Categories
Tag: SRC
python – Reading files asynchronously hangs within Pytorch Dataset when DataLoader.num_workers > 1
I’m training a classifier on raw-bytes in binary files. Each file can be several megabytes long. I have a dataset with several millions of binaries in it. Loading all this data at once and keeping it all in memory is very expensive, so I wanted to write an IterableDataset to…
Error in neigh_modify configuration – LAMMPS Beginners
Dear community of LAMMPS users I am simulating a complex system consisting of a biomolecule (1876 atoms), a nantube of an oxide (4200 atoms) and a box of water (30000 atoms) and I get the following error: ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (src/npair_half_bin_newton.cpp:156) I am…
Gradients disabled globally? – autograd
Hi, so I have this very basic and unrealistic example: a = torch.linspace(-1,1,100).reshape(-1,1) b = a c = torch.nn.Sequential( nn.Linear(1,10), nn.ReLU(), nn.Linear(10,1) ) opt = torch.optim.Adam(c.parameters(), lr=1e-3) for i in range(10): opt.zero_grad() b_hat = c(a) loss = F.mse_loss(b_hat,b) loss.backward() opt.step() So sure, it’s not a realistic training, however it should…
Can’t Access Multiple GPUs when Using PPPM GPU Acceleration – LAMMPS
Dear developers and user, I’m running the simulation using an unmodified LAMMPS (2 Aug 2023) version. I want to use multiple GPUs and CUDA API to accelerate the PPPM alogrithm. However, I can’t access more than one GPU when running program. I have tried numerous ways to solve this problem,…
ADR: OpenAPI SDK Generator | Unleash
Background In our current frontend setup we have a lot of code that can be generated out of the OpenAPI schema. Types have not been updated in a while, and even some new features rely on hard-coded types instead of auto-generated files in src/openapi. Fetchers and actions in the frontend…
Bug#1060149: src:extrepo: fails to migrate to testing for too long: autopkgtest regression
Hi Wouter, On 06-01-2024 20:51, Wouter Verhelst wrote: The Release Team considers packages that are out-of-sync between testing and unstable for more than 30 days as having a Release Critical bug in testing [1]. Your package src:extrepo has been trying to migrate for 33 days [2]. This should have been…
slurm fails on disconnected standalone computer/node
Hi, I have a setup similar to the one of the original reporter. My NodeName is localhost . The error messages at booting time scared me, so I dug the issue. I also related this issue to my observation that slurm fails to launch jobs when my standalone computer is…
rstudio – Cannot deploy R-shiny app due to “fribidi was not found”
Local app runs fine, but I keep encountering this error when attempting to publish it. I have already installed fribidi & harfbuzz using brew install fribidi & brew install harfbuzz on my Mac, but I am still encountering the error. I am using: Installing urltools (1.7.3) … Using cached urltools….
r – How to add a title on the center-left of the plot in ggplot2?
As a very late contribution to TidyTuesday challenge of Bob Ross’s Paintings, I have tried to plot 10 paintings of Bob Ross. Without further background, here is my code; library(tidyverse) library(showtext) library(showtextdb) library(ggthemes) library(ggtext) library(magick) library(ggimage) library(cropcircles) library(cowplot) library(patchwork) font_add_google(“Lora”, bold.wt = 700, family = “plottitle”) font_add_google(“Roboto Slab”, family =…
installing DESeq2 on Windows
installing DESeq2 on Windows 0 I have a problem with installing DESeq2 on Windows. The problem started with installing libraries that DESeq2 uses so I’m installing them individually. I do it by: ‘BiocManager::install(‘zlibbioc’)’ . I got an error that suggests that is something wrong with compilation: C:\rtools43\x86_64-w64-mingw32.static.posix\bin\windres.exe: can’t popen `C:\rtools43\x86_64-w64-mingw32.static.posix\bin\gcc.exe…
gcc – Error compiling giac (inside SageMath) in poly.h function
Environment: CentOS 7.9 GCC 13.1.0 SageMath 10.0 When compiling SageMath, the compilation gets to the “giac” program and fails. The failure occurs in the “poly.h” function. I’m on a closed network so I cannot upload the logfile. Here is the last part of the error: modpoly.cc:16082:1: internal compiler error: Aborted…
Generate topology file for glucose – User discussions
horlust December 29, 2023, 10:15am 1 GROMACS version: 2021.4-2GROMACS modification: No Hello everyone! I am fairly new to GROMACS. I’ve been able to successfully run simulations for some small molecules with the OPLS-AA force field. My problem has always been the generation of the topology files. Using pdb2gmx seems impossible…
Running GROMACS with OpenCL on accelerator – User discussions
Aastha December 19, 2023, 11:23am 1 GROMACS version:2023.3GROMACS modification: YesHere post your questionI am trying to run GROMACS on an accelerator connected to PCI bus.I made the following modifications to the code: changed CL_DEVICE_TYPE_GPU to CL_DEVICE_TYPE_ALL Added my accelerator vendorcheckGpu returns value TRUE, so the dummy kernel is able to…
Lipid vesicle(CHARMM Gui files) simulation in GROMACS – User discussions
GROMACS version: 2022.1 and 2020GROMACS modification: Yes/NoHere post your questionHello, I am trying to simulate Lipid based vesicle in GROMACS on Frontera super-computer. The following command I am using to run the simulation. But I am getting error messages. Since I am new I don’t understand the error message perfectly….
