#openmpi

[codingprolab]

CS 4000 Homework # 4: Phylogenies, Pandemics, and OpenMPI

This assignment is inspired by the recent global COVID-19 pandemic caused by the coronavirus SARS-CoV-2. The virus, while deadly, is a relatively simple organism that consists of an RNA sequence that is less than 30,000 characters long. We have already sequenced the genetic data that makes up the virus, along with many, many versions of it. You can get the data for variants from around the world…

[ankitcodinghub]

CSC718 - Homework 2 OpenMPI Programming Assignments Solved

The homework assignment will be graded based on the following criteria: • Accuracy: 1) the solution meets specific requirements in the problem description; 2) the solution produces correct results; 2) the procedures adopted in the solution are technically sound. • Efficiency: efficiency will be one of the criteria when grading programing assignment. The solution should produce the desired results…

[oldbookshop]

guys are any of you really good with a) working remotely on HPCs / computing clusters, specifically ones that use slurm job scheduling b) MPI / OpenMPI / PMI stuff

I keep getting this one error that nobody can figure out and i am at my wit's end here lol

[myprogrammingsolver]

Lab 6: Using OpenMPI to Estimate the Value of a Definite Integral using the Monte Carlo method

Objective: Use OpenMPI to estimate the value of a definite integral using the Monte Carlo method. How to use Monte Carlo simulation to estimate an integral: 1The Monte Carlo technique takes advantage of a theorem in probability that is whimsically called the Law of the Unconscious Statistician. The theorem is basically the chain rule for integrals. If is a continuous random variable and is a…

[cat-26]

i'm trying to compile my code on my computer and all the help forums are miles ahead of my skill level

like. i didn't write this code. i barely know how it works. i just need mpif90 to work so i can check out my oscillating airfoil :(

[774]

まず、ターミナルを立ち上げ ---------------------------- apt-get update （更新) ---------------------------- apt-get install openmpi-bin libopenmpi-lib (MPI本体の入手) ---------------------------- うまくインストールできているかを見るには、 例えば、 ---------------------------- mpiexec ---------------------------- などと打ってみるとよい。コマンドの使い方のヘルプページようなメッセージが出るはず。 mpieとうったくらいでタブキーを押して、補完されるはずである。 ---------------------------- mpicc または mpic++ ---------------------------- などでもよいかもしれない。こっちはメッセージが短い。

寄せ集めPCでクラスターを作る（第一回；システム構築） - #include"blog.h"

[zhengyj]

compile openmpi in Sierra

due to the bug of  gcc 7.1for mac osx, it prompts  such kind of error messages “error: ‘LOG_INFO’ undeclared” when compiling openmpi 3.0. But using clang and clang++ succeeded to compile openmpi in Sierra:

./configure --prefix=install_dir CC=clang CXX=clang++

make -j 4

make install

[insignificantdan-blog]

Is that more nodes for my #thincluster #supercomputer I think it is... 20 Wyse Cx0 #thinclients Yay!!!! #istillneedmore #timetowork #itwillwork #computersaremylife #computer #cluster #doingit #makeithappen #budget #builditwithwhatigot #brokeasscomputernerd #hireme #debian #cluster #openmpi #reuse #lowpower #ihaveacomputerproblem #cyclethatcpu #doinitforme #compute

[brishtiteveja-blog]

Message Passing using OpenMPI : Production and Consumption via Broker

Message Passing using OpenMPI : Production and Consumption via Broker

I am working on several assignments and through the problem solving process, I am learning OpenMPI. OpenMPI is a great library that gives you capability of using multiple CPUs in parallel. Think about you are given 100 random numbers which are not sorted. Normally you would write a sequential program where you will implement a O(nlogn) sorting algorithm like quick sort or merge sort to sort those…

[veworvt]

Python install gfortran

PYTHON INSTALL GFORTRAN INSTALL

PYTHON INSTALL GFORTRAN SIMULATOR

PYTHON INSTALL GFORTRAN DOWNLOAD

PYTHON INSTALL GFORTRAN FREE

Addition of path manually for Openmpi (Parallel Run).

