Tag: CMake

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…

If you are not very familiar with building software from source and using/editing makefiles (as it seems to be the case here), then we recommend to use the CMake based build procedure instead. It will autodetect and configure available features like JPEG or PNG libraries and MPI etc. That said,…

“Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.3.tar.gz (18 Aug 11:51, 37987972 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 but used also for e.g. polymers). Release of 2020 series….