Extend Functionality of Generator Plugin
OpenAPI Specification is a standard for documentation of HTTP REST services. You can try it using the Swagger editor. Based on specification files, code generators generate all model, server, and client classes required for development. This article is about the OpenAPI generator. It allows the generation of API client libraries…
Creating a dataset that returns two images efficiently – vision
madkr December 16, 2023, 5:40pm 1 I am working on a project where I have to simultaneously load an image along with the features of the image. I have pre-computed the features (single channel, same dimensions as the image) and they’re present on the same disk with the same name…
PRRG4 regulates mitochondrial function and promotes migratory behaviors of breast cancer cells through the Src-STAT3-POLG axis | Cancer Cell International
Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality Worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. doi.org/10.3322/caac.21660. Article PubMed Google Scholar Hu G, Chong RA, Yang Q, Wei Y, Blanco…
PyTorch Multi-Class Classification Using a Transformer with Custom Accuracy and Interpretability
I put together a PyTorch neural network multi-class classification demo. For the neural architecture, I dropped in a TransformerEncoder hidden layer. For model accuracy, I implemented a custom confusion matrix. For interpretability, I implemented custom input gradient monitoring. I used one of my standard synthetic datasets. The data looks like:…
Undefined reference to mbedTLS functions – Nordic Q&A – Nordic DevZone
Hi all! So I’m trying to use mbedTLS methods in my project. I got it to work on SDK v1.9.0 but when upgrading to v.2.4.0 I get a lot of “undefined references” to methods regarding mbedTLS.I see that there is some other issues regarding this but those haven’t solved my…
R Studio doesn’t open – RStudio IDE
Yesterday, R Studio suddenly closed, and it didn’t open again afterward. I could never figure out why. Even after uninstalling and reinstalling R, Rtools, and RStudio applications with the latest versions, it still doesn’t open. Additionally;uninstalling RStudio and reinstallinguninstall/reinstall of RStudio and R. (here I also tracked down any R…
Formononetin | FGFR2 inhibitor | Axon 4067
All All Products Enzymes Receptors Ion Channels Research Areas Oxidoreductases Transferases Lyases Isomerases Ligases Nuclear Receptors Ligand-gated ATP-Sensitive Angiogenesis Apoptosis Cardiovascular Cell Cycle Regulation Cell Signaling & Oncology CNS Diabetes & Metabolism Epigenetics Immunology Miscellaneous Pain & Inflammation Stem Cell Oxidases MAO Cys-loop, cationic Cis-Trans Isomerase CypA DNA Topoisomerase Synthetases…
CP2K QMMM Calculation seems to randomly crash
Dear all, I have encountered a very disturbing phenomena. My system is fairly simple: One Na+ in water (up to 800 water molecules). I generated the system using tleap. The plan is the following: Since full semi empirical MD with XTB is costly for 801 atoms, I tried to calculate…
Installing JupyterHub via Stackable Demo on K8s | by Alex McLintock | Dec, 2023
docs.stackable.tech/home/stable/demos/jupyterhub-pyspark-hdfs-anomaly-detection-taxi-data So, this is an article in an ongoing series where I investigate the deployment tools of Stackable.tech This firm supplies supported versions of many open source data engineering tools to easily build data platforms on Kubernetes (k8s) clusters. These can be on your own premises, in a data centre,…
[llvm-bugs] [Bug 75428] clang crash when build IPEX code.