If everything goes fine, then you should see the following message on running the command mpirun in the terminal : mpirun could not find anything to do Step –5: Setup environment path and test mpirun export PATH="$PATH:/home/user/.openmpi/bin"Įxport LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/" configure -prefix="/home/$sandeep/.openmpi" #sandeep is my username, change it accordingly# Step – 4: Configure the installation file, after entering the package folder by using:- cd openmpi #if your archive-name is openmpi# Or use these commands for extraction:- tar -xzf Step – 3: Extract the openmpi package and open the directory if you have problem in extraction, then go through this link

PYTHON INSTALL GFORTRAN DOWNLOAD

Step – 2 : Download the latest openmpi package from here

PYTHON INSTALL GFORTRAN INSTALL

Step – 1 : Install the basic dependency packages sudo apt-get install libibnetdisc-dev Install FFTW libraries:- sudo apt-get install libfftw3-devīefore installation of Openmpi, you have to install some dependencies manually, please go through these steps for installation Sudo apt-get install sqlite3 libsqlite3-devįor libpng use this command in your terminal: sudo apt-get install libpng-devĪfter these installations two important installations are required, Or sudo apt-get install make build-essential zlib1g-dev libbz2-dev libreadline-dev Sudo apt-get install python2.7 #for python 2.7# Or sudo add-apt-repository ppa:fkrull/deadsnakes Sudo apt-get install libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev If it is not installed in your system, then go for these commands:- sudo apt-get install build-essential checkinstall Install all necessary gcc and fortran compilersĬheck if python is already installed python -version.Change it according to your Linux operating system wherever it is required. Pre Installation Steps:- These installation steps are for Ubuntu/ kubuntu.

PYTHON INSTALL GFORTRAN SIMULATOR

It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, mesoscale, or continuum scale.” LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code.“LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems.

PYTHON INSTALL GFORTRAN FREE

Instead of the $1000 Aerospace Toolbox, use this free IGRF12 for Matlab.Lammps Installation For Parallel Run in Linux Matlab can seamlessly call Python modules, as in igrf12.m. The IGRF model may be specified with the igrf12.igrf(model=) option: Using as a Python module at geodetic coordinates 65N, 148W: import igrf12 mag = igrf12. py build_ext -inplace -compiler = mingw32 Example If you get ImportError on Windows for the Fortran module, try from the iri2016 directory: del *. Optionally, test the install with: pytest Otherwise, for the latest release from PyPi: python -m pip install igrf12 To get the IGRF12 development version, git clone and then: python -m pip install -e. Windows only: from Powershell: echo " `n compiler=mingw32" | Out-File -Encoding ASCII ~/ pydistutils. International Geomagnetic Reference Field IGRF12 and IGRF11.in simple, object-oriented Python ≥ 3.6 or Matlab.Ī Fortran compiler is required, such as gfortran:

[kwvewor]

Brew install openmp

#BREW INSTALL OPENMP HOW TO#

#BREW INSTALL OPENMP INSTALL#

This command forces Homebrew to build OpenMPI from source with the gcc-6 compiler.

#BREW INSTALL OPENMP INSTALL#

To build OpenMPI, type in the following command $ brew install openmpi -build-from-source -cc=gcc-6 If you installed the binary distribution, it’s compiled with clang without any OpenMP support. Here we also want to build it from source because then our MPI compiler is using the gcc we built just now with OpenMP support. Therefore, there are several MPI implementations, such as MPICH, OpenMPI, and Intel MPI. After you installed it, you should be able to compile programs with OpenMP support with gcc-6 -fopenmp If you have installed gcc before on your Mac using Homebrew, then reinstall it with the following command $ brew reinstall gcc -without-multilibĪccording to my experience, it takes about half an hour to one hour to build gcc since it’s quite a large piece of program.

