Tag: CMake

#!/bin/sh # Measure heap usage (and performance) of ECC operations with various values of # the relevant tunable compile-time parameters. # # Usage (preferably on a 32-bit platform): # cmake -D CMAKE_BUILD_TYPE=Release . # scripts/ecc-heap.sh | tee ecc-heap.log set –eu CONFIG_H=‘include/mbedtls/config.h’ if [ –r $CONFIG_H ]; then :; else echo…

Description: In python-pytorch’s PKGBUILD, CMake files are moved from `/usr/lib/python3.11/site-packages/torch/share/cmake` to `/usr/lib/cmake`, which makes sense, however, the `torch.utils.cmake_prefix_path` variable still points to `/usr/lib/python3.11/site-packages/torch/share/cmake`. Some other libraries may use this variable as part of their build system to find TorchConfig.cmake. Either `torch/utils/__init__.py` should be patched to point to ArchLinux’ location, or…

Source: boost1.81 Version: 1.81.0-5 Severity: normal —–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Dear maintainer, starting with CMake 3.26, a new warning is issued if cmake_minimum_required() is not called before project(), as some policy settings affect the behavior of project(). Your package is affected: autopkgtest [23:01:45]: @@@@@@@@@@@@@@@@@@@@ summary atomic FAIL stderr: CMake Warning (dev) at…

yzs May 26, 2023, 3:42pm 1 Hi, I’m experiencing performance degradation when trying to compile from source, and I’m wondering if there are some details I’m missing. Using pytorch v2.0.0 as an example, I used both cuda 11.7 and cudnn 8.5 (consistent with builder/install_cuda.sh at main · pytorch/builder · GitHub…

GROMACS version: 2021.4GROMACS modification: Yes/No Hi, I am getting this error while installing gromacs 2021.4 please help me with it. I configured cmake as follows: cmake … -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DGMX_MPI=ON -DGMX_GPU=CUDA -DGMX_SIMD=AVX2_256 -DCMAKE_PREFIX_PATH=/usr/local/gromacs2021 -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs2021 -DBUILD_SHARED_LIBS=ON -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-11.7 after this I am getting an error as follows: [ 92%] Building…

I’m trying to run docker for alphafold but it says that there is no ‘/home/administrator/alphafold/run_alphafold.py’ in the directory even if it does exist Code I’m trying to run python3 docker/run_docker.py \ –fasta_paths=your_protein.fasta \ –max_template_date=2022-01-01 \ –data_dir=/data8/Alphafold_database\ –output_dir=/data8/Alphafold_output_dir OBS: this is just a test to know if docker is working (your_protein.fasta…

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…

Erik May 24, 2023, 5:01pm 1 GROMACS version: 2023.1GROMACS modification: No I’m trying to compile GROMACS 2023 using Intel’s LLVM compilers and have run into a number of issues. The first is that they don’t seem to play nicely with nvcc because of a bug with the way nvcc sets…

Source: pytorch-audio Severity: normal Tags: patch User: reproduci…@lists.alioth.debian.org Usertags: buildpath X-Debbugs-Cc: reproduc…@lists.alioth.debian.org The RPATH contains the build path resulting in different buildid and various other differences: tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pytorch-audio.html The attached patch to the upstream tools/setup_helpers/extension.py fixes this by passing -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON to CMake. With this patch applied, based on my local tests, pytorch-audio should build…

GROMACS version:2023.1GROMACS modification: NoHere post your question System: Ubuntu on WSL2 with Windows 11 I try to cmake gromacs using the following tags: cmake .. -DGMX_GPU=CUDA -DGMX_CUDA_TARGET_SM=”75″ -DGMX_CUDA_TARGET_COMPUTE=”75″ -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_BUILD_OWN_FFTW=ON -DGMX_PYTHON_PACKAGE=ON But the configure returns an error with the following statement: Traceback (most recent call last): File “<string>”, line 1,…

Il giorno mer 17 mag 2023 alle 20:26:52 +02:00:00, Matthias Geiger <matthias….@tutanota.de> ha scritto: > please update mbedtls to 3.4.0 . The 3.x release track includes the > .cmake file > I’d need for another library I’m trying to package. Hi Matthias, thanks for the report. I’d love to package…

I want to run detectron2 prediction as a Python Code embedded in a WebRTC C++ code. I am using webrtc-streamer as a C++ server in which I want to embed detectron2 Python code to call a prediction function. Everything works fine when I run the executable of webrtc-streamer and call…