Issue 75428 Summary clang crash when build IPEX code. Labels clang Assignees Reporter xuhancn The error msg: “`cmd Stack dump: 0. Program arguments: /usr/bin/clang++ -DAT_PARALLEL_OPENMP=1 -DUSE_C10D_GLOO -DUSE_DISTRIBUTED -DUSE_RPC -DUSE_TENSORPIPE -Dintel_ext_pt_cpu_EXPORTS -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/aten -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/tpp -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/libxsmm/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/build/Release/csrc/cpu/csrc/cpu/cpu_third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/include -I/home/xu/anaconda3/envs/ipex_cpu/include/python3.12 -I/home/xu/anaconda3/envs/ipex_cpu/include -I/home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include/torch/csrc/api/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/src/../include -isystem /home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include -fPIC…
Charge your APIs Volume 20: Navigating the OpenAPI Initiative Workflows Specification
In the ever-changing world of API development, the OpenAPI Initiative stands as a beacon of standardisation and best practices. This collaborative and open-source project, under the auspices of the Linux Foundation, has been instrumental in establishing the standards for how APIs are described and utilised. Amongst its most notable contributions…
autopkgtest regression on architectures where char is unsigned
Source: rust-rusqlite Version: 0.29.0-2 Severity: serious tracker.debian.org/pkg/rust-rusqlite Issues preventing migration: ∙ ∙ autopkgtest for rust-rusqlite/0.29.0-2: amd64: Pass, arm64: Regression or new test ♻ (reference ♻), armel: Regression or new test ♻ (reference ♻), armhf: Regression or new test ♻ (reference ♻), i386: Pass, ppc64el: Reference test in progress, but real…
Bug#1058627: src:zope.proxy: fails to migrate to testing for too long: autopkgtest regression
Source: zope.proxy Version: 4.5.0-1 Severity: serious Control: close -1 5.1-2 Tags: sid trixie User: release.debian….@packages.debian.org Usertags: out-of-sync Dear maintainer(s), The Release Team considers packages that are out-of-sync between testing and unstable for more than 30 days as having a Release Critical bug in testing [1]. Your package src:zope.proxy has been…
Wall simulations with GPU – User discussions
stephan December 13, 2023, 4:46am 1 GROMACS version: 2022.3GROMACS modification: No Dear all, I want to run a simulation with two repulsive walls to keep the system finite in z while having non-periodic boundary conditions in that dimension.Everything works fine except when offloading bonding interactions to the GPU. I think…
python – What is the function _transformer_encoder_layer_fwd in pytorch?
I ran into the function _transformer_encoder_layer_fwd of pytorch in the lib/python3.11/site-packages/torch/_C/_VariableFunctions.pyi file, the function is called here but I didn’t find any details about this function. Why could this function be called? And how? def _transformer_encoder_layer_fwd(src: Tensor, embed_dim: _int, num_heads: _int, qkv_weight: Tensor, qkv_bias: Tensor, proj_weight: Tensor, proj_bias: Tensor, use_gelu:…
cfgrib failing to find eccodes
I cannot reproduce this locally yet – running the tests in a clean chroot works fine. However ecmwflibs was failing when I tested it – but worked ok when rebuilt, so I’ve added a superficial test for autopkgtest to it, to see if it breaks on its own in the…
Sage 10.2.rc2 released
On Mon, Nov 13, 2023 at 1:30 PM David Coudert <david….@gmail.com> wrote: > Yesterday I have synchronized my fork on GitHub with 10.2.rc2 and it went well, but today I see that « This branch is 1 commit ahead, 1 commit behind sagemath:develop » O_o. See github.com/dcoudert/sage/ > It seems that I…
python – Pytorch I3D Resnet model on a custom dataset
This is a follow-up to a couple of questions I asked before…I want to fine-tune the I3D model for action recognition from Pytorch hub (which is pre-trained on Kinetics 400 classes) on a custom dataset, where I have 4 possible output classes. I’m loading the model and modifying the last…
Building sagemath 10.2 on Fedora 38
Hi!, I have successfully build sagemath 10.1 on a Fedora 38 computer but now, when a I try to build sagemath 10.2 in the same computer, I have a lot of errors in Cythonizing files The first one is: [ 19/557] Cythonizing sage/arith/rational_reconstruction.pyx Error compiling Cython file: ———————————————————— … …
html – Automatic wikipedia image script
So I made this script to automatically download the picture of a species from the general info box on Wikipedia. I have this data frame containing all the (latin) names of the species where I then want to automatically download the Wikipedia species picture and put them on a map….
