Tag: HPC

Job description Seeking a highly motivated Research Associate with expertise in deep learning and spatial biology within the field of translational cancer research. The project will entail algorithm development and deployment of deep learning approaches for histomorphological characterisation of triple negative breast cancers. Through spatial transcriptomics, diverse transcriptional profiles will…

Axle Informatics is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations around the globe. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques…

job summary: As the largest staffing and recruitment agency in the world, we can commit to finding you the perfect role that gives you the opportunity to learn and grow in the life sciences arena. Utilizing a recruiter for your job search gives you access to a large network of…

Bioinformatics Software Engineer II/III Job ID: req3384Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…

Hi everyone, There’s a monthly meeting on the use of JupyterHub in HPC and general Jupyter in HPC topics. Everyone interested in the intersection of Jupyter and HPC is invited. Standing items include a check in on developments with Batchspawner and Wrapspawner but the agenda typically covers a wide variety…

I am very new to ATAC-seq pipeline from Encode and trying to run on a HPC but not sure the steps after reading their instruction. github.com/ENCODE-DCC/atac-seq-pipeline Here is my json file: { “atac.title” : “atac)”, “atac.description” : “Encode”, “atac.pipeline_type” : “atac”, “atac.align_only” : false, “atac.true_rep_only” : false, “atac.genome_tsv” : “https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v4/hg38.tsv”,…

Junior Bioinformatician position in BiNGS   We are seeking a junior bioinformatician for the Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) core, to lead transcriptomics and epigenetics data analysis projects related but not limited to cancer biology, skin biology, developmental biology, diabetes, and neuron biology.   The mission…

Optimum setting for local blastp for ~10K sequences 0 Hi all, I’m trying to blast around 10,000 protein sequences against nr with blastp. In the past, using 100-sequence chunks and a single CPU each had worked well for blastn, but blastp seems to be much slower. A .fasta file with…

Hi everyone, I have a following configuration: cryosparc_master running on a local workstation (where I have sudo) a university HPC cluster with wonderful GPUs (where I don’t have sudo) I want to connect the HPC cluster as a separate lane for our local cryosparc. However, when I try using example…

Help with running ATAC using Encode pipeline 0 Hi all, I am trying to run atac pipeline of Encode on a HPC but not sure the correct command after reading their instruction. github.com/ENCODE-DCC/atac-seq-pipeline If you want to run your data, what will you put in the INPUT_JSON? INPUT_JSON=”https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled.json” caper hpc…

Overview At the heart of QIAGEN’s business is a vision to make improvements in life possible. We are on an exciting mission to make a real difference in science and healthcare. We are still the entrepreneurial company we started out as and have today achieved a size where we can…

Michigan Imputation Server – Local docker image 0 Hi, Due to clinical data and not meeting the minimum sample of 20, I hope to use the Michigan Imputation Server locally via its’ Docker image. I got couple of questions that I hope others can help: I tried to do this…

How do I restrict to only hm3 SNPs for plink analyses? 0 Hello! I am trying to use plink to select only hm3 snps from the ukb bgen files that I have, but I am at a total loss as to how to proceed. I am really new to all…

The way I see it, artificial intelligence (or AI), really leapt into the zeitgeist in late-2022 or early-2023 with the public introduction of DALL-E2 and ChatGPT. Both are provided by OpenAI and are software products that use AI to generate art and writing, respectively (and often at astounding quality). Since…

I am running DADA2 through QIIME and my demux.qza file is 110GB. After 24Hr I saw it consumed more than 4TB of disk space and the log file is not updating from a certain point.Here I am curious whether it is normal or if there is any glitch and I…

Fixed-term: The funds for this post are available for 2 years in the first instance. This is an exciting opportunity for a highly motivated computational researcher to join Professor Sir Shankar Balasubramanian’s pioneering research programme playing a key role in advancing the understanding of sequence, structure and chemical modifications in…

