My first MOOSE simulation

MOOSE is a tool that allows the use of many physics and maths libraries to run simulations of finite elements of any shape, including unstructured meshes.

My purpose is to run simulations in parallel. My laptop that already is using Fedora 32, has four cores to process calculations.

According to the official MOOSE Website, we can install MOOSE using Conda.

1. In case you already have installed Conda, and its configuration; please go to the step 3.

You might install conda on Linux, by executing the following command:

curl -L -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3

2. Then, please set the global environment in our system to use conda:

export PATH=$HOME/miniconda3/bin:$PATH

3. Let’s add the channel conda-forge that will allow us to create the moose environment:

conda config --add channels conda-forge
conda config --add channels https://mooseframework.org/conda/moose
conda create --name moose moose-libmesh moose-tools

4. You need to activate the new moose env to use it. Do an update if it is possible:

conda activate moose
conda update --all

5. Clone the moose code and the examples provided in the new moose environment:

mkdir ~/projects
cd ~/projects
git clone https://github.com/idaholab/moose.git
cd moose
git checkout master

6. You can run the project in parallel, in this case we are using only four cores:

cd ~/projects/moose/test
make -j 4
./run_tests -j 4

If everything is a success, a message that the passed tests done in parallel, is displayed:Now, were are ready to run our first MOOSE program. I followed this workshop

cd ~/projects/moose/tutorials/darcy_thermo_mech/step01_diffusion
make -j 4 # use number of processors for your system
cd problems
../darcy_thermo_mech-opt -i step1.i

Remember to copy the content of sept1.i, and execute the output with Peacock, as follows:

~/projects/moose/python/peacock/peacock -r step1_out.e

Now, we have our simulation in action 🙂Thanks to my friend Manuel Merino for his support during my new age as a scientist.

Posted in τεχνολογια :: Technology | Tagged , , , , , , , , , | Leave a comment

Dolfin on Podman

Since Docker is not useful on Fedora 32 anymore, I decided to install podman in order to use the dolphin (previously called fenics) to run some solutions of PDEs.

Install podman on Fedora 32. If you want further information of podman, click here.

sudo dnf install -y podman

You might check that you are running podman by executing the ps command. This process might take a while. It is a new environment that use Fedora 32 resources.

[yulytas@fedora ~]$ podman ps -s
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES SIZE
[yulytas@fedora ~]$

Now, we are going to create a folder where all the dolfin work will be stored in our laptop:

sudo mkdir ~/dolfin

From the file recently created, we can access interactively to the container register in quay.io/fenicsproject/stable:current. This will happen by using the port 8000 and mounting the work space /home/fenics/shared into my local folder ~/dolfin, as follows:

cd ~/dolfin && podman run -ti -p 8000:8000 -v ~/dolfin:/home/fenics/shared -w /home/fenics/shared quay.io/fenicsproject/stable:current

repofenics

*** If everything goes well, you will see the following message displayed ***

# FEniCS stable version image

Welcome to FEniCS/stable!

This image provides a full-featured and optimized build of the stable
release of FEniCS.

To help you get started this image contains a number of demo
programs. Explore the demos by entering the 'demo' directory, for
example:

cd ~/demo/python/documented/poisson
python3 demo_poisson.py

What I am going to do from now on is, calculate the PDEs using dolfin (fenics), and then copy the results to /home/fenics/shared which is linked automatically to my local /dolfin.

Thanks to Dan for the explanation about containers.

Posted in τεχνολογια :: Technology | Tagged , , , , , , , , | Leave a comment

Jupyter Notebook on Fedora 32

Hello world, I am back again to science… and this time I will program PDEs using Python!