AWH very large free energy barriers – User discussions
Noob December 10, 2023, 12:43am 1 GROMACS version: 2023.3GROMACS modification: NoI have been trying to run a Free energy simulation using AWH and no matter what I set some of the values too I keep getting the same error: ——————————————————- Program: gmx mdrun, version 2023.3 Source file: src/gromacs/applied_forces/awh/pointstate.h (line 355)…
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…
Charmm36-jul2022.ff – User discussions – GROMACS forums
GROMACS version:GROMACS modification: Yes/NoHere post your question I am trying to generate amylin 2L86.top using CHARMM36-jul2022.ff and TIP3P. Amylin has 37 residues but the last NH2 is considered as residue 38. Although AMBERsb-star-ILDN.ff works with 38 resiues”, Charmm36-jul2022 does not work (see below):Fatal error:Residue type ‘NH2’ not found in residue…
How to set awh1-dim1-diffusion and awh1-error-init properly – User discussions
Noob December 6, 2023, 9:13pm 1 GROMACS version: 2023.3GROMACS modification: NoI have been trying out the AWH accelerated sampling for gromacs to better sample the conformational space of a protein. I followed the AWH tutorial for gromacs using more or less the same mdp parameters just adjusted to fit my…
pytorch 2.2.0-rc1 – Download, Browsing & More
pytorch 2.2.0-rc1 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of pytorch-2.2.0-rc1.tar.gz (7 Dec 00:30, 118528815 Bytes) About: PyTorch provides Tensor computation (like NumPy) with strong GPU acceleration and Deep Neural Networks (in Python) built on a tape-based autograd system. Release…
Rstudio Starting fatal error – General
I failed to start Rstudio:here is the error: R Session Startup Failure Report RStudio Version RStudio 2023.09.1+494 “Desert Sunflower ” (cd7011dc, 2023-10-16) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.09.1+494 Chrome/116.0.5845.190 Electron/26.2.4 Safari/537.36 Error message [No error available] Process Output The R session exited…
AWS IoT core mbedtls error – Programming Questions
I’m trying to connect a weather station to an AWS IoT core server and I get the error “Arduino/libraries/WiFiClientSecure/src/ssl_client.h:7:10: fatal error: mbedtls/platform.h: No such file or directory” and I have no idea how to fix it, I’m using an r4 Wifi #include <WiFi.h> #include <WiFiClientSecure.h> #include <Wire.h> #include <Adafruit_Sensor.h> #include…
Panic: Could not run ‘torchvision::roi_pool’ with arguments from the ‘CUDA’ backend – Jetson Nano
Hi, Team! I have such errors, when I run my code in docker container: root@de87551d73cf:/app/src# ./main WARN[0032] CUDA is valid WARN[0044] CUDA is valid INFO[0044] Forwarding… [W TensorImpl.h:1156] Warning: Named tensors and all their associated APIs are an experimental feature and subject to change. Please do not use them for…
Trouble installing Electrode Package using traditional make – LAMMPS Installation
dlee5 December 4, 2023, 2:37am 1 Hello, I am new to LAMMPS, and I am using the stable 2, August 2023 version. I am trying to build LAMMPS using make mpi, and I have the Molecule, Manybody, KSPACE, and Rigid packages installed. I am trying to install the Electrode Package….
Issue with Accessing Thermo Data in Pylammps – LAMMPS Installation
Dear members of the LAMMPS mailing list, I have been attempting to build and install the LAMMPS Python interface (Pylammps) to leverage the advantages of accessing thermos data. However, I am encountering the following error: Based on my understanding from the documentation, if I set up a simulation with a…
locuszoom error
locuszoom error 1 Hi there, I downloaded locuszoom in it’s entirty from their github page. I have everything in order but when I attempt to run the following I get an error: locuszoom_test/bin/locuszoom –metal chr7.snx13.marker.locuszoom.metal –ld chr7.imputed.concat.sorted.nomono.80.recode.maf01.pheno.vcf.2.ld.locuszoom.input –refsnp rs1533245 –prefix chr7.snx13.rs1533245 /share/hennlab/progs/locuszoom_test/bin/../src/m2zfast.py:82: SyntaxWarning: invalid escape sequence ‘\d’ RE_SNP_1000G = re.compile(“chr(\d+|[a-zA-z]+):(\d+)$”);…
BLAST: overflow error
Hi, I’m using blastn in BLAST 2.11.0 and it keeps failing for specific sequences for a reason that I’m yet to understand. Any lead on what he problem might be? The error message is Error: NCBI C++ Exception: T0 “/tmp/BLAST/2.11.0/gompi-2020b/ncbi-blast-2.11.0+-src/c++/src/serial/objistrasnb.cpp”, line 499: Error: (CSerialException::eOverflow) byte 132: overflow error ( at…
Bioconductor Code: metagenomeSeq
metagenomeSeq ============= Statistical analysis for sparse high-throughput sequencing [![Travis-CI Build Status](https://travis-ci.org/HCBravoLab/metagenomeSeq.svg?branch=master)](https://travis-ci.org/HCBravoLab/metagenomeSeq) <a href=”www.bioconductor.org/packages/devel/bioc/html/metagenomeSeq.html#since”><img border=”0″ src=”www.bioconductor.org/shields/years-in-bioc/metagenomeSeq.svg” title=”How long since the package was first in a released Bioconductor version (or is it in devel only).”></a> <a href=”bioconductor.org/packages/stats/bioc/metagenomeSeq.html”><img border=”0″ src=”www.bioconductor.org/shields/downloads/metagenomeSeq.svg” title=”Percentile (top 5/20/50% or ‘available’) of downloads over last 6 full months. Comparison…
140releng-powerpc64le-quarterly][misc/py-pytorch] Failed for py39-pytorch-2.0.1 in configure
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/140releng-powerpc64le-quarterly/84b4661ec108/logs/py39-pytorch-2.0.1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=140releng-powerpc64le-quarterly&build=84b4661ec108 Log: =>> Building misc/py-pytorch build started at Sun Dec 3…