GROMACS version:2022.5-Colvars_2023_05_01GROMACS modification: YesI am attempting to use ABF in the colvars module for my simulation. I have tried installing several versions of Gromacs (gromacs2021.6-colvars, fresh download of gromacs2022.5 that I patched with colvars). I have tried installing them on my own laptop in Ubuntu22.04 on WSL2 as well as…

Hello, I am new to using containers and was wondering if anyone has experience using cp2k singularity container on Expanse or any other resource in the ACCESS ecosystem. I found the container for v. 9.1.0 at catalog.ngc.nvidia.com/orgs/hpc/containers/cp2k.  I intend to use the container in an HPC setting that uses slurm…

How to download iGenomes from S3 1 Hi all, I run a pipeline on HPC that got an error with pulling iGenomes from S3 so I try to download it to my cluster but don’t know how. Would you have a suggestion? Thank you so much. ewels.github.io/AWS-iGenomes/ iGenome • 45…

GROMACS version: 2022.3, 2022.5, 2023.1GROMACS modification: NoHello, I’ve been having issues, trying all three of these GROMACS distributions. I’m running on an HPC, and I have included the basic error logs for the outputs of cmake and make check for the blank run after logging into the HPC. After gcc-7.5.0…

I am new to Slurm. Let’s say we have a computing system with 24 cores CPU & 32GB system memory. I need to divide that system resources by each user in my job queue dynamically. How should I set Slurm to achieve something like this: If nothing is running in…

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

Now that you are connected to the head node, familiarize yourself with the cluster structure by running the following set of commands. SLURM SLURM from SchedMD is one of the batch schedulers that you can use in AWS ParallelCluster. For an overview of the SLURM commands, see the SLURM Quick…

Looking to be a part of a highly innovative organization in your next opportunity!? Our client is currently looking for a Bioinformatics Scientist to join the Mississauga team! If you are looking for a new challenge, and have a great interest in technology, we want to hear from you! What…

Hi all,I have the following issue when trying to execute a simulation file on a gpu hpc cluster.The following error. ._____________________________________________________________________________________|| Initial checks…| All good.|_____________________________________________________________________________________[gpu008:162305] OPAL ERROR: Not initialized in file pmix3x_client.c at line 112————————————————————————–The application appears to have been direct launched using “srun”,but OMPI was not built with SLURM’s…

HI,   So I’m testing the use of Open MPI 5.0.0 pre-release with the Slurm/PMIx setup currently on NERSC Perlmutter system. First off, if I use the PRRte launch system, I don’t see the issue I’m raising here.   But, many NERSC users prefer to use the srun “native” launch…

Below you will find the details for the position including any supplementary documentation and questions you should review before applying for the opening. To apply for the position, please click the Apply for this Job link/button.If you would like to bookmark this position for later review, click on the Bookmark…

Challenges & Requirements [SPONSORED GUEST ARTICLE]   International Supercomputing Conference (ISC) is an annual conference that showcases the key technologies in the supercomputing field. It brings together experts from multiple specialist fields, including research into life sciences and genetics to shed light on the origins and mysteries in our lives. HPC,…

Molecular profiling reveals common changes in matched pairs of HNSCC primary tumor and metastasis-derived cell lines Identification of both genetic and functional differences between primary and metastatic variants of HNSCC would be enabled by in vitro models derived independently from these sites from the same patient. Unfortunately, HNSCC tumor cells…

//php echo do_shortcode(‘[responsivevoice_button voice=”US English Male” buttontext=”Listen to Post”]’) ?> Nvidia will make Cambridge-1, the supercomputer it launched for the U.K. healthcare and life sciences research sector, accessible through its DGX-Cloud offering. One of the first Nvidia installations to join the DGX-Cloud, Cambridge-1 has been “hugely successful” since it launched…

New Delhi: A Supreme Court bench comprising Chief Justice D.Y. Chandrachud and Justice P.S. Narasimha expanded on May 12 the remit of a High-Powered Committee (HPC) constituted for the purpose of stopping the capture of wild elephants. The bench issued the direction while disposing of an interlocutory application (IA) in…