Firstly, we need to download the Anaconda package, in my case for Linux and python 3.xCopy the package downloaded to the path for out installation and execute the script:

bash Anaconda3-2020.02-Linux-x86_64.sh

Press yes if you accept running the installer to initialize, as follows:

To reload the modification of the bashrc file, we need to execute the source command:

source ~/.bashrc

To navigate on Anaconda applications like Jupyter Notebook, you might run on terminal:

anaconda-navigator

Finally you can launch Jupyter which will be work locally as you can see:Check out into your browser to see the tree of files presented by Jupyter. I am going to create a folder called FEniCS to run some PDEs programs. Then, locate into the new created folder, and click on New > Notebook: Python3To execute your code, press SHIFT + ENTER

Posted in τεχνολογια :: Technology | Tagged , , , , , , , , , , | Leave a comment

Tuning my Fedora 32 after installation

There are plenty of articles online related to this topic, but I will share my own humble basic experience to set up an environment as a developer.

First of all, the size of the fonts on the system is (in my eyes) too small. I have a myopia, then I need to large the fonts. One way to do it is by the modifying the setting of the system, in the Universal Access option: In the same settings menu, you might choose other features to tune according to your necessities.

Another crucial change that Fedora has to do is updating the Firmware. In my case, it was done automatically after Turn off and Turn on again. I did this instead of Reset because it got many issues such as not turn it on again.In case you do not see that happening automatically, I strongly suggest that you do it automatically, by using the Software Manager application, as this:Additionally, you can setup the power battery management to increase the life of the battery of your laptop, by executing these commands:

sudo dnf -y install tlp tlp-rdw
sudo systemctl enable tlp.service
sudo systemctl restart tlp

Finally, to install an IDE to code in C++, it was decided to use Flathub to avoid dependency issues that I might have in the way of the installation.Good luck! Any suggestion for improvement or comment is welcomed!

Posted in FEDORA, τεχνολογια :: Technology | Tagged , , , , , , | Leave a comment

Upgrading Fedora 31 to Fedora 32

Why do we upgrade Fedora each year?

Since 2003, Fedora contributors around the world have been working on improvements in favour of this free software. The support of each developed version can last for a year, then it is important to do an upgrade to get t. Nowadays the Fedora project has released the Fedora 32 version, and by upgrading my Fedora 31, I can get also the new improvements for GNOME ❤︎

Upgrading using GUI methods

In case you are not familiar with the Command Line Interface (CLI), then you can click on the Software option to do the Upgrade as it follows:Upgrading using CLI methods

According to the Official Fedora documentation, we can follow these steps:

sudo dnf upgrade --refresh 
sudo dnf install dnf-plugin-system-upgrade
sudo dnf system-upgrade download --releasever=32
sudo dnf system-upgrade reboot

Some screen-shots of the upgrading process in my laptop:Finally, I got Fedora 32 and GNOME 3.36.2:Alternative with one line:

This process took me a while… if you are reading this post and you just installed the Fedora 31 with no much data in your laptop, you might try the upgrading with only one line:

sudo dnf -y --releasever=32 --setopt deltarpm=false distro-sync

#stayHome #staySafe #stayEducated

Posted in FEDORA, GNOME, τεχνολογια :: Technology | Tagged , , , , , , , , , , , | Leave a comment

Installing Fedora 31 on Windows 10 using MacOS Catalina

This installation has been done on a Dell 7400 laptop…

On the MacOS

It was downloaded Fedora 31 ISO , and a USB was inserted. Then, open a terminal to use the command diskutil list which will display the current disks:

We can identify that my USB is represented by the /dev/disk2 file, and it has 4 GB. This file will be unmounted to delete any instance attached to the USB.

Now, with the help of the command dd, we will copy the standard input (the Fedora ISO) to the standard output (my USB). This might take several minutes.You might now remove safely the USB flash drive as it follows:

Life is not too short to do it…

On Windows 10

Insert the bootable USB flash drive you have created in the MacOS. Then, Restart the Windows 10’s laptop, and press F2 to enter the UEFI settings.

Due to the restrictions that the new DELL 7400 presents, we need to disable some options such as Secure Boot option to boot from our USB stick:The Advance Boot Options has to be Enable in order to read the USB content.Finally, the Boot Sequence has to present as our first option: the USB Disk.Click on APPLY after setting the changes to save the new configuration.