#BREW INSTALL OPENMP HOW TO#

This helped me finally figure out how to install R from source with the capabilities I desired. To do that, type in the following command $ brew install gcc -without-multilib Install R 100 Homebrew Edition With OpenBlas & OpenMP My Version Luis Puerto ALazaro 2 years ago Thank you for this awesome guide It helped me to get running R with OpenMP in my Mac livelaughriley 2 years ago Hey, thanks for this post. We’ll use Homebrew to build the GNU Compiler Collection (GCC) on our Mac from source, with OpenMP support. We also take this opportunity to install pkg-config. Therefore, what we need to do is to compile a compiler with OpenMP support. Open up a Terminal and use Homebrew to install OpenMP support for the clang compiler that comes by default with Yosemite. One thing you should know is that OpenMP is not really a package that you install on your computer. Remember to run brew update before you continue. It’s very easy to install, just go to their website and follow the steps. /configure -t openmp -p /blis auto make -j8 make check -j8 make install Use Homebrew to install the gcc compiler: brew install. It is in some way similar to package managers in Linux distributions, such as apt-get and yum. Make sure you have Homebrew installed on your Mac.

[ankitcodinghub]

ECE 4122/6122 Lab 6: Using OpenMPI to Estimate the Value of a Definite Integral using the Monte Carlo method Solved

(100 pts) Category: OpenMPI Objective: Use OpenMPI to estimate the value of a definite integral using the Monte Carlo method. How to use Monte Carlo simulation to estimate an integral: The Monte Carlo technique takes advantage of a theorem in probability that is whimsically called the Law of the Unconscious Statistician. The theorem is basically the chain rule for integrals. If 𝑋𝑋 is a continuous…

[homeworkdave]

High-Performance Computing Lab 1

High-Performance Computing Lab 1

COSC 420 – High-Performance Computing Lab 1 1 Objectives In this lab you will focus on the following objectives: 1. Develop familiarity with C programming language 2. Develop familiarity with parallel computing tool OpenMPI 3. Explore empirical tests for program efficiency in terms of parallel computation and resources 2 Tasks 1. You may work in groups of one or two to complete this lab. Be sure…

[okura-anything]

openmpi + fortran なプログラムをある程度は快適に読み書きできる環境を Docker を用いて構築した

必要なもの

vscode docker

使い方

1 後ほど紹介するファイル群を一つのディレクトリにまとめる。 2 vscode の remote container で開く。

ディレクトリ構成

$ tree -al . ├── .devcontainer │   ├── devcontainer.json │   └── docker-compose.yml ├── Dockerfile └── docker-compose.yaml

それぞれのファイルについて

.devcontainer/devcontainer.json

// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at: // https://github.com/microsoft/vscode-dev-containers/tree/v0.224.3/containers/docker-existing-docker-compose // If you want to run as a non-root user in the container, see .devcontainer/docker-compose.yml. { "name": "Existing Docker Compose (Extend)", // Update the 'dockerComposeFile' list if you have more compose files or use different names. // The .devcontainer/docker-compose.yml file contains any overrides you need/want to make. "dockerComposeFile": [ "../docker-compose.yaml", "docker-compose.yml" ], // The 'service' property is the name of the service for the container that VS Code should // use. Update this value and .devcontainer/docker-compose.yml to the real service name. "service": "fortran", // The optional 'workspaceFolder' property is the path VS Code should open by default when // connected. This is typically a file mount in .devcontainer/docker-compose.yml "workspaceFolder": "/workspace", // Set *default* container specific settings.json values on container create. "settings": { "code-runner.clearPreviousOutput": true, "code-runner.saveFileBeforeRun": true, "code-runner.runInTerminal": true, "terminal.integrated.fontSize": 18, "code-runner.executorMap": { // 👇 is for normal fortran // "FortranFreeForm": "cd $dir && gfortran $fileName -o $fileNameWithoutExt && $dir$fileNameWithoutExt", // "fortran_fixed-form": "cd $dir && gfortran $fileName -o $fileNameWithoutExt && $dir$fileNameWithoutExt", // 👇 is for openmpi fortran "FortranFreeForm": "cd $dir && mpif90 $fileName -o $fileNameWithoutExt && mpirun -np 4 --allow-run-as-root $dir$fileNameWithoutExt", "fortran_fixed-form": "cd $dir && mpif90 $fileName -o $fileNameWithoutExt && mpirun -np 4 --allow-run-as-root $dir$fileNameWithoutExt", }, "fortran.gfortranExecutable": "/usr/bin/gfortran", "fortran-ls.executablePath": "/usr/local/bin/fortls", "fortran.formatting.formatter": "findent", }, // Add the IDs of extensions you want installed when the container is created. "extensions": [ "krvajalm.linter-gfortran", "formulahendry.code-runner", "hansec.fortran-ls", ] // Use 'forwardPorts' to make a list of ports inside the container available locally. // "forwardPorts": [], // Uncomment the next line if you want start specific services in your Docker Compose config. // "runServices": [], // Uncomment the next line if you want to keep your containers running after VS Code shuts down. // "shutdownAction": "none", // Uncomment the next line to run commands after the container is created - for example installing curl. // "postCreateCommand": "apt-get update && apt-get install -y curl", // Uncomment to connect as a non-root user if you've added one. See https://aka.ms/vscode-remote/containers/non-root. // "remoteUser": "vscode" }