Summary The Human Genome Sequencing Center (HGSC) provides a unique opportunity to gain high-throughput data production experience in an academic research environment, with opportunities for publication, conference travel and international scientific collaboration. As a member of the NGSI Clinical Informatics team, you will directly contribute to the HGSC’s pioneering work…

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…

About The RoleWe have an exciting opportunity for an experienced bioinformatician who is interested in working at the forefront of the gene editing (CRISPR knock-out, base editing) and gene modulation (CRISPRa, CRISPRi, RNAi) fields. We are seeking a Cambridge-based Senior Bioinformatics Scientist 1 to join our global Bioinformatics team, which…

The Department of Medicine, Division of Cardiovascular Medicine at Stanford University is seeking a talented Bioinformatics Engineer to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC). As part of this groundbreaking national research consortium, you will help unravel the molecular mechanisms underlying the benefits…

We are looking for a highly motivated postdoc for the Kempe Foundations funded project “Analysis of miRNA function during embryo development in Norway spruce” in the research group of Dr. Egertsdotter. The postdoctoral scholarship will be placed at the Department of Forest Genetics and Plant Physiology (Swedish University of Agricultural Sciences), which…

Job Portal Postdoc position in circadian biology and bioinformatics Novo Nordisk Foundation Center for Basic Metabolic Research University of Copenhagen The University of Copenhagen is seeking a highly motivated and dynamic researcher with expertise in analysis and interpretation of high-throughput sequencing (transcriptomics, epigenomics etc.) and mass spectrometry (proteomics, metabolomics etc.)…

Hello all, I’m looking for guidance on how to write a non-interactive job script for qiime2. The HPC I have access to uses LSF and docker images, which are both new to me. So far, I have been creating an interactive shell to use qiime2 (I created a .sh file…

OUTLINE   On total of the cluster systems (except Nobel and Tigressdata), addicts run programs of submitting scripts into the Slurm mission scheduler. A Slurm script must execute three-way things: prescribe the resource requirements for the workplace set the environment specify the work to be carrying going in the form of cup commands Below…

jiji May 12, 2023, 9:25am 1 GROMACS version: 2021GROMACS modification: /NoHere post your question I have a trajectory files of 200 ns simulation of a system with 488007 atoms, around 20000 frames and it takes about 10-20 minutes to read one frame on my HPC environment of 1 GPU, 10…

Cloud providers are building armies of GPUs to provide more AI firepower. At its annual Google I/O developer conference today, Google announced an AI supercomputer with 26,000 GPUs. The Compute Engine A3 supercomputer is one more proof point that it is throwing more resources in an aggressive counteroffensive in its…

Dear CP2K community, Is CP2K 2022.1 a development or released version? Our HPC cluster will go through maintenance soon, and old version 5.1 will be removed, so I am checking to see if our HPC facility installed this 2022.1 version correctly.  The output file (screenshot below) says it is a development version, but…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Wed, 10 May 2023 00:14:41 +0200 Source: slurm-wlm Architecture: source Version: 22.05.8-4 Distribution: unstable Urgency: medium Maintainer: Debian HPC Team <debian-…@lists.debian.org> Changed-By: Gennaro Oliva <oliv…@na.icar.cnr.it> Closes: 1034950 1034955 1034978 1034987 1034992 1035562 Changes: slurm-wlm (22.05.8-4) unstable; urgency=medium . * Fix Breaks/Replaces…

Foundation models, and generative AI, have captivated our collective imagination and enabled the discovery of new ways to improve the way we live and work. From more seamless interactions with technology via natural language, to automatic generation of code or other data, to use cases across various domains of science,…

The Bioinformatics Research Associate is part of the Creative Data Solutions (CDS) Shared Resource at Vanderbilt University and is a key individual contributor responsible for performing bioinformatics analyses of genomic data sets, developing and implementing (genetic and other) statistical models, and contributing to research studies. This position requires that the…