Restart again, and this time press F12 to choose the USB Disk option:A list of options to run Fedora 31 will appear. You might test it first to see how does it work. We are going to install on disk, then select Start Fedora-Workstation-Live-31:

On our Fedora 31

Click on Install to Hard Drive

Select the language you prefer. I will chose English (United Kingdom):Configure these three basic options on Fedora 31 according to your resources:In my case, I usually write in English UK, English USA, and Spanish. Select the appropriate timezone, in my case I will choose London – UK: If you want to use the whole Hard Disk, then click on the Disk icon, then Done.

In case you need to set a password to encrypt the disk, you might check on Encrypt my data option. This option will appear after Restarting.To use all the space for the hard disk, I will Reclaim space and Delete all.Finally, click on Begin Installation to start the installation on disk:Now you have Fedora 31! :gratula:

* Now you can install basic packages on your laptop following this script.

Posted in FEDORA, GNOME, τεχνολογια :: Technology | Tagged , , , , , , , , , | 1 Comment

Report of GNOME PERU FEST 2020

1. Before the event

A. Coordination

a) The speakers 

The idea was gathering all the Peruvian GNOME lovers to share our experiences with GNOME throughout all the past ten years to all our viewers around the world.

Jose Quiñones (juazisco) is currently a chief in the IT area of the Health Public sector in Peru. He has been previously involved in the initiative GNOME PERU Challenge 2017-1

Fabian Orccón (cfoch) is a member of the GNOME Foundation, GSoC mentor and ex-GSoC student. He also supported GNOME Peru events such as HACKCAMP 2016.

Martin Vuelta (zodiafireworks) is a FLOSS enthusiastic person who helped me in organizing previous GNOME events such as Linux Playa,  LinuxAtUNI and PeruRumboGSoC2018.

Alex Aragón (aragcar) has been a designer for many FLOSS events I have organized for years. He participated in the LinuxCamp2012. One of the first designs he did here.

Fiorella Effio (aweba) is a Frontend developer who has also participated in several GNOME events in Peru since 2016. She wrote most of her experiences with GNOME here.

Angelou Alexander (aggalex) is a student from Greece, and our only international guest. We have met in the GUADEC 2019 and we did together a workshop at FOSSCOMM 2019.

  • We had two previous meetings before the event online as you can see in the pictures:

B. Advertising 

First of all, the GNOME marketing team was informed, as well as the GNOME members through the GNOME Planet. I also documented this event in the wiki.

The event was promoted using the fan page from GNOME PERU FEST, Linux at UNI and in the fan page of Fedora Peru.

Special thanks to Maricielo Isabel Vergara Lao who designed the poster for the event.

C. Setting up the technology 

We basically did a streaming on Facebook using OBS and Jitsi to present GNOME 3.36.

2. During the event 

As it was planned, the streaming started at 9am (Peruvian time). The speakers and myself were ready on time for the transmission. However, we only saw a few of people connected. This is understandable due to time difference between UK and other parts of the world. During this quarantine time, people usually sleep late, and might wake up late to prepare their brunch around 11 am… Anyway, we officially started 9:30 a.m. (Peruvian time).Our transmission lasted around 5 hours as it was planned. Thank to all the speakers that were connected the five hours in a raw. Fiorella Effio had prepared her GNOME on Ubuntu, but she did not do a presentation due to a technical issue. We had very few views online ranging from 9 to 25 people. Some of them expressed interested in joining GNOME.In the UK, the event started in the afternoon and it finished at night time. I was so glad to arrange my first online event. Special thanks to Angelou for his kind help. Greece has two hours ahead UK, but Angelou was always there for the meetings with our team.This quarantine time made me change the format of the GNOME parties I use to organize. We have celebrated the new version 3.36.1 with the usual balloons and selfies. I used cereals instead of a consistent cake.

3. After the event 

Overall, I am satisfied and happy that new people showed interest in the GNOME project. The streaming has reached so far more than 6,500 people, and more than 1,700 views.

You are so welcomed to see our event here!

Thanks to all the world! #stayHome #staySafe #stayEducated

Posted in FEDORA, GNOME, τεχνολογια :: Technology | Tagged , , , , , , , , , , , , , | 2 Comments