more jobs get done, the less resources sit idle, the greater the return on the HPC investment. Greater power efficiency means greater organizational…

Continue Reading Lenovo Maximizes HPC Resources via Partnership with SchedMD and Slurm Workload Manager – High-Performance Computing News Analysis