.devcontainer/docker-compose.yml

version: '3' services: # Update this to the name of the service you want to work with in your docker-compose.yml file fortran: # If you want add a non-root user to your Dockerfile, you can use the "remoteUser" # property in devcontainer.json to cause VS Code its sub-processes (terminals, tasks, # debugging) to execute as the user. Uncomment the next line if you want the entire # container to run as this user instead. Note that, on Linux, you may need to # ensure the UID and GID of the container user you create matches your local user. # See https://aka.ms/vscode-remote/containers/non-root for details. # # user: vscode # Uncomment if you want to override the service's Dockerfile to one in the .devcontainer # folder. Note that the path of the Dockerfile and context is relative to the *primary* # docker-compose.yml file (the first in the devcontainer.json "dockerComposeFile" # array). The sample below assumes your primary file is in the root of your project. # # build: # context: . # dockerfile: .devcontainer/Dockerfile volumes: # Update this to wherever you want VS Code to mount the folder of your project - .:/workspace:cached # Uncomment the next line to use Docker from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker-compose for details. # - /var/run/docker.sock:/var/run/docker.sock # Uncomment the next four lines if you will use a ptrace-based debugger like C++, Go, and Rust. # cap_add: # - SYS_PTRACE # security_opt: # - seccomp:unconfined # Overrides default command so things don't shut down after the process ends. command: /bin/sh -c "while sleep 1000; do :; done"

Dockerfile

FROM python:slim-bullseye RUN apt-get update && \ apt-get install -y --no-install-recommends \ build-essential=12.9 \ gfortran=4:10.2.1-1 \ openmpi-bin=4.1.0-10 \ openmpi-common=4.1.0-10 \ openmpi-doc=4.1.0-10 \ libopenmpi-dev=4.1.0-10 && \ pip install fortran-language-server==1.12.0 findent==4.2.0 && \ apt-get clean && \ rm -rf /var/lib/apt/lists/*

docker-compose.yaml

version: '3' services: fortran: restart: always build: . container_name: 'fortran' working_dir: '/root/src' tty: true volumes: - ./:/root/src command: "bash"

感想

個人的にはfortranを読みたい・書きたいなどの動機は全くないのですが、研究の都合上必要となってしまったので、このような環境を整えて、気の進まないタスクは始末したいです。

[evoldir]