The pytorch DEBUG build crashes cicc nvcc error : ‘cicc’ died due to signal 11 (Invalid memory reference) nvcc error : ‘cicc’ core dumped Here’s a sample (generated) command that causes a crash /opt/cuda/bin/nvcc -forward-unknown-to-host-compiler -DAT_PER_OPERATOR_HEADERS -DHAVE_MALLOC_USABLE_SIZE=1 -DHAVE_MMAP=1 -DHAVE_SHM_OPEN=1 -DHAVE_SHM_UNLINK=1 -DIDEEP_USE_MKL -DMINIZ_DISABLE_ZIP_READER_CRC32_CHECKS -DONNXIFI_ENABLE_EXT=1 -DONNX_ML=1 -DONNX_NAMESPACE=onnx_torch -DTORCH_CUDA_BUILD_MAIN_LIB -DUSE_C10D_GLOO -DUSE_C10D_MPI -DUSE_C10D_NCCL -DUSE_CUDA…

This is an idiomatic Rust wrapper for MbedTLS, allowing you to use MbedTLS with only safe code while being able to use such great Rust features like error handling and closures. Additionally, building on MbedTLS’s focus on embedded use, this crate can be used in a no_std environment. Building This…

GROMACS version: 2023.01GROMACS modification: No I installed GROMACS 2023.01 using the cmake command below. cmake … -DGMX_USE_RDTSCP=ON -DGMX_SIMD=AVX2_256 -DGMX_BUILD_MDRUN_ONLY=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=ON -DGMX_GPU=CUDA -DCMAKE_C_COMPILER=gcc-9 -DCMAKE_CXX_COMPILER=g+±9 But, When I execute mdrun like below,I got the error, THREAD_MPI is not complied during installation.mpirun -np 2 gmx mdrun -v -deffnm ${mini_prefix} -ntmpi…

I am attempting to build Pytorch/XLA on a new Windows 11 laptop (16″ Lenovo AMD Ryzen Ideapad 5 pro to be specific) under WSL (Ubuntu 22.04) following the Linux instructions at github.com/pytorch/pytorch#from-source However, no matter what I try I get compilation errors (mostly warnings that are promoted to errors). If…

I am not sure what your issue is.I have fedora 37 and fedora 38. Both with nvidia GPUs and both with the latest nvidia (530.41.03) and cuda (12.1) from rpmfusion. Using the command given on the pytorch site – (pip3 install torch torchvision torchaudio) to do the install as my…

GROMACS version: 2023.1GROMACS modification: No Dear GROMACS community I have been trying to run QM/MM calculations using the CP2K interface in GROMACS.I have compiled the codes in multiple occasions, using different configurations. CP2K 2023.1: using Eiger arch file, using full toolchain installation (-install all), using other variations: fftw=install –with-plumed=no –with-sirius=no…

As the title, I tried to use the C++ version of Pytorch i.e. LibTorch on win11, but when I do the mingw32-make operation I get a missing file error as follows: [ 50%] Building CXX object CMakeFiles/app.dir/example-app.cpp.obj g++.exe: error: /Z7: No such file or directory g++.exe: error: /EHsc: No such…

ncs 2.3.0 Good morning,for a few days, I can no longer compile a firmware that I use regularly. I don’t understand what could have happened. I’ll post the compilation with the errors if anyone has any ideas about it.Thank you CMAKE/BUILD [cmake] CMake Error at /opt/nordic/ncs/v2.3.0/zephyr/cmake/modules/extensions.cmake:2520 (message): [cmake] BOARD is not…

I’m trying to train a deep learning model using my GPU yet only my CPU was in use. I called the cuda is available function and false was returned. Here’s the detail of my python environment. (base) C:\Windows\System32>python -m torch.utils.collect_env Collecting environment information… PyTorch version: 2.0.0 Is debug build: False…

ximik April 25, 2023, 2:29pm 1 GROMACS version: 2023.1GROMACS modification: NoI want to install gromacs with cp2k. I used cmake … -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/home/ximik/grcp2k -DGMX_CP2K=ON -DCP2K_DIR=/home/ximik/cp2k/lib/local/psmp -DCP2K_LINKER_FLAGS=/home/ximik/cp2k/lib/local/psmp/libcp2k.a -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON After that make -j 4And a have errorshome/ximik/cp2k/obj/local/psmp/exts/dbcsr/dbcsr_mm_hostdrv.F90:440: undefined reference to __libxsmm_MOD_libxsmm_sgemm0′ /usr/bin/ld: /home/ximik/cp2k/lib/local/psmp/exts/dbcsr/libdbcsr.a(dbcsr_mm_hostdrv.o): in function xsmm_process_mm_batch_s’:/home/ximik/cp2k/obj/local/psmp/exts/dbcsr/dbcsr_mm_hostdrv.F90:440: undefined reference…

pytorch 2.0.1-rc2 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of pytorch-2.0.1-rc2.tar.gz (24 Apr 15:27, 111342048 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. PyTorch…