Hi Slurm community, Slurm-web is an open source web interface for Slurm workload manager : rackslab.github.io/slurm-web/ The project was born in 2015(*), it was originally funded by EDF [2] (huge thanks to them!) and it reached a nice and unique feature set with versions 2.x. Unfortunately, the software has suffered…

Full time, 12 month fixed term contract with the possibility of extension contingent on funding A fantastic opportunity to perform data analysis to support the School of Mathematics & Statistics, located on Camperdown Campus Base Salary HEO5/6, $79,717 – $98,796 p.a. + 17% superannuation About the…

Package: slurm-wlm Version: slurm-wlm-basic-plugins Severity: normal Dear Maintainer, since commit e9e3e521 (salsa.debian.org/hpc-team/slurm-wlm/-/commit/e9e3e5211c76bacded1c0b55695f21545a2f48fa), package slurm-wlm-basic-plugins does not include /etc/slurm/plugstack.conf consequently files in /etc/slurm/plugstack.conf.d are ignored. Thank you. — System Information: Debian Release: bookworm/sid APT prefers jammy-updates APT policy: (500, ‘jammy-updates’), (500, ‘jammy-security’), (500, ‘jammy’), (100, ‘jammy-backports’) Architecture: amd64 (x86_64) Kernel: Linux…

New generations of CPUs offer a significant performance improvement in machine learning (ML) inference due to specialized built-in instructions. Combined with their flexibility, high speed of development, and low operating cost, these general-purpose processors offer an alternative to other existing hardware solutions. AWS, Arm, Meta and others helped optimize the…

Igbokwe, I. O. Evolving anti-disease strategies from biochemical pathogenesis of African trypanosomiasis. Adv. Cytol. Pathol. 3(2), 33–39 (2018). Google Scholar  Njiru, Z. K., Constantine, C. C., Gitonga, P. K., Thompson, R. C. & Reid, S. A. Genetic variability of Trypanosoma evansi isolates detected by inter-simple sequence repeat anchored-PCR and microsatellite….

I am new here and a relative beginner in Ubuntu, I want to install slurm to manage properly my DIY cluster,. I want to use the cluster (HPC) for parallel simulations I have 3 nodes (1 master 2 slaves) ubuntu 20.04 server I followed the instructions from nekodaemon.com (I can’t…

AMD has released the new ROCm 5.5 GPU compute stack for the open-source Linux community which adds improved RDNA 3 support. ROCm 5.5 releases with several new updates and provides better support to the new AMD RDNA 3 architecture This update brings changes and better support for the Radeon RX…

We are looking to hire a brilliant Bioinformatics Scientist to join our diverse team at Dovel Technologies, LLC in Bethesda, MD.Growing your career as a Full Time Bioinformatics Scientist is a great opportunity to develop relevant skills.If you are strong in cooperation, planning and have the right experience for the…

Im trying to combine lightning and torchdata using datapipes and dataloader2 but is running into this error when i try to train. I also end up having to kill some left over processes with pkill -9 -f “python src/train.py” I think that the problem is that the teardown doesn’t get…

At BaseSolve, we are transforming Genomics Data Science Technologies. We provide smart solutions for efficient analysis and management of Next Generation Sequencing data facilitating accurate insights for clinical diagnostics as well as scientific research. Post : Sr Bioinformatics Scientist (2 positions) Your Role As a Senior Bioinformatics Scientist; You will…

mkweber (Margo) April 26, 2023, 3:15pm 1 I used this command to extract reads to prepare for training a silva classifier for a paired-end 18S sequencing:qiime feature-classifier extract-reads –i-sequences silva-138-99-seqs.qza –p-f-primer TTAAARVGYTCGTAGTYG –p-r-primer CCGTCAATTHCTTYAART –o-reads ref-seqs.qza I am training the SILVA classifier using the command for aligning 18S reads:qiime feature-classifier…