140releng-powerpc64le-quarterly][biology/cytoscape] Failed for cytoscape-3.6.1 in build
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/140releng-powerpc64le-quarterly/84b4661ec108/logs/cytoscape-3.6.1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=140releng-powerpc64le-quarterly&build=84b4661ec108 Log: =>> Building biology/cytoscape build started at Sat Dec 2…
RStudio doesn’t work on Debian 12 with R version 4.3.2 – General
Hello, From the download website, it seems RStudio support Debian 12. I have installed R 4.3.2 R version 4.3.2 (2023-10-31) — “Eye Holes”Copyright (C) 2023 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain…
Automating API Documentation: A Journey from TypeScript to OpenAPI and Schema Governence with Optic
In the previous blog post Documenting and Testing Schemas of Serverless Stacks with Optic & Cypress, we focused on the benefits of schema testing and governance. Briefly, some of the core problems addressed were: Effortless API Documentation: Automating the API documentation creation and update, ensuring that our API documentation evolves…
Bioconductor Code: distinct
# distinct: a method for differential analyses via hierarchical permutation tests <img src=”inst/extdata/distinct.png” width=”200″ align=”right”/> `distinct` is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. `distinct` is…
Testing an OpenAPI specification in PHP
Introduction OpenAPI has become the de facto standard for API specifications. According to its description, “It is a specification language for HTTP APIs that defines structure and syntax in a way that is not wedded to the programming language the API is created in”. The specification is independent of the…
Problem in installing ‘magick’ R package
Problem in installing ‘magick’ R package 0 Hi everyone: I have attempted to install the R package ‘magick’ on R (version: 4.3.1) using the following command: install.packages(“magick”) However, it turns out that there were some warning messaged popped out in the R console: Installing package into ‘/home/billychan/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is…
Rstudio cant install packages – General
Hi together i am currently doing an introductory course in R but having trouble with Rstudio.i want to install a package but just get a really, really long error.Below is what i get in return but i’m already struggling to understand the first bit because i have got rtools installed…
linux – cannot install R package in Rstudio cloud
I am just starting using Rstudio Cloud in Linux and encountered issue installing the package. I just started with tidyverse #install tidyverse packages options(repos = c(CRAN = “https://cloud.r-project.org”)) options(download.file.method = “libcurl”) install.packages(“tidyverse”) #Error I got > install.packages(“tidyverse”) Warning in install.packages : unable to access index for repository cloud.r-project.org/src/contrib: cannot open…
unicycler error : [Errno 13] Permission denied:
I was running unicycler and encountered an error in permisson, what steps should I take to resolve this issue? [Errno 13] Permission denied: Command line: /home/default1/miniconda3/envs/unicycler/bin/spades.py -o /mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly -k 27 –threads 9 –isolate -1 /mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.1qc.fq -2 /mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.2qc.fq -m 1024 System information: SPAdes version: 3.15.5 Python version: 3.10.8 OS: Linux-4.4.0-19041-Microsoft-x86_64-with-glibc2.31 Output…
Vertex AI Search : How to configure/set JWT or OA…
Hi I have a couple question and recommendation regarding Configuration Search Widget to integrate with Django Web App. 1. How to get token from my Django Web Application? To be honest, I realize that it is out of Google Vertex Search product . Yet if anyone have any better idea…
java – Generate only one specific endpoint from API
My current setup for OpenAPI Generator in build.gradle. def openApiGeneratorConfig = { classpath configurations.openApiGenerator systemProperties = [“apis”: “”, “models”: “”] mainClass=”org.openapitools.codegen.OpenAPIGenerator” args ‘generate’ args ‘-o’, “$rootDir/external” args ‘-t’, “$rootDir/external/src/main/resources/codegen/templates/” args ‘–skip-validate-spec’ args “–import-mappings”, “Instant=java.time.Instant,YearMonth=java.time.YearMonth,LocalDateTime=java.time.LocalDateTime” args “–type-mappings”, “double=BigDecimal” } def configFilesRoute = “$rootDir/external/src/main/resources/config/swagger” task generateExternalApiClient(type: JavaExec) { configure openApiGeneratorConfig systemProperties =…
Gemini is coming to Makersuite & so are Stubbs | by Variahy | Nov, 2023
PaLM 2 is going to be replaced by Gemini. A more powerful, multimodal version of PaLM 2. And Gemini is coming — right to Makersuite, for everyone to try out. Makersuite has some basic features, supports text to text outputs, but we want more. We want multimodality. Look at Bard…
Error: Atomtype N3 not found while trying to obtain ions.tpr – User discussions
sam13 November 27, 2023, 12:33am 1 GROMACS version: 🙂 GROMACS – gmx grompp, 2023.3-Homebrew (-:GROMACS modification: No Hello,I have been trying to do MD simulation for a protein whose 3D structure is predicted by AlphaFold. The ligand is Aspartate molecule. I am following a similar approach to the Protein-Ligand GROMACS…
Microservices for beginners. Spam service. Python. Scikit-learn. Kafka.