Fwd: Job: Washington.MachineLearningEvolution

Begin forwarded message: > From: evoldir@web.rhpcs.mcmaster.ca > Subject: Job: Washington.MachineLearningEvolution > Date: 18 November 2021 at 05:19:18 GMT > To: rdmpage@gmail.com > > > Hello EvolDir Members: > > Hiring Now: NSF-funded Consultant or Postdoctoral Fellow (1 year, with > potential for extension), Washington, D.C., USA; remote work space > possible > > Project title: NSF Convergence Accelerator Track E: Innovative seafood > traceability network for sustainable use, improved market access, and > enhanced blue economy > > Project Overview: This proposal will build a cross-cutting traceability > network to accelerate the path towards accurate and inclusive monitoring > and management of marine bioresources, whose sustainability is vital to > feed the global population. Leveraging wide-ranging expertise in fisheries > science, marine biology, environmental anthropology, computer science, > trade policy, and the fisheries industry, we will develop a powerful > tool to achieve long-lasting & transferable solutions. Addressing the > global challenge of feeding the human population will require the ocean > as a solution. > > This NSF Convergence Accelerator project will: > > 1.Develop a prototype traceability tool that allows affordable > identification of species and area of capture for wild octopus fisheries > within the United States and abroad using our proposed machine learning > (ML) model “SeaTraceBlueNet” trained on legacy data of environmental > metadata, species occurrence and images; > > 2.Develop a community-based citizen-science network (fishers, researchers, > industry partners, students, etc.) to gather new data (images, metadata > and environmental DNA (eDNA)), train on and test the portable eDNA > kits and SeaTraceBlueNet dashboard prototype to build the collaborative > capacity to establish a standardized traceability system; and, > > 3.Set a system in place to connect traceability, sustainability and > legality to support the development of a blue economy around the octopus > value chain, incorporating the best practices and existing standards > from stakeholders. > > > Background and skills sought: > > Expertise (5+ years of combined work and/or academic experience) > preferably in one of the following fields: Bioinformatics, Machine > Learning, Computer Sciences, Biological Sciences, Molecular Biology Note: > PhD is not required, as long as applicant shows demonstrated abilities > in the following. > > Experience required: Software: Agile software i.e., Jira, GitHub, > Anaconda, pyCharm, Jupyter notebooks, OpenCV Must have languages: Python, > SQL, bash scripting, linux command-line Optional: C++, R, Spark, Hive > > Programming environments and infrastructure: Cloud, HPC, Linux, Windows > Familiar with Machine learning platform and libraries such as, TensorFlow, > PyTorch, Caffe, Keras, Scikit-learn, scipy, etc.  Implementing computer > vision models such as ResNet, Deep learning models using Recurrent > Neural Networks (CNNs, LSTMs, DNNs), using Support Vector Machines > (SVMs) models, probabilistic and un/regression models, data processing > and handling activities including data wrangling, computer vision. > > Bonus skills: Using BERT NLP models, computer software like OpenVino, > targeting GPUs, familiarity with GCP tools and applications, > such as BigTable, cloudSQL, DataFlow, CloudML, DataProc, etc., > dashboard development and implementation, Compiling and configuring HPC > environments, developing applications using MPI, OpenMPI, pyMIC, using job > schedulers such as PBS, Scrum; Bioinformatics tools such as BLAST, Qiime2 > > Job Physical Location: Washington, D.C. USA; remote work station is > an option. > > Compensation: $65,000 (annual) with benefits, and some travel > > Although, US citizenship is not required, proper work status in the USA > is required. Unfortunately, we cannot sponsor a visa at this time. > > Expected start date: November/December 2021 (up to 12 months depending > on start date) > > Application Deadline: Applications will be reviewed and interviews > will take place on a rolling basis until the position is filled. > Application submission process: Please send the following documents via > email to Demian A. Willette, Loyola Marymount University (demian.willette > @ lmu.edu). > > 1.Curriculum Vitae: Including all relevant professional and academic > experience; contracts, collaborations, on-going projects, grants > funded, list of publications (URLs provided), presentations, workshops, > classes; Machine Learning and bioinformatics skills and languages; > Gitbub/bitbucket; any experience with processing molecular sequence data > (genomics and/or metabarcoding) > > 2.Reference contacts: Names, affiliations and contact information (email, > phone) for up to three professional references that we will contact in > the event that your application leads to an interview. > > 3.Transcripts: Transcript showing date of completion of your most relevant > degree(s) and grades. > > Please send all inquiries to: Demian A. Willette, Loyola Marymount > University (demian.willette @ lmu.edu) > > > Cheryl Ames > via IFTTT

[felord]

EE451 Homework4-  Pass Message in a Ring Solved

EE451 Homework4-  Pass Message in a Ring Solved

Examples The “mpi examples” folder includes the source codes used in discussions and a pbs file ‘queue.pbs ’. To run an mpi program, for example, the ‘scatter.c’, follow the steps: login hpc-login3.usc.edu source /usr/usc/openmpi/default/setup.sh Go to your working directory which has ‘job.sl’ and ‘scatter.c’. mpicc -o go scatter.c sbatch job.sl After you get the email saying your job is…