Hi there, I eventually managed to get the gres AutoDetect=rsmi to sort of work. It correctly found the AMD GPU, a Instinct MI210. I am using ROCm 5.4. Unfortunately, the reported gpu type is “Instinct MI210” which I can’t configure in the GresType parameter in the slurm.conf because of the…

Penguin Solutions released Scyld ClusterWare software v12.0, designed to streamline HPC and AI server provisioning to get HPC and AI server clusters up and running faster, securely, and at scale. Scyld ClusterWare software provides administrators with a complete, scalable, and flexible HPC and AI cluster management and monitoring environment. Penguin…

GATK error on HPC clusters 1 I run GATK pipeline but at stage of BaseRecalibrator step , I got this error : Unrecognized VM option ‘PrintGCTimeStamps’ Error: Could not create the Java Virtual Machine. how could I solve this error. is anyone have idea. highly appreciate for your help. Thank…

Our goal is to measure genotype discordance between samples across all pairwise sample combinations. We start by defining a region of positions to query as a BED file. Although any positions can be defined, common human variant positions will be the most informative. We used 1000 Genomes positions with population…

ISC High Performance 2023 connects public and industry users and technology developers in Hamburg, Germany, from May 21 – 25. Expect an active collaborative exchange on high performance computing, machine learning, data analytics and quantum computing. The ISC 2023 Exhibition is the only Europe-based global HPC tradeshow for vendors and…

Batch script to run many serial jobs parallel on a HPC with slurm I want to run a large number of independent serial jobs in parallel using slurm. However, I run into the maximum number of 100 jobs that a user can submit. Therefore only 100 jobs are processed simultaneously…

This version was released on April 21st, 2023. These release notes document the changes that have taken place in GROMACS since the previous 2023 version, to fix known issues. It also incorporates all fixes made in version 2022.5 and earlier, which you can find described in the Release notes. Fixes…

klterwelp (Kat Terwelp) April 20, 2023, 2:45pm 1 Version of qiime2: qiime2-2023.2 installed with conda on an HPC. I’m following the classifier training tutorial. Below is the code I’m using for importing the reference sequences from HOMD to a .qza file. I’ve also attached the resulting .qza file: ref-seqs.qza (19.3…

Description Kelly Government Solutions is a strategic supplier and business partner to the federal government and its key suppliers. Through our partnership with the National Institutes of Health, Kelly Government Solutions offers administrative, IT, engineering, scientific, and healthcare professionals the opportunity to work with the leading medical research center in…

Details Posted: 20-Apr-23 Location: Evanston, Illinois Salary: Open Categories: Information Technology Staff/Administrative Department: MED-Hematology OncologySalary/Grade: EXS/8 Job Summary: Partners with clients to design, develop, implement and maintain business solutions regarding data management and analysis.  This includes database administration, data consolidation, data analysis and management reporting.  Utilizes software to generate metrics…

sinteractive is a tiny wrapper on srun to create interactive jobs quickly and easily.It allows you to get a shell on one of the nodes, with similar limits as you would do for a normal job. Load the module file slurm/utils (EEMCS-HPC Cluster) or download the provided script below. To…

Bioinformatics Analyst II/III Job ID: req3427Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

The 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…

How much resources does HiCanu need to assemble PacBio sequence 0 Hi, I am planning to assemble a diploid genome using pacBio reads. We have 900GB of raw reads. The genome size is ~1 Gbps. What resources do we need to get this done? How much RAM and how many…

Responsibilities Location Cambridge, CambridgeshireGB Job ID JR-036129 About The PerkinElmer Life Sciences And Diagnostics Company The PerkinElmer Life Sciences and Diagnostics company – which is to be renamed during the second quarter of 2023 – provides end-to-end solutions that help scientists, researchers and clinicians better diagnose disease and discover new…

GROMACS version: 2022-3GROMACS modification: NoHi,using HPC with SLURM, I noticed loss of performance if MD runs in a node shared with other jobs using other GPUs (Tesla) with respect to use an exclusive node, where no jobs are running. Other jobs are other programs running on different GPUs in the…