Whole series: Microservices for beginners Microservices for beginners. Front-end service. Vue js. Socket.io. Microservices for beginners. Api Gateway service. Nest js. Kafka. Microservices for beginners. User service. Nest js. Mongodb. Kafka. Microservices for beginners. Message service. Nest js. Mongodb. Kafka. Microservices for beginners. Spam service. Python. Scikit-learn. Kafka. Microservices for…
Building Pytorch for Conda from source with GLIBCXX_USE_CXX11_ABI=1
GdMacmillan (Gordon MacMillan) November 26, 2023, 4:17pm 1 Before I begin, I’ve checked the topics similar to this one and they all have linking issues and PR’s that are outdated. I am attempting to compile the libtorch binaries and build pytorch from source with GLIBCXX_USE_CXX11_ABI=1 The reason for this, I…
Rstudio Server not working for only one user – RStudio IDE
Hello I am an admin of an rstudio-server, I was asked to create a new account today everything seemed to work fine but this new user can’t use Rstudio inside the server. He logs in normally but when selecting new session and using Rstudio as editor the session wont start…
[Frontend] Preserving Pytorch Spans – pre-RFC
Hey all, wanted to discuss a new feature proposal with the community. I’ve not contributed to TVM before so please let me know if there is a strict process to follow. When loading a traced pytorch model using tvm.relay.frontend.from_pytorch, TVM auto assigns span names since 0.14.0 based on the operator…
SLURM: RuntimeError: CUDA error: CUDA-capable device(s) is/are busy or unavailable – distributed
I am trying to train EG3D on a slurm cluster using multiple gpus. But am getting the following error: File “/home/dmpribak/ondemand/data/sys/myjobs/projects/default/4/train.py”, line 395, in main launch_training(c=c, desc=desc, outdir=opts.outdir, dry_run=opts.dry_run) File “/home/dmpribak/ondemand/data/sys/myjobs/projects/default/4/train.py”, line 105, in launch_training torch.multiprocessing.spawn(fn=subprocess_fn, args=(c, temp_dir), nprocs=c.num_gpus) File “/home/dmpribak/.conda/envs/eg3d3/lib/python3.11/site-packages/torch/multiprocessing/spawn.py”, line 246, in spawn return start_processes(fn, args, nprocs, join,…
Different learning rates for different parameters
Hello! How can I specify a different learning rate for each parameter of my model. In my case I have something of the form: x_index = torch.tensor([14.,15.,8.,9.,10.,11.,13.,12.,5.,4.,3.,2.,0.,1.]) wavenumber_vals = torch.tensor([284829.132,284829.132,284840.730,284840.730,284854.732,284854.132,284864.420,284864.920,284884.170,284884.620,284898.434,284898.814,284910.218,284910.218],dtype=torch.float64) params = torch.tensor([B_0, D_0, gamma_0, b1_0, c1_0, b2_0,eqQ_0],dtype=torch.float64, requires_grad=True) opt = optim.Adam([params], lr=1e-3) for i in range(10): opt.zero_grad() loss =…
Using openapi-typescript-codegen, why does this Swagger schema produce a model of Record?
My swagger.json includes this schema: “schemas”: { “BuildFruitBody”: { “properties”: { “id”: { “type”: “number”, “format”: “double” }, “name”: { “type”: “string” } }, “type”: “object”, “additionalProperties”: true } }, However, when I generate the axios client via npx openapi-typescript-codegen -i ./swagger.json -o src/services/api -c axios, the resulting model is…
Having troubel in understanding what loss is currently in use
aquorio15 (Amartya) November 24, 2023, 10:49am 1 I was going through this hugging face code and I am having trouble understanding what loss the model is currently using . Although I know most seq2seq models uses CrossEntrophy loss but I don’t see the definition anywhere in the code huggingface/transformers/blob/aca6288ff42cebded5421020f0ff088adeb446dd/examples/language-modeling/run_clm.py Actually…
main-powerpc64le-default][misc/py-pytorch] Failed for py39-pytorch-2.1.1 in configure
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/main-powerpc64le-default/p5b346a1c0cc2_sfb51ddb20d/logs/py39-pytorch-2.1.1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=p5b346a1c0cc2_sfb51ddb20d Log: =>> Building misc/py-pytorch build started at Fri Nov 24…
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…
RStudio session failed to start – RStudio IDE
Error Information: Description of issue –I’ve used RStudio for many years without problem. I was using it yesterday without problem; then, it crashed and won’t restart. I’ve reinstalled R and RStudio. I believe that I have removed RStudio state files. Attempted steps taken to fix – System Information: RStudio Edition:…
Compiling Deep-md with GROMACS – User discussions
GROMACS version: 2020.2GROMACS modification: Yes/NoI was trying to install Deep-md with GROMACS following the link1.6. Install GROMACS with DeepMD — DeePMD-kit documentation. To do this, I have followed the link to install Deep-MD: 1.2. Install from source code — DeePMD-kit documentationHere I have successfully completed the 1.2.1 ( install-the-python-interface) and…
merge .pdata and .xdata sections from host object files
diff –git a/src/cmd/cgo/internal/test/callback_windows.go b/src/cmd/cgo/internal/test/callback_windows.gonew file mode 100644index 0000000..95e97c9— /dev/null+++ b/src/cmd/cgo/internal/test/callback_windows.go@@ -0,0 +1,133 @@+// Copyright 2023 The Go Authors. All rights reserved.+// Use of this source code is governed by a BSD-style+// license that can be found in the LICENSE file.++package cgotest++/*+#include <windows.h>+USHORT backtrace(ULONG FramesToCapture, PVOID *BackTrace) {+#ifdef _AMD64_+ CONTEXT context;+…