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…

bansa01 (Bansa01) April 20, 2023, 12:22am 1 Hello Folks, I am looking to launch a docker container using 3 files which are DockerFile, build.sh and run.sh respectively. Where I have all my configuration mentioned in DockerFile. I mention explicitly the python version which I need to be present on the…

pmbm13 April 18, 2023, 12:20pm 1 Hi!When I try to install dash-bio package I constantly get this error: C:\Users\pmbm1>pip install dash-bio==1.0.1Collecting dash-bio==1.0.1Using cached dash_bio-1.0.1-py3-none-any.whlCollecting dash>=1.6.1 (from dash-bio==1.0.1)Using cached dash-2.9.3-py3-none-any.whl (10.2 MB)Requirement already satisfied: pandas in c:\users\pmbm1\appdata\local\programs\python\python311\lib\site-packages (from dash-bio==1.0.1) (1.5.3)Requirement already satisfied: scipy in c:\users\pmbm1\appdata\local\programs\python\python311\lib\site-packages (from dash-bio==1.0.1) (1.10.1)Collecting scikit-learn>=0.20.1 (from dash-bio==1.0.1)Using…

This question stems from me trying to compile PyTorch from source. The build fails with: — Performing Test SUPPORT_GLIBCXX_USE_C99 — Performing Test SUPPORT_GLIBCXX_USE_C99 – Failed CMake Error at cmake/MiscCheck.cmake:63 (message): The C++ compiler does not support required functions. This is very likely due to a known bug in GCC 5…

GROMACS version: 2022.5GROMACS modification: No CP2K Installation:./install_cp2k_toolchain.sh –enable-cuda=no –libint-lmax=5 –with-sirius=no –with-mkl=system –with-openblas=no –with-scalapack=no –with-cosma=no –with-spla=no –with-spfft=no –with-hdf5=no –with-spglib=no –with-libvdwxc=no –with-plumed=no After this, I end up with several arch files. I am just listing the content of the local.psmp file here. The local.psmp has the following contents:CC = /home/Packages/intel/oneapi/mpi/2021.5.1/bin/mpiiccCXX = /home/Packages/intel/oneapi/mpi/2021.5.1/bin/mpiicpcAR…

Hello everyone, I’ve been working on installing CP2K on a system with IBM Power9 processors and Nvidia V100 GPUs. I’m using the toolchain with these options: ./install_cp2k_toolchain.sh -j –with-cmake=system –mpi-mode=openmpi –enable-cuda –gpu-ver=V100 It installs all the dependencies without any errors so that I copy over the files to the arch…

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 \…

Dear Community,   This is Pim, a new EPYC user. I just DIYed a workstation as following:     – Supermicro H11DSi     – EPYC 7B12 * 2     – Samsung RECC 3200 32G * 16     –  Samsung 980 Pro 2t     – Centos 7…

The Center for Quantitative Genetics and Genomics (QGG) at Aarhus University invites applications for a position as Postdoc in the field of bioinformatics and sequence analysis as per 1 August 2023 or as soon as possible thereafter. Expected start date and duration of employmentThe position is a fixed-term full-time position…

We are looking to hire a motivated Postdoc in bioinformatics and sequence analysis to join our stellar team at Aarhus Universitet in Århus C.Growing your career as a Full Time Postdoc in bioinformatics and sequence analysis is a great opportunity to develop useful skills.If you are strong in cooperation, people…

bugzilla.redhat.com/show_bug.cgi?id=2179414 Bug ID: 2179414 Summary: Review Request: python-scikit-build-core – Build backend for CMake based projects Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Assignee: nobody@xxxxxxxxxxxxxxxxx Reporter: redhat@xxxxxxxxx QA Contact: extras-qa@xxxxxxxxxxxxxxxxx CC: package-review@xxxxxxxxxxxxxxxxxxxxxxx Target Milestone: — Classification: Fedora Spec URL: download.copr.fedorainfracloud.org/results/lecris/fedora-scikit-build-core/fedora-38-aarch64/05656194-python-scikit-build-core/scikit-build-core.spec SRPM URL: download.copr.fedorainfracloud.org/results/lecris/fedora-scikit-build-core/fedora-38-aarch64/05656194-python-scikit-build-core/python-scikit-build-core-0.2.2-1.fc38.src.rpm…

jeanc March 17, 2023, 3:35pm 1 Hello, I have made some changes to some files in the src directory to do some tests. The documentation says that I will have to re-compile and relink the LAMMPS executable with make. While the initial build was successful with an executable created in…