Issue in installing any package in R 0 Hello everyone! I am facing a very weird issue. I am working on hpc where R is preinstalled. As I am trying to install any package, I am getting this error: **Warning message: package ‘BiocManager’ is not available for this version of…

HelloI’ve got some issues when running pvserver on HPC(Slurm) by singularity. Looking for some help sincerely. VersionParaView-5.11.0-MPI-Linux-Python3.9-x86_64.tar.gz (download from this link) Run EnvHPC Cluster managed by Slurm (CentOS 7) without any mpi QuestionI packet paraview to singularity SIF. Dockerfile like FROM centos:7 COPY paraview /usr/local/paraview RUN yum install -y libXcursor…

Hi —, I have a question about a silent feature removal. It is about the –dependency:expand feature, that was present in Slurm for 10 years until its removal in version 21.08.03. Until Slurm 21.08.02, the expand option had an extensive documentation with the dynamic job elasticity features, with resource…

I recently needed to make the group’s cluster computing environment available to a third party that was not fully trusted, and needed some isolation (most notably user data under /home), but also needed to provide a normal operating environment (including GPU, Infiniband, SLURM job submission, toolchain management, etc.). After thinking…

plink2 bgen to vcf ukbiobank 2 Hello I have imputed data from ukbiobank in bgen format. I would like to convert it to a vcf file. I can use plink2 to make pgen files and then use plink2 again to create a vcf plink2 –bgen ukb_imp_chr17_v3.bgen –sample ukimp_chr17_v3_s.sample –make-pgen plink2…

About the team/job The Dodonova group at EMBL Heidelberg is looking for a Postdoc with a Structural Biology background to investigate the 3D organization of Archaeal Chromatin. This position is funded by the ERC Starting Grant. The Dodonova group (www.embl.org/groups/dodonova/) aims to understand the mechanisms and evolutionary principles of genome packaging…

The PositionPrincipal Software Bioinformatics EngineerLocation: Mississauga or across CanadaHybrid position if living in Grand Toronto AreaImpact HealthcareRoche 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…

How many CPUs should I use in my SLURM job for my BLAST? 1 Hello, I am trying to perform a blastp search of 23 sequences against a BLAST database containing approximately 15,000 sequences (in a for loop that will give me seperate outputs). As a newcomer to HPC systems,…

Hi, It has recently come to our attention default Spack builds of GROMACS use RelWithDebInfo instead of Release which is the default in our build system. Due to the lower optimization levels in RelWithDebInfo such build will run up to 20% slower than release builds. Therefore, I strongly recommend to…

Good afternoon community! I am new in the field and need you help with an ongoing issue I have with velocity analysis. I am running a velocyto analysis on HPC cluster, and using command run. This is the full script I am using:* module load Anaconda3 source activate tutorial export…

Hello! I am working on assembling a transcriptome of the terminal ganglion of the cricket (Gryllus bimaculatus). We are working on a non-model species and thus did not remove ribosomal contamination during library prep. We want to remove ribosomal contamination bioinformatically, and I am mapping our sequences, which have been…

Stanford University is seeking a Bioinformatics Engineer to manage and analyze large amounts of information, typically technical or scientific in nature, independently with minimal supervision. About the Department of Pathology Comprised of extraordinary faculty and staff, our mission is to improve the ability to diagnose, treat and understand the origin…

GROMACS version: 2016.3GROMACS modification: No Hello Folks, I’m new to the HPC world and I’m playing around with Spack and Gromacs. I currently have the following Dockerfile FROM ubuntu:22.04 RUN apt-get update && DEBIAN_FRONTEND=”noninteractive” \ TZ=”America/New_York” apt-get install -y tzdata RUN apt install -y environment-modules \ wget gpg build-essential \…

I am using Manta (github.com/Illumina/manta/blob/master/docs/userGuide/README.md) but whenever I try to specify the –exome command using the following code I get the error below: The code in my script: # Accept path to reference fasta file as a parameter: reference=$1 # Accept input and output directories as parameters: input_dir=$2 output_dir=$3 #…