slurm 23.11.0 – Download, Browsing & More
slurm 23.11.0 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of slurm-23.11.0.tar.bz2 (22 Nov 00:04, 7353218 Bytes) About: Slurm is a fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters. Fossies downloads: / linux /…
Pass reads file form host to container
Docker: Pass reads file form host to container 0 Hello, I need your help please. I want to create docker container to analyse my reads, to run it via nextflow or wdl worflow. I have a python script, and I would like to pass my reads as argument something like…
HDF5 brew issue // conda installation issue
I have used kallisto in the past, but now am struggling to get bootstrapping to work on a new computer (MacBook M1). I have searched through the issues that others encountered and tried three different methods of installation, but still no luck. Could you please help or direct me to…
Possible inclusion of PLUMED interface – Developers discussions
Dear GROMACS developers, we (PLUMED developers) noticed that GROMACS now makes it possible to easily add plugins modifying forces. We would like to investigate if it makes sense for us to implement an interface for PLUMED in the spirit of the one introduced for the Colvars package in this commit:…
A Step-by-Step Guide to building a BERT model with PyTorch (Part 2c) | by Tahir Rauf | Nov, 2023
So far in the series, we have accomplished several tasks: In Part 1, we prepared our dataset for BERT training. In Part 2a, we prepared fixed input embeddings for the BERT. Following that, in Part 2b, we implemented multi-head attention and the feedforward block. However, we still need to implement…
[slurm-users] Default SelectTypeParameters option
Hi, I have noticed our site relies on the default value SelectTypeParameters (e.g. not specified in slurm.conf) which should be same as: SelectTypeParameters=CR_Core_Memory I have noticed some strange behaviour where the compute nodes do not seem to use memory cgroup e.g. in the log without the above…
Object Detection with PyTorch Mobile
In this article we will set up a Mobile Application for Object Detection. We will use PyTorch Mobile to optimize and run the YOLOv5 on an Android app. AI mobile app development Challenges Developing AI applications in mobile is difficult due to slow loading speeds and scalability problems. They heavily…
Bug#1056217: src:rust-async-task: fails to migrate to testing for too long: autopkgtest regression
Source: rust-async-task Version: 4.4.1-1 Severity: serious Control: close -1 4.5.0-1 Tags: sid trixie User: release.debian….@packages.debian.org Usertags: out-of-sync Control: block -1 by 1055099 Dear maintainer(s), The Release Team considers packages that are out-of-sync between testing and unstable for more than 30 days as having a Release Critical bug in testing [1]….
python 3.x – Can’t create Vertex AI (GCP) notebook with custom container
I’m trying to create a Vertex AI notebook using a Custom Container to train my torch model on GCP. I wasn’t able to correctly generate a notebook using this custom container and I can’t understand why. I tried to look at the documentation but wasn’t able to identify any pages…
node.js – Vertex AI – NodeJS SDK – Error: 3 INVALID_ARGUMENT: 0 is out of supported range [1, 1025);
I’m following the example for calling the predict endpoint: : I am getting this error in Vertex ai: ⨯ Error: 3 INVALID_ARGUMENT: 0 is out of supported range [1, 1025); for the maximum number of tokens. at callErrorFromStatus (webpack-internal:///(rsc)/./node_modules/@grpc/grpc-js/build/src/call.js:31:19) at Object.onReceiveStatus (webpack-internal:///(rsc)/./node_modules/@grpc/grpc-js/build/src/client.js:192:76) at Object.onReceiveStatus (webpack-internal:///(rsc)/./node_modules/@grpc/grpc-js/build/src/client-interceptors.js:344:141) at Object.onReceiveStatus (webpack-internal:///(rsc)/./node_modules/@grpc/grpc-js/build/src/client-interceptors.js:308:181) at eval…
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 &&…
Gmx trjconv -fit – User discussions
Lili November 16, 2023, 8:00pm 1 Program: gmx trjconv, version 2021.3-MODIFIEDSource file: src/gromacs/pbcutil/pbc.cpp (line 101)Function: numPbcDimensions(PbcType)::<lambda()>Hi,I am preparing gmx_MMPBSA calculations after production mdrun,Bellow are my two commands. I first command survive but the second give errores as I pasted bellow.Command 1:gmx trjconv -s topol.tpr -f traj.xtc -o md_noPBC_center.xtc -pbc atom…
Installation of DESeq2 package while utilizing free Posit cloud – General
Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager)Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)BiocManager::install(“DESeq2”)‘getOption(“repos”)’ replaces Bioconductor standard repositories,…
DESeq2 installation failures
DESeq2 installation failures 0 Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager) Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2…
Pytorch network -> onnx -> tensorrt performance(run frequency) question – Jetson AGX Xavier
hi, dear Nvidia engineers,I have been working on a state of art neural network and tried to deploy it on jetson xavier . one major consideration is the realtime perforamance. I tried the int8, cuda-graph, method and it gives some performance indeed, but it still doesnot meet a realtime requirement….