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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…

pytorch 1.8.2 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of pytorch-1.8.2.tar.gz (18 Aug 00:15, 14923822 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. LTS…

I-Zac March 8, 2023, 10:58am 1 I got this error after making yes-all packages and tried to recompile lammps.How can i resolve this please? zac3553@i-Zac:~/lammps-23Jun2022/src$ make mpiGathering installed package information (may take a little while)make[1]: Entering directory ‘/home/zac3553/lammps-23Jun2022/src’make[1]: ‘lmpinstalledpkgs.h’ is up to date.Gathering git version informationmake[1]: Leaving directory ‘/home/zac3553/lammps-23Jun2022/src’Compiling LAMMPS…

itandy March 8, 2023, 1:24pm 1 GROMACS version: 2023 GROMACS modification: No Here post your question I am having problems getting GROMACS-2023 to work for users other than the one who built it. If a user other than the one who built the binary calls gmx_mpi, the following error message…

GROMACS version: 2023GROMACS modification: No Hi all, I am trying to install Gromacs 2023 on my M2 MacBook Air. I am using the following compilation line: CC=/opt/homebrew/bin/gcc-12 CXX=/opt/homebrew/bin/g++-12 cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs -DGMX_FFT_LIBRARY=fftw3 -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=OpenCL The compilation seems to go smoothly, and then I issue make check. After building gmock, I…

GROMACS version: 2023GROMACS modification: Yes/NoHere post your questionI try to install the latest version of gromacs “gromacs 2023” on my mac pro having M1. I used the following command to perform cmake. cmake -D CMAKE_C_COMPILER=/usr/local/bin/mpicc -D CMAKE_CXX_COMPILER=/usr/local/bin/mpicxx -D CMAKE_INSTALL_PREFIX=/usr/local/gromacs_new -D GMX_FFT_LIBRARY=fftw3 -D GMX_MPI=ON -D GMX_BUILD_OWN_FFTW=ON -D REGRESSIONTEST_DOWNLOAD=ON -D GMX_GPU=OpenCL …/…

GROMACS version:2022.5GROMACS modification: Don’t think soOS -CentOS 7.9cmake 3.17.3local anaconda3 for python3CUDA 11.7 I am looking for help on what i might have missed. Gromacs compiled ok without any reported errors. I had to install openMPI and symlink it for the compiler to see it.All the mdrun tests fail with…

I have encountered problems compiling LAMMPS with NVIDIA GPU’s using CUDA.It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. I am…

GROMACS version:2018GROMACS modification: Yes/NoHere post your questiongmx mdrun -v -deffnm em Back Off! I just backed up em.log to ./#em.log.7#Compiled SIMD: None, but for this host/run AVX2_256 might be better (see log).The current CPU can measure timings more accurately than the code ingmx mdrun was configured to use. This might…

Dear all, I am compiling LAMMPS 8Feb23 on an old cluster. Here are the details: OS: Linux “Ubuntu 16.04.4 LTS” 4.13.0-39-generic Compiler: GNU C++ 5.4.0 20160609 with OpenMP not enabled C++ standard: C++11 MPI v3.1: Open MPI v4.1.5, package: Open MPI otello@vikos Distribution, ident: 4.1.5, repo rev: v4.1.5, Feb 23,…

rpsingh February 26, 2023, 7:12am 1 GROMACS version: 2023GROMACS modification: NoHere post your question I tried installing Gromacs 2023 on Ubuntu 20.04 LTS using the following command:mkdir buildcd buildsudo cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs2023(without sudo, a large number of permission errors were obtained) When running the above, I get…

Dear all, I’m trying to build CP2K 2023.1 in WSL Ubuntu 20.04 LTS by tools/toolchain/install_cp2k_toolchain.sh in my laptop. I use the following command: ./install_cp2k_toolchain.sh –with-gcc=install –with-openmpi=install –math-mode=openblas –mpi-mode=openmpi –with-pexsi=install –with-quip=install –with-plumed=install –with-libtorch=install –with-sirius=install -j 12 Everything is OK until compiling SIRIUS. The toolchain returns an error as following: –– Found…

