Tag: mig

bootstraped treemix show no migration event

bootstraped treemix show no migration event 0 I run treemix with bootstraping using Treemix_bootstrap.sh (BITE R package) with one migration event. it worked without any error. Now when I want to draw the tree, the tree is drawn but without any migration event and I get the following warning message….

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[slurm-users] Dynamic MIG Question

Hello All, I am currently working in a research project and we are trying to find out whether we can use NVIDIAs multi-instance GPU (MIG) dynamically in SLURM. For instance: – a user requests a job and wants a GPU but none is available  – now SLURM will reconfigure a…

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[slurm-users] Usage of particular GPU out of 4 GPUs while submitting

Hi Daniel Letai Thanks for the quick response and guidance. I have done the changes as mentioned in gres.conf and slurm.conf and now I am able to submit the jobs to a particular GPU. Regarding MIG, it was just a thought came in m mind, in case studentA wants to…

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[slurm-users] Usage of particular GPU out of 4 GPUs while submitting jobs to DGX Server

Hello Everyone   I am just beginner of slurm and started to use the same on our DGX Server which has 4 numbers of A100, 80GB GPUs. Everything works fine, jobs goes to random GPUs (free available). My question is related to submission of jobs to those GPUs. How…

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Nccl_external fails while trying to compile pytroch from source – torch.compile

Hello, I’m trying to compile pytorch from source and encountering the following build error. $ CC=gcc-10 CXX=g++-10 python setup.py develop … [5995/6841] Linking CXX executable bin/HashStoreTest Warning: Unused direct dependencies: /home/netfpga/research/collective/pytorch/build/lib/libc10.so /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_intel_lp64.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_gnu_thread.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_core.so.1 /lib/x86_64-linux-gnu/libdl.so.2 /home/netfpga/anaconda3/envs/pytorch_base/lib/libgomp.so.1 [5996/6841] Performing build step for ‘nccl_external’ FAILED: nccl_external-prefix/src/nccl_external-stamp/nccl_external-build nccl/lib/libnccl_static.a /home/netfpga/research/collective/pytorch/build/nccl_external-prefix/src/nccl_external-stamp/nccl_external-build /home/netfpga/research/collective/pytorch/build/nccl/lib/libnccl_static.a cd /home/netfpga/research/collective/pytorch/third_party/nccl/nccl &&…

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Student research celebrated at Health Sciences Research Day

MU School of Medicine students presented roughly 250 research projects at the annual 2023 Health Sciences Research Day (HSRD), held Nov. 10, 2023, and featured the work of undergraduates, medical and nursing students, PhD students and postdoctoral trainees. The research posters covered a variety of topics within the health care…

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Open-Label PROPEL Study Results Highlight Longterm Impact of Cipaglucosidase Alfa and Miglustat in Late-Onset Pompe Disease

New data from the phase 3 PROPEL study (NCT04138277) showed that treatment with cipaglucosidase alfa (Pombiliti)/miglustat (Opfolda), a recently approved 2-component agent, was effective in patients with late-onset pompe disease (LOPD) for up to 104 weeks. These data, presented at the 2023 American Association of Neuromuscular and Electrodiagnostic Medicine (AANEM)…

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Building multi-tenant JupyterHub Platforms on Amazon EKS

Introduction In recent years, there’s been a remarkable surge in the adoption of Kubernetes for data analytics and machine learning (ML) workloads in the tech industry. This increase is underpinned by a growing recognition that Kubernetes offers a reliable and scalable infrastructure to handle these demanding computational workloads. Furthermore, a…

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How to run multiple jobs, one per GPU, with SLURM?

Apologies if this has be asked/answered before, but even after reading everything I can find, I am struggling to get SLURM to do what I want. Let’s say I have a machine with 4 GPUs. I want to train 4 models in parallel, each job running on a single GPU….