transformers 4.35.1 – Download, Browsing & More
transformers 4.35.1 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of transformers-4.35.1.tar.gz (14 Nov 15:37, 15700182 Bytes) About: Transformers supports Machine Learning for Pytorch, TensorFlow, and JAX by providing thousands of pretrained models to perform tasks on different modalities such as…
RStudio won’t start, but R will, on MacOS Sonoma
In preface: This problem has persisted through two operating system upgrades and numerous reinstallations of R, RStudio, and XQuartz. My MacBook Pro is from 2018, and shouldn’t have any problem running up-to-date software. I’ve tried other fixes, but nothing’s worked; running RStudio.app from the command line fails consistently, it’s not…
Sage 10.0 released
Congratulations to Volker and to all Sage contributors on the new release. 2023-05-21 01:00 UTC, Matthias Köppe: Thanks. > Some notes: > > – The list of “New Contributors” was also automatically generated > by GitHub. It did not know the contributors of previous versions. > I’ve manually removed many…
Workbench project sharing issue: system error 13 (Permission denied) – NFSv4 on Ubuntu 20.04 – RStudio IDE
Hi there,I have a new Posit Workbench installation on Ubuntu 20.04 and I’m attempting to replicate what I had on my old servers – project sharing working across an NFSv4 share which contains all my user home directories. Both the sharing machine and Workbench machine are running the same version…
@options() decorators in sagemath library code and Sphinx 7.1+
We have instances of @options() (from src/sage/misc/decorators.py) applied to functions in the library, e.g. github.com/sagemath/sage/blob/41031292ff1ae518cd5b5a29ce277aa1ff8ced9e/src/sage/plot/contour_plot.py#L1394 where an argument name of the form foo=bar in @options matches an argument name foo of the function, e.g. @options(plot_points=100, incol=’blue’, outcol=None, bordercol=None, borderstyle=None, borderwidth=None, frame=False, axes=True, legend_label=None, aspect_ratio=1, alpha=1) def region_plot(f, xrange, yrange, plot_points, incol, outcol, bordercol, borderstyle, borderwidth,…
Bug#1055848: cfgrib: autopkgtest regression
Source: cfgrib Version: 0.9.10.4-2 Severity: serious User: debi…@lists.debian.org Usertags: regression Hi Maintainer The upload of cfgrib 0.9.10.4-2 is failing its own autopkgtest [1]. I’ve copied what I hope is the relevant part of the log below. Regards Graham [1] ci.debian.net/packages/c/cfgrib/testing/amd64/ 80s autopkgtest [21:14:56]: test tryload: [———————– 80s Traceback (most recent call last): 80s File…
Pytorch Transformer only generating NaN when using mask
When I generate a src_mask like this mask = torch.triu( torch.ones(batch_size, batch_size).bool(), diagonal=0 ) >> tensor([[ True, True, True, True, True], [False, True, True, True, True], [False, False, True, True, True], [False, False, False, True, True], [False, False, False, False, True]]) then the transformer only generates NaN values. If I…
Error in compiling lammps after interfacing with AENET
Dear Dr. Artrith and team, Greetings! I’m new to aenet. Thank you Dr. Artrith and team for develping aenet and opensourcing it. I downloaded USER-AENET and interfaced with lammps 4Feb2020-version. However, I’m getting the following error (complete error response attached ) when I compile the lammps using “make mpi”. Kindly…
java/OpenAPITools/openapi-generator/samples/client/petstore/java/okhttp-gson-dynamicOperations/src/main/java/org/openapitools/client/auth/RetryingOAuth.java
We and our partners use cookies to Store and/or access information on a device. We and our partners use data for Personalised ads and content, ad and content measurement, audience insights and product development. An example of data being processed may be a unique identifier stored in a cookie. Some…
Will sagemath return to the Fedora 39 repository?
bgregs (Brian Snyder) November 11, 2023, 5:12pm 1 I upgraded from Fedora 38 to 39 without paying close attention to the warnings about incompatible packages on my system (rookie mistake). After upgrading, I realized that sagemath is not in the Fedora 39 repository. Is this permanent or could sagemath come…
Gromacs: src/gromacs/nbnxm/kernel_common.h File Reference
#include “gromacs/math/vectypes.h” #include “gromacs/utility/real.h” #include “atomdata.h” #include “pairlist.h” This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Declares the nbnxm pair interaction kernel function types and kind counts, also…