Job:PhD Position to Develop Machine Learning Methods for Microbiome Analysis 0 Looking for a highly motivated PhD student for Computational Biology research, with an algorithm development focus. The Ecological and Evolutionary Signal-processing (EESI) and Informatics lab is doing a restart from the pandemic and will be composed of a dynamic,…

Hello allI am trying to install GROMACS on GPU. I have installed latest cmake 3.26.0_rc3 but when i am trying to configure GROMACS as per instructions given, it gives me the error of cmake: command not found. Now as per my understanding I am probably not giving the path variable…

Hi, thank you for your reply. I’m not from programming background and trying to self learn bioinformatics, so I don’t know the exact problem. I will try to be more descriptive this time. When I use conda install -c conda-forge ambertools It gives me error for package. Which I see…

mojito February 19, 2023, 12:41pm 1 GROMACS version: 2023CUDA – 12.0System- Ubuntu (WSL2)GPU- GTX1650Here post your questionI am trying to make a GPU build of Gromacs but it’s failing everytime tanishque@DESKTOP-7V2NMM0:~/gromacs-2023/build$ sudo cmake … -DGMX_GPU=CUDA– Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Development Development.Module Development.Embed) (found suitable version “3.10.6”, minimum required…

Dear lammps users, I wanna install LAMMPS (stable release 2022) on Linux and install some packages like GPU and KSPACE. I have tried two different approaches.In the traditional method, I ran these lines in terminalmake yes-GPUI installed the packages that I wanted.then I run, make mpi, but I get this…

akram February 16, 2023, 10:41am 1 Dear experts,I want to use the “group2ndx” command to create an index file where the IDs of the any atoms belonging to a certain group is determined.This command needs to install the COLVARS package, but I can’t compile Lammps after installing this package because…

roozi February 16, 2023, 2:28am 1 GROMACS version:2021.7 , 2021.6 , 2022.5 , 2023GROMACS modification: No Hey all,I am trying to build gromacs 2021.7 using Mingw64 on Windows 10 (pro , x64) (without gpu support). & cpu: core-i7.Used Cmake-GUI (3.25.2) for configuration. (FFTW , BUILD_SHARED_LIBS=On , GMX_PREFERE_STATIC_LIBS=Off , GMX_BUILD_SHARED_EXE=On). The…

pytorch 2.0.0-rc1 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of pytorch-2.0.0-rc1.tar.gz (16 Feb 00:08, 111326579 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…

Kehan: The LAMMPS version is 3 Nov 2022 Please note that the latest feature release of LAMMPS is version 8 Feb 2023. Kehan: -DCMAKE_INSTALL_PREFIX=`pwd` This looks very wrong. From your description it seems that the “full install” is not the best choice. That would be the case, if your target…

gromacs_stmv_job_script – HackMD # gromacs_stmv_job_script ###### tags: `Gromacs` “`= #!/bin/bash #PBS -N gromacs_stmv #PBS -q ct400 #PBS -l select=8:ncpus=32:mpiprocs=25 #PBS -l walltime=3:00:00 #PBS -P ACD110038 #PBS -j oe #PBS -o pbsout_gromac_8nodes_25ppn.txt export PATH=/home/nckuhpclab03/cmake/cmake/bin:$PATH module load gcc/9.3.0 module load mpi/openmpi-4.0.5/gcc930 module load intel/2018_u1 module show intel/2018_u1 export PATH=/home/nckuhpclab03/gromacs/gromacs-2020.2/gromacs/bin:$PATH export MKLROOT=/pkg/intel/2018_u1/compilers_and_libraries_2018.1.163/linux/mkl cd…

The GROMACS (GROningen MAchine for Chemical Simulations) molecular dynamics package testing with the water_GMX50 data. This test profile allows selecting between CPU and GPU-based GROMACS builds. To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark gromacs. Test Created 15 June 2019 Last Updated 8…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 10 Feb 2023 03:05:28 +0800 Source: pytorch-audio Architecture: source Version: 0.13.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Deep Learning Team <debian…@lists.debian.org> Changed-By: Aron Xu <a…@debian.org> Closes: 990627 1008922 Changes: pytorch-audio (0.13.1-1) unstable; urgency=medium . [ Mo Zhou ] * New…

gromacs-devel-2021.5-1.fc36 – Fedora Packages ↵ Return to the main page of gromacs-develView buildSearch for updates Package Info (Data from x86_64 build) Changelog Dependencies Provides Files Changelog Date Author Change 2022-01-29 Christoph Junghans <junghans at votca dot org> – 2021.5-1 – Version bump to v2021.5 (bug #1787785) 2022-01-20 Fedora Release Engineering…

gromacs 2023 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2023.tar.gz (6 Feb 19:24, 41863526 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

votca-devel-2022.1-1.fc36 – Fedora Packages ↵ Return to the main page of votca-develView buildSearch for updates Package Info (Data from x86_64 build) Changelog Dependencies Provides Files Changelog Date Author Change 2022-12-21 Christoph Junghans <junghans at votca dot org> – 2022.1-1 – Version bump to v2022.1 2022-11-29 Christoph Junghans <junghans at votca…