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[slurm-users] Slurm versions 23.02.6 and 22.05.10 are now available (CVE-2023-41914)

Slurm versions 23.02.6 and 22.05.10 are now available to address a number of filesystem race conditions that could let an attacker take control of an arbitrary file, or remove entire directories’ contents (CVE-2023-41914). SchedMD customers were informed on September 27th and provided a patch on request; this process is documented…

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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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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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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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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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CUDA and pytorch versions mismatch – CUDA Setup and Installation

AK51 September 21, 2023, 4:47pm 1 Hi, I got a new computer and installed the CUDA 12.2, it works fine, nvidia-smi works fine. But when I tried some projects in github, many projects give this mismatch error, please advance. Do I need to downgrade the CUDA? What is a proper…

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How does the GPUs in WSL2 get surfaced for something like SLURM (Gres) – Container: CUDA

in a traditional Ubuntu install, you can see the nvidia devices in /dev/nvidiaX. In a WSL2 implementation, they do not exist there, and I cant seem to find out how to surface them. as part of a SLURM cluster, if I want to use GPUs I need to create a…

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nvidia – Looking for the Nvida devices in my WSL2 Ubuntu implementation for SLURM GRES

I am trying something odd. I have a slurm cluster configured that has 4 compute nodes. 2 of which are Windows 11 machines running WSL2 and I have it working. right now, I am trying to add GPU support to the SLURM cluster. For the 2 compute nodes that are…

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How to run replica exchange with NVIDIA MPS/MIG – User discussions

roozi September 7, 2023, 1:21am 1 GROMACS version:2023GROMACS modification: No Hi,Just came upon below link while trying to find tricks to increase output of a REMD run on gmx using a GPU based HPC server: developer.nvidia.com/blog/maximizing-gromacs-throughput-with-multiple-simulations-per-gpu-using-mps-and-mig/ As per the content of above link(coauthored by @pszilard ) using NVIDIA MPS(Multi-Process Service)…

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Step-by-Step Guide to Setup Pytorch for Your GPU on Windows 10/11

In this competitive world of technology, Machine Learning and Artificial Intelligence technologies have emerged as a breakthrough for developing advanced AI applications like image recognition, natural language processing, speech translation, and more. However, developing such AI-powered applications would require massive amounts of computational power far beyond the capabilities of CPUs…

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Using full GPU node without MPI – User discussions

Hrishi August 30, 2023, 9:16am 1 GROMACS version: 2019GROMACS modification: Yes Hello, I am trying to run the gromacs on a multi-instance GPU (MIG). I tried several commands to run Gromacs but each time it used part of the GPU and not the full node. 1. gmx mdrun -v -deffnm…

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Emadlangeni Mayor leads TROIKA on oversight visit to Kerk Street phase 3 project

An oversight visit at the Balele Game Park. (Image sourced). Emadlangeni’s Mayor M.L. Buthelezi recently led a municipal troika to assess the progress of the Kerk Street Phase 3 MIG project and to evaluate the developments on the refurbishment of the Balele Game Park. The municipality’s communications department, said the…

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Utrecht sees renovations as mayor and officials monitor developments

Promising developments are unfolding in the heart of Utrecht, as the eMadlangeni (Utrecht) Municipality takes a vigilant stance on two major community projects. Click HERE to visit AME Amajuba’s website Utrecht Mayor, Cllr Mzwakhe Buthelezi, recently led a municipal TROIKA delegation to assess the advancement of the Kerk Street Phase 3 Municipal Infrastructure…

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Not detecting GPU RTX 4000 – Opacus

HelloI am trying to install pytorch in Ubunut Mint 21 and use it with RTX 4000. First I’ve installed all drivers and cuda (from cuda_12.2.1_535.86.10_linux.run). Here are some outputs (local user – not root): $ nividia-smiMon Aug 7 08:50:44 2023±————————————————————————————–+| NVIDIA-SMI 535.86.05 Driver Version: 535.86.05 CUDA Version: 12.2 ||—————————————–±———————±———————+| GPU…

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Down-regulation of stimulator of interferon genes (STING) expression and CD8+ T-cell infiltration depending on HER2 heterogeneity in HER2-positive gastric cancer

Smyth EC, Nilsson M, Grabsch HI, van Grieken NC, Lordick F. Gastric cancer. Lancet. 2020;396:635–48. Article  CAS  PubMed  Google Scholar  Siegel RL, Miller KD, Fuchs HE, Jemal A. Cancer statistics, 2022. CA Cancer J Clin. 2022;72:7–33. Article  PubMed  Google Scholar  Yarden Y, Sliwkowski MX. Untangling the ErbB signalling network. Nat…

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python – PyTorch Profiler: CUPTI initialization failed