Wednesday, 12. April ► 9:00 – 10:30 Abstract The HPC JupyterHub service at the RWTH allows all eligible users of the RWTH Compute Cluster to utilize the existing compute hardware interactively with the use of Jupyter Notebooks. This HPC JupyterHub provides customization of Profiles with a variety of programming kernels,…

In this week’s real-time analytics news: The Gartner Data & Analytics Summit and the NVIDIA GTC conference generated numerous announcements. Keeping pace with news and developments in the real-time analytics market can be a daunting task. Fortunately, we have you covered with a summary of the items our staff comes…

Description New York University Abu Dhabi seeks to recruit a Research Associate with expertise in bioinformatics to work within the newly established Abu Dhabi Precision Medicine Virtual Research Institute (ADPMVRI). The role of the bioinformatician will focus on supporting the Institute’s mission to develop a comprehensive research infrastructure – whereby…

Augustin Bussy1*, Ole Schütt2, Jürg Hutter1* 1 Department of Chemistry, University of Zurich, CH-8057 Zürich, Switzerland 2 CP2K Foundation, CH-8006 Zurich Switzerland * Corresponding authors emails: augustin.bussy@chem.uzh.ch, hutter@chem.uzh.ch How to cite this record Augustin Bussy, Ole Schütt, Jürg Hutter, Sparse tensor based nuclear gradients for periodic Hartree–Fock and low-scaling correlated…

Today at its GPU Technology Conference, Nvidia discussed four new platforms designed to accelerate AI applications. Three are targeted at inference workloads for generative AI applications, including generating text, images, and videos, and another is aimed boosting recommendation models, vector databases, and graph neural nets. Generative AI has surged in…

Join top executives in San Francisco on July 11-12, to hear how leaders are integrating and optimizing AI investments for success. Learn More Nvidia’s H100 Hopper GPUs, which promise to revolutionize artificial intelligence (AI) with unprecedented speed and power, are now widely available to customers across various platforms, the company…

Job Purpose Scientific Computing Support, Senior Specialist is responsible for assisting researchers with running their codes and applications on the research computing facilities, training them on the correct usage of those resources, assisting with analysis of performance, code optimization, and parallel scaling of scientific applications, as well as the implementation…

Hi all, I was looking to see if we can use the InitScript of the job_container/tmpfs to setup quotas for the /tmp directory. The InitScript key of the job_container.conf file is documented here [1]. We are using Slurm 23.02.0. However, when I try to use this option I get the…

The Fanciulli Lab at IRCCS Regina Elena National Cancer Institute is seeking a highly motivated Bioinformatician with expertise in Scientific Computing Support. The selected candidate will play a key role in the development, implementation, and maintenance of various IT systems, with a primary focus on scientific software and services. Additionally,…

Hi, My lammps version is lammps-23Jun2022, and I want to run MD simulations with ML hdnnp, and then use plumed to do the enhanced samplings. I encountered a issue when I run the MD simulations: terminate called after throwing an instance of ‘PLMD::Plumed::ExceptionError’ what():+++ PLUMED error+++ at Communicator.cpp:89, function void…

Bioinformatics Analyst II/III Job ID: req3427Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…

Downloading NCBI Blast nt database 0 I would like to download the full nt database to run a BLAST search on a large genome through HPC. I have installed BLAST using conda and set up accordingly. When I run the step below (edited from the manual (www.ncbi.nlm.nih.gov/books/NBK569850/) for the nr…

Abstract: Training models from scratch requires way too much data, time, and computing power (or money) to be a practical option. This is why transfer learning has become such a common practice: by starting with models trained on related problems, you are saving time and achieving good results with little…

Hi, I am new to slurm. I am setting up a multi cluster environment. I  have 1 small doubt with respect to the user accounting. My setup will look like below: Cluster name A: Alpha (Slurmctld) Cluster name B: Beta (Slurmctld) Both controllers are pointing to the same database server….