Successfully built Sagemath 9.6 on Bookworm (“apt dist-upgrade”-ed as of 25 January 2023) using the following script. (It seems to have partially built 9.7, and that build might be fixable by an interested someone.) The important piece seems to be ./configure –without-system-gcc –without-system-pari –without-system-singular to avoid the version conflicts reported…

GROMACS version:2022.1GROMACS modification: Yes/No I am trying to compile GROMACS with CP2K package to do QM/MM simulation. I have installed CP2K and the cmake process for GROMACS configured without any problem. But the make -j N process failed at 100% Lining CXX executable …/…/bin/gmx_mpi.It started to print out a long…

Hi, I have now attempted to install cp2k on a slurm HPC with K40ms. I used: ./install_cp2k_toolchain.sh –with-openmpi=system –with-openblas –enable-cuda –gpu-ver=K40 –with-cmake=system –with-libxc –with-pexsi=no –with-ptscotch=no –with-superlu=no –with-quip –with-plumed –with-elpa=no –with-sirius=no –with-libxsmm –with-fftw=system Also, using —————————- Modules ————————————-Currently Loaded Modulefiles: 1) libraries/cuda-11.4   2) mpi/openmpi-x86_64   3) pmi/pmix-x86_64  Installation works fine, no…

Narges January 24, 2023, 9:16am #1 Hello all, In GROMACS installation in a cluster, after running the command: ‘cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON’ I have faced the error (attached pictures). I would be thankful if you could help me to fix it. al42and January 24, 2023, 11:19am #2 Hello. That looks…

bugzilla.redhat.com/show_bug.cgi?id=2156243 Bug ID: 2156243 Summary: Review Request: python-scikit-build – Improved build system generator for CPython extensions Product: Fedora Version: rawhide Status: NEW Component: Package Review Assignee: nobody@xxxxxxxxxxxxxxxxx Reporter: troy@xxxxxxxxxxxxxxxx QA Contact: extras-qa@xxxxxxxxxxxxxxxxx CC: package-review@xxxxxxxxxxxxxxxxxxxxxxx Target Milestone: — Classification: Fedora Spec URL: troycurtisjr.fedorapeople.org/python-scikit-build/python-scikit-build.spec SRPM URL: troycurtisjr.fedorapeople.org/python-scikit-build/python-scikit-build-0.16.3-1.fc38.src.rpm Description: Improved build system generator…

Issue Title State Comments Created Date Updated Date Closed Date Cannot import flax after installing while using TPU open 4 2022-11-12 2022-12-08 – Request new package `functorch` open 0 2022-11-02 2022-12-08 – pythreejs is installed, but widgets are not shown open 4 2022-10-30 2022-12-08 – Is it kaggle env issue…

Hello all,I have created a Linux cluster with ssh and NFS. I have installed lammps in the NFS folder. I have verified that the cluster works properly with openmpi and the communication is good. But when I run lammps, after reading the data file it gets stuck on the first…

[Buildroot] [PATCH] package/mbedtls: use pre-configure, not post-patch, hooks to configure * [Buildroot] [PATCH] package/mbedtls: use pre-configure, not post-patch, hooks to configure @ 2022-08-28 19:54 Yann E. MORIN 0 siblings, 0 replies; only message in thread From: Yann E. MORIN @ 2022-08-28 19:54 UTC (permalink / raw) To: buildroot; +Cc: Yann…

GROMACS version: 2021.2GROMACS modification: No Hello GROMACS users and developers. I have a demand to compile GROMACS 2021.2 with CP2K 9.1. Is this combination supported? If so, how to do it? I noticed that the cmake variables DGMX_CP2K, DCP2K_DIR and DCP2K_LINKER_FLAGS are available only in the 2022 version. And from…