I’m working on a few profilings with PyTorch and am not able to see my CUDA activity. The exact error I am getting is: WARNING:2023-08-01 21:00:10 561983:561983 init.cpp:146] function cbapi->getCuptiStatus() failed with error CUPTI_ERROR_NOT_INITIALIZED (15) WARNING:2023-08-01 21:00:10 561983:561983 init.cpp:147] CUPTI initialization failed – CUDA profiler activities will be missing INFO:2023-08-01…

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Torch.cuda.is_available() is False – CUDA:12.2 – rtx 4070

TTTest July 28, 2023, 12:02pm 1 Machine learning newbie here, stuck on the first step of learning PyTorch of installing CUDA. I’ve been trying to get CUDA working on my system for the past day to no avail. I’ve created multiple environments then tried installing pytorch using the below config…

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[slurm-users] MIG-Slice: Unavailable GRES

Dear Slurm Mailing List, I am experiencing a problem which affects our cluster and for which I am completely out of ideas by now, so I would like to ask the community for hints or ideas. We run a partition on our cluster containing multiple nodes with Nvidia A100 GPUs…

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[slurm-users] GRES and GPUs

Hey, I am currently trying to understand how I can schedule a job that needs a GPU. I read about GRES slurm.schedmd.com/gres.html and tried to use: GresTypes=gpu NodeName=test Gres=gpu:1 But calling – after a ‘sudo scontrol reconfigure’: srun –gpus 1 hostname didn’t work: srun: error: Unable to allocate resources: Invalid…

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python – PyTorch torch.cuda.is_available() returns False for Windows

First run nvidia-smi. This will give you your driver and what CUDA version you can support up to. e.g., for me, the top box says this: +—————————————————————————–+ | NVIDIA-SMI 527.41 Driver Version: 527.41 CUDA Version: 12.0 | |——————————-+———————-+———————-+ | GPU Name TCC/WDDM | Bus-Id Disp.A | Volatile Uncorr. ECC |…

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[slurm-users] GPU Gres Type inconsistencies

Hi all,   I’m trying to set up GPU Gres Types to correctly identify the installed hardware (generation and memory size). I’m using a mix of explicit configuration (to set a friendly type name) and autodetection (to handle the cores and links detection). I’m seeing two related issues which I…

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Nvcc fatal : Unsupported gpu architecture ‘compute_89’ – CUDA Setup and Installation

After installing cuda in my laptop it apparently is still missing the support for the specific GPU, on ubuntu 22.04. I have followed the instructions in CUDA Toolkit 12.1 Update 1 Downloads | NVIDIA Developer When running some of the examples I get a message like this: cuda-samples/Samples/6_Performance/LargeKernelParameter$ make/usr/bin/nvcc -ccbin…

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IAF Heritage Centre in Chandigarh to spread wings with Phase 3

Following encouraging response to the country’s first Indian Air Force Heritage Centre that was launched in Chandigarh’s Sector 18 on May 8, the air force is now working on expanding the centre under Phase 3. A visitor experiencing an MiG-21 cockpit at the Indian Air Force Heritage Centre at Sector…

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Transcriptional patterns of sexual dimorphism and in host developmental programs in the model parasitic nematode Heligmosomoides bakeri | Parasites & Vectors

Mapping of bulk RNA-seq data and differential gene expression (DGE) Using the splice-aware aligner STAR, we mapped the RNA-seq reads to the H. bakeri genome assembly obtained from WormBase ParaSite (PRJEB15396). Among all the datasets, 93.26–95.62% of the reads uniquely mapped to the reference genome (Table 1), reflecting the high…

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3 Tests Fail: MDRunIOTest – User discussions

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…

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python – Pytorch can’t find gpu

I begin to learn ML on my windows11 machine. But torch can’t find my gpu. In [2]: device = torch.device(“cuda:0” if torch.cuda.is_available() else “cpu”) In [3]: device Out[3]: device(type=”cpu”) This is my nvidia-smi outputs +—————————————————————————————+ | NVIDIA-SMI 531.68 Driver Version: 531.68 CUDA Version: 12.1 | |—————————————–+———————-+———————-+ | GPU Name TCC/WDDM…

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Pytorch 2.0 is not a “stable” version

Timo_D (Timo D) April 24, 2023, 11:22am 1 Hey, first of all, I am grateful for this library and that it is open source, I know there is a massive amount of hard work behind this. However, I have to say with the amount of rather critical bugs related to…

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Gromacs 2023 GPU support not working for some reason – User discussions

