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Showing posts with the label Tips and tricks

Quick PBS Commands for GEOframe Simulations

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In these days, I have had the need to run several jobs on a High-Performance Computing (HPC) system. Specifically, I wanted to perform multiple kriging simulations with the GEOFrame hydrological modeling system. GEOFrame already supports parallel processing, so each job can perform multiple simulations simultaneously using a topology file—typically synthetic to avoid unnecessary waits at leaf nodes. To further accelerate the workflow, I split my topology into multiple files and submitted each as part of an array job. Below, I share some useful commands, starting with the PBS file for submitting array jobs. Each simulation file is named grap${PBS_ARRAY_INDEX} , where ${PBS_ARRAY_INDEX} varies from 1 to 90. PBS Array Job Submission Example: #!/bin/bash #PBS -l select=1:ncpus=20:mem=30GB #PBS -N kriging_array_1 #PBS -m abe #PBS -M my_mail@mail.com #PBS -l walltime=03:00:00 #PBS -J 1-90 #PBS -q myQueue module load jdk-11.0.1 cd /home/daniele.andreis/articolo_kriging/ SIM...

How I Keep My Research Papers and Bibliography Organized

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Keeping your paper library well-organized is essential for finding the right document at the right time. A good organization system helps you stay focused on your research, save time, and improve productivity. Over the years, I have experimented with several digital tools for managing bibliographies and taking notes. I’ve read blogs, watched tutorials, and incorporated advice from others, adapting these methods to fit my personal workflow. My requirements are quite common: organizing papers, taking notes, and accessing them seamlessly across devices such as my laptop and tablet. There are many sources for discovering research papers: recommendations from supervisors, references within papers I’ve read, and social media posts about new studies—both on general platforms like X (formerly Twitter) and research-specific networks like ResearchGate. This results in a massive collection of interesting papers to read and organize. My primary tools are Zotero and Notion. I followed Holl...

How I Organize Myself: From Bullet Journal to Notion

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Organizing my daily tasks and long-term goals is essential as I balance my work, PhD research, personal growth, and leisure time. Over time, I've developed a system that blends analog and digital tools to keep everything in order. Here's an overview of how I use these tools and resources to manage work, track habits, and pursue new interests. Although the system can be a bit complex, it works for me, and I regularly try to update and improve the steps. Bullet Journal for Daily Planning and Habit Tracking My bullet journal is the heart of my organization. I track daily tasks, important thoughts, and monitor new habits. I started using this method after reading The Bullet Journal Method by Ryder Carroll [2] , which serves as the foundation for my approach. I adapt the method to suit my needs. For example, I don’t use it for appointments or general note-taking—only for specific to-dos and habit tracking. My structure includes: Index: This is the ...

On the smartphone GPS accuracy

 As i started playing around Android programming, as soon I got the grip on the basic, I had go deep into "localization". So I had read a lot of manual pages, web pages and post about it. My first step was to create a class which allow me to select the best location provider, in several study case. So my mainly choice parameter were the requested accuracy, the  status of the battery, and if I get the passive data then the age of the Location Object. Two fact drawing my attention: the passive provider , and the improve of precision of coordinates when the wi-fi was turned on. So I have investigate how it was work, and I found several blog article or post [2], which explain how it work, and support it by example on how happen when people relocate  without changes ("relocate") theirs  their's wi-fi hot spot: a catastrophic lack in accuracy of the Location. However in the last days I have had some spare time so I have tried to better understand the accurac...

My first plot with xkcd

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  xkcd R package is a tool to enhance the R plot. Usually, I use ggplot2 to build my plot, but I wanted to create "more informal" plot so I found this library [2]. 1) Install the extrafont e xkcd and sysfonts packages (I have had some problem with update packages, so before I have run update.packages(checkBuilt = TRUE, ask = FALSE) And then install xkcd from R repository and extrafont from downloaded code. The sysfonts required to install free-type (sudo apt-get install freetype*)  2) Install fonts from http://simonsoftware.se/other/xkcd.ttf within the R console library(ggplot2) library(extrafont)  if(! "xkcd" %in% fonts()) { xkcdFontURL <- "http://simonsoftware.se/other/xkcd.ttf" download.file(xkcdFontURL,dest="xkcd.ttf") font_import(".")  ## because we downloaded to working directory loadfonts() } 3) Install ggplot (In R) library(ggplot2) library(xkcd) library(extrafont) library(lubridate) wind<- r...