Scientific SoftwareDevelopment InfrastructureRossen ApostolovKTH/[email protected] A use case:GROMACS GROMACS Project started 1995 in Groningen, most of the core developersare now in Sweden Highly tuned code for molecular dynamics, minimization, normalmode analysis; post-processing tools ( 100) Open source & Free software: L-GPL 3000-5000 users world wide, through [email protected] 300kactive CPUs, Apr. 2012…

Dear all, I am using LAMMPS to simulate some thermodynamic properties of b-SiGe. I found the potential file in the official github repository for LAMMPS . The first part of my code is this ############################################################### #1 general units metal dimension 3 atom_style atomic neighbor 0.3 bin #2 structure boundary p…

PRSice (pronounced ‘precise’) is a software package for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS). PRSice can run at high-resolution to provide the best-fit PRS as well as provide results calculated at broad P-value thresholds, illustrating results corresponding to either, can thin SNPs according to…

hi,i am working on jetson Xavier NX box,i updated to jetpack 5.0.1 and deepstream6.1 right now.before i setup ARCH= -gencode arch=compute 72 for NX to train some models.but i cmake another file yesterday it detected arch-gencode 75!so i am confuse right now, should i setup 72 or 75 for jetson…

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: beefy17.nyi.freebsd.org/data/main-i386-default/p429f3de9bdcd_s2573e6ced9/logs/cp2k-9.1.0.log Build URL: beefy17.nyi.freebsd.org/build.html?mastername=main-i386-default&build=p429f3de9bdcd_s2573e6ced9 Log: =>> Building science/cp2k build started at Sat Jun 4…

Good day to all,I am trying to apply Monte Carlo method within the intervals of MD simulation.Specifically, I am trying to write python code that could be invoked from lammps(or vice versa) so that I could add a new calculation method. To begin with, I am currently running Lammps on…

I am trying to install an external module to lammps called “USER-CONP2” for applying external electric field. I am installing using the traditional make approach instead of cmake. But while building lammps, I am getting the message fix_conq.cpp:63: undefined reference to `ddot_’ please tell me how I can link Lapack/Blas…

Source: opm-grid Version: 2021.10-3 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of opm-grid the autopkgtest of opm-grid fails in testing when that autopkgtest is run with the binary packages of opm-grid from unstable. It passes when run with only packages from testing. In tabular form:…

Goal Hi guys, is there an option to enable MBEDTLS debugging as with the CONFIG_MBEDTLS_DEBUG_LEVEL=4 for the MBEDTLS_BUILTIN? I am trying to setup a DTLS client based in order to establish a CoAP Secure Session via Openthread to a Borderrouter and I am struggling in the handshake process. It would…

LAMMPS Patch 24 March 2022 Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of…

. /path/to/gromacs/bin/GMXRC You used the actual installation path here, right? ╰─> [124 lines of output] We can’t help without the full output. Please copy the raw text from the terminal window. Note that you can format the terminal output in the forum post either by using the </> button or…

HTSlib Compiler/GCCcore/11.2.0 1.14 Description =========== A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix More information ================ – Homepage: www.htslib.org/ – Site contact: Support <sc@fz-juelich.de>, software installed by Alexandre Strube <a.strube@fz-juelich.de> EBROOTHTSLIB /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0 EBVERSIONHTSLIB 1.14 EBDEVELHTSLIB /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0/easybuild/Compiler-GCCcore-11.2.0-HTSlib-1.14-easybuild-devel +CMAKE_PREFIX_PATH /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0 +CPATH /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0/include +LD_LIBRARY_PATH /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0/lib…

I have a project using NCS v1.8.0 where I enabled openthread. For some reason, when trying to build `mbedtls/library/ecjpake.c`, the make command uses `-DMBEDTLS_CONFIG_FILE=”nrf-config.h”` and fails on: > nrf-config.h: No such file or directory I’m not sure why it tries to use this file because `MBEDTLS_CFG_FILE` is set to `config-tls-generic.h`….