GROMACS version: 2023GROMACS modification: NoHere post your questionSo I have beee trying to get GPU support for gromacs in my WSL2 Ubuntu system, for a few days and have come up short so I thought I’d try here. I have already run the comands to compile gromacs form source code…

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machine learning – pytorch cannot built running processes on Tesla V100-PCIE-32GB (type: (7, 0))

On remote server, PyTorch can access the GPU that can place variables and models on GPUs, but the GPU shows no running processes found on the GPU. Thu Apr 20 09:21:59 2023 +—————————————————————————–+ | NVIDIA-SMI 511.65 Driver Version: 452.39 CUDA Version: 11.0 | |——————————-+———————-+———————-+ | GPU Name TCC/WDDM | Bus-Id…

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[slurm-users] Slurm and MIG configuration help

Hi all! I’ve successfully managed to configure slurm on one head node and two different compute nodes, one using “old” consumer RTX cards, a new one using 4xA100 GPUS (80gb version). I am now trying to set up a hybrid MIG configuration, where devices 0,1 are kept as is, while…

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Developments in gene therapy for inherited optic neuropathies

Other gene therapy strategies under preclinical investigation are mtDNA heteroplasmy shifting and mitochondrial base editing. (Adobe Stock image) By Benson S. Chen, MBChB, MSc, FRACP; Joshua P. Harvey, MA, BM BCh,Pg Cert, FRCOphth; and Patrick Yu-Wai-Man, PhD, BMedSci, MBBS,FRCPath, FRCOphth Inherited optic neuropathies (IONs) are disorders that result in degeneration…

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EBV-positive pyothorax-associated lymphoma expresses CXCL9 and CXCL10 chemokines that attract cytotoxic lymphocytes via CXCR3

doi: 10.1111/cas.15782. Online ahead of print. Affiliations Expand Affiliations 1 Department of Microbiology and Infection, Kochi Medical School, Kochi University, Nankoku, Japan. 2 Division of Chemotherapy, Kindai University Faculty of Pharmacy, Higashi- Osaka, Japan. 3 Science Research Center, Kochi University, Nankoku, Japan. 4 Department of Pathology, Kochi Medical School, Kochi…

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Exploring developments in gene therapy for inherited optic neuropathies

By Benson S. Chen, MBChB, MSc, FRACP; Joshua P. Harvey, MA, BM BCh, Pg Cert, FRCOphth; and Patrick Yu-Wai-Man, PhD, BMedSci, MBBS, FRCPath, FRCOphth; Special to Ophthalmology Times® Inherited optic neuropathies (IONs) are a group of disorders that result in degeneration of the retinal ganglion cells (RGCs) and optic atrophy,1…

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Presentation: Ph 3 open-label extension study (ATB200-07) of AT-GAA

Long-term efficacy and safety of cipaglucosidase alfa/miglustat in ambulatory patients with Pompe disease: a Phase III open- label extension study (ATB200-07) Benedikt Schoser Friedrich-Baur-Institut, Neurologische Klinik, Ludwig-Maximilians-Universität München, Munich, Germany Cipaglucosidase alfa plus miglustat is a novel, investigational, two-component therapy designed to address current challenges in ERT…

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[slurm-users] Issue with AMD SMT, CUDA_VISIBLE_DEVICES and MiG AutoDetect=nvml

Hi Everyone,   Has anyone seen an issue where the CUDA_VISIBLE_DEVICES environmental variable is set to an integer (0, 1, 2 or 3 for us) instead of the UUID (MIG-xxx) when AMD SMT is enabled? Not sure if this is a bug but it feels like one. Certain libraries like…

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[slurm-users] gres/gpu count lower than reported

Hello Fellow Slurm Admins,   I have a new Slurm installation that was working and running basic test jobs until I added gpu support. My worker nodes are now all in drain state, with gres/gpu count reported lower than configured (0 < 4)   This is in spite of the…

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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis

Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS  PubMed  Google Scholar  Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…

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Toll-like receptor 2/4 in Chinese patients with sepsis

Introduction Sepsis is a life-threatening organ dysfunction that results from an exaggerated host immune response to disseminate infection.1 Despite improvements in treatment strategies, sepsis remains a leading cause of death in critically ill patients worldwide.2 Low platelet number, known as thrombocytopenia, is common in infectious diseases (also sometimes referred to…

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