Sign Up Log In Log In Popular FireworksFireWorks Using fix GCMC to plot adsorption isothermsLAMMPS General Discussion Topic of the Month: What are your favorite pre- and postprocessing toolsLAMMPS Why is My lattice size increasing during the initial NPT run for equilibrating Si diamond crystal?LAMMPS General Discussion About fix smdLAMMPS…

Please provide complete information as applicable to your setup. • Hardware Platform (Jetson / GPU) Jetson nano• DeepStream Version 6.00• JetPack Version (valid for Jetson only)• TensorRT Version• NVIDIA GPU Driver Version (valid for GPU only)• Issue Type( questions, new requirements, bugs)• How to reproduce the issue ? (This is…

Dear Irslan Ulalh Ashraf, Please reply to the mailing-list when asking for more help, not to me personally. Concerning your question it appears that a ‘liblammps.a’ library and ‘lmp’ executable are in your directory. Congrats! If you can execute it in the build directory you’re nearly there (typing ‘./lmp -h’…

Dear LAMMPS experts, I am trying to build lammps with cmake command with cmake3 by using this command line: cmake3 -C ../cmake/presets/most.cmake ../cmake It seemed that installation was successful according to the below report: — <<< Build configuration >>> Operating System: Linux CentOS Linux 7 Build type: RelWithDebInfo Install path:…

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

I want to use mbedtls for my stm32 projects, but I have some problems with building. I have to build mbedtls with arm-none-gcc compiler, right? My command is :(in build directory). CC=/home/jareeeeczek/Arczbit/Firmware/ProgramingRelated/ARM_GCC/gcc-arm-none-eabi-10-2020-q4-major/bin/arm-none-eabi-gcc CFLAGS=’-fstack-protector-strong’ cmake -DUSE_SHARED_MBEDTLS_LIBRARY=On ../ and I have error while compiling test program: none-eabi-10-2020-q4-major/bin/arm-none-eabi-gcc CFLAGS=’-fstack-protector-strong’ cmake – DUSE_SHARED_MBEDTLS_LIBRARY=On ../…

after making ubuntu in windows and installing the prerequisite commands ( sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip python3-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tool)I downloadedLAMMPS Patch Release 14 Dec 2021 From www.lammps.org/download.htmland after extracting, I put it on the desktop. Next I entered…

[Buildroot] [PATCH 1/2] package/mbedtls3: new package * [Buildroot] [PATCH 1/2] package/mbedtls3: new package @ 2021-12-28 15:33 Fabrice Fontaine 2021-12-28 15:33 ` [Buildroot] [PATCH 2/2] package/hiawatha: needs mbedtls3 Fabrice Fontaine 2021-12-28 15:49 ` [Buildroot] [PATCH 1/2] package/mbedtls3: new package Thomas Petazzoni 0 siblings, 2 replies; 5+ messages in thread From: Fabrice…

$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi (base) bash-4.2$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi [+] /opt/intel/cmake (external cmake-3.20.0-3teotjsa6webcsazofydfkk2v3pn2hb6) [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/alsa-lib-1.2.3.2-yctbppr2tcdayclbt32xjgagmmwbct2v [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/libiconv-1.16-ilxedtsoqggtmtbrjxehh6ojznmtdni3 [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/yasm-1.3.0-7y4fvxshqkmikii3cvelccaiajj4dboc [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/zlib-1.2.11-k24vg36ubsrvwfgrdipndmpqn4eo5jq7 ==>…

🐛 Describe the bug I am working on a constrained optimization problem using the augmented lagrange method. However, after calculating the first loss term in the optimization, I received the following error after trying to calculate the gradients with loss.backward(). /home/ihowell/Projects/validity/validity/generators/bern_vae.py:23: UserWarning: To copy construct from a tensor, it is…

TL;DR: Using a variation on Amazon’s “Herring” technique, which leverages reduction servers, we can perform the all-reduce collective faster than NCCL: up to 2x as fast as NCCL in microbenchmarks up to 50% speedup in end-to-end training workloads You can use it right away in your project, with no code…

jetson nano To configure pytorch and torchvision Environmental Science +tensorrt Model transformation +Deepstream Deploy yolov5（ Close test available ） Because a game came into contact with jetson nano, Need to use pycharm Train your own model plus yolov5 Target detection , And deployed to jetson nano On , It didn’t…

install pytorch in jetson nano Done! Getting Started with Jetson Nano In this tutorial, you will learn how to set up the NVIDIA ® Jetson ™ Nano and install everything you need to use the full power of the tiny embedded board. Git – Version Contol…

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: ampere2.nyi.freebsd.org/data/main-arm64-default/p7539e33f88ff_s169b368a62/logs/RStudio-2021.09.1+372.log Build URL: ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p7539e33f88ff_s169b368a62 Log: =>> Building devel/RStudio build started at Wed Dec 8…

Job:PhD Student Needed for Machine Learning (Deep Learning and Classical) in Molecular Biology 0 Several openings are available immediately (or as late as Fall 2022) Looking for a highly motivated PhD student for Computational Biology research, with an algorithm development focus. The Ecological and Evolutionary Signal-processing (EESI) and Informatics lab…