Ilyass's books

The Perfect Theory: A Century of Geniuses and the Battle over General Relativity
Martian Dawn and Other Novels
The Android's Dream
An Unwelcome Quest
A Calculated Life
Spell or High Water
Off to Be the Wizard
Brave New World Revisited
Tartarin De Tarascon
Star-Dust
Startup Growth Engines: Case Studies of How Today's Most Successful Startups Unlock Extraordinary Growth
The 7 Day Startup: You Don't Learn Until You Launch
Have Space Suit—Will Travel
Calculating God
Stuff Matters: Exploring the Marvelous Materials That Shape Our Man-Made World
Spin
Vortex
The Formula: How Algorithms Solve all our Problems … and Create More
What If?: Serious Scientific Answers to Absurd Hypothetical Questions
The Twilight Zone: The Original Stories


Ilyass's favorite books »

In a \documentclass{article} Latex document, the \usepackage{cite} will automatically compact your citations from [1, 2, 3, 4] to [1-4] for example (check here to learn more about it).

Now if you are using the \documentclass{elsarticle} to send your manuscript to an Elsevier journal, the previous solution does not work. The reason is that the elsarticle.cls class document is designed to work with natbib which uses the cite command and creates a conflict with \usepackage{cite}. A solution to get your compacted citations to work without \usepackage{cite} is provided in the elsarticle class documentation, add the following line before the document’s end:

\biboptions{sort&compress}

PS: I tested everything with bibtex.

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Formatting

Press the up arrow to edit your last message, then press Enter.

  • Bold: *text*

  • Italics: _text_

  • ~Strikethrough~: ~text~

  • Verbatim: insert the text in-between ` marks

Channels

You can mute any channel to stop getting notifications by typing /mute in the channel. Use it for channels that you only check from time to time. You will still be notified if someone directly mentions you.

You can leave a channel by typing /leave in the channel.

You can invite anyone to a channel simply by typing their username in that channel. You must then click on Invite.

Use the Do Not Disturb mode if you do not want to be disturbed at all for some time. Simply type /dnd 1 hour and you will not be bothered for the next hour.

To send a notification to all users in a channel, use @channel in your message. To send a notification to a specific user use @username. Use @here to send a notification to the presently active users in a channel (anyone using DND or absent will not be notified). Use @everyone to send a notification to every member of the team.

Set reminders

Get started with: /remind help

Typical usage: /remind me to Call Tamir next Thursday at 3PM

You will receive a reminder at Thursday 3PM that you can either mark as completed, or ask Slackbot to remind you again some other time. You can setup reminders for anyone in the same Slack team using their username instead of me. You will be noitifed by SlackBot once that person marks the reminder as complete.

Check you existing reminders by typing: /remind list

Other examples:

/remind me to drink water at 3pm every day
/remind @jessica about the interview in 3 hours

Tiny database

It is possible to setup custom SlackBot answers. These answers are triggered by specific keywords or sentences. Its most common usage is for the Wifi password. If a message contains both words wifi and password or key, then SlackBot should provide the WiFi key.

It can be used as electronic post-its to remember things…

Integrations or apps

A large number of apps or integrations are available for Slack. An integration either adds functionality to Slack or plugs it to other services. The most common integration to expand functionality is Giphy; once installed, it is possible to type @giphy [text] in any channel to display a gif related to the [text] written.

Slack can also be connected to Github and Trello for example. In that case, any update in a Github repo will appear in a certain channel. Other users can immediately react and discuss the update, wether it is a Github update, a Trello one, Google Drive, etc…

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Thanks to Patrick Diehl, I have been working at the Bonn University, more precisely at the Institut für Numerische Simulation in order to develop some new tools to better explore some of my experimental results through the Peridynamics framework (writing it in italics because I am still not sure that it is what we are actually doing, welcome to Research). While I am there, Patrick guided me installing Peridigm on my machine. In this blogpost, I will re-write the steps to do so in such a way that it is clear even for someone who is not familiar with the Linux environment. If you are pretty familiar with the Linux environment, you should head toward Patrick’s blogpost, which is more for experienced users.

First, you need a Virtual machine sfotware if you are on Windows, then grab the image of Fedora 23. Create a new Virtual Machine and install Fedora on the VM.

Once your machine is installed and working, you need to install a few packages. To do so, open a terminal and type:

sudo dnf install mpich-devel mpich netcdf-mpich-devel netcdf-mpich hdf5-mpich-devel hdf5-mpich netcdf-fortran-mpich-devel boost-mpich-devel boost-mpich blas-devel blas lapack-devel lapack gcc-c++

DNF is the equivalent of apt-get from Ubuntu in Fedora.

You will also need to get a group of softwares. This is a great feature of DNF which will get and install a bunch of packages necessary for a certain field or usage, in this case, you will need to:

sudo dnf  groupinstall "X Software Development"

Once you have the necessary packages, you will need to get an compile Trilinos on your machine. This guide considers that you are using Trilinos 12.6.2, you can get it here. Unpack Trilinos on your machine, and use the terminal to enter the unpacked folder. We are going to create a build folder inside it in order to compile it properly.

mkdir build && cd build

We will then need to load the previously installed mpich package, which is necessary for multiprocessor computations. We need it to compile Trilinos:

module load mpi/mpich-x86_64

Now, let’s create an empty text file in the previously created build folder and paste a list of instruction for the C compiler, explaining how it should actually compile Trilinos. This file should be called build.sh:

cmake \
-D CMAKE_INSTALL_PREFIX:PATH=/home/ilyass/trilinos-12.6.2-source \
-D CMAKE_CXX_FLAGS:STRING="-O2 -ansi -pedantic -ftrapv -Wall -Wno-long-long" \
-D CMAKE_BUILD_TYPE:STRING=RELEASE \
-D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" \
-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
-D Trilinos_ENABLE_Teuchos:BOOL=ON \
-D Trilinos_ENABLE_Shards:BOOL=ON \
-D Trilinos_ENABLE_Sacado:BOOL=ON \
-D Trilinos_ENABLE_Epetra:BOOL=ON \
-D Trilinos_ENABLE_EpetraExt:BOOL=ON \
-D Trilinos_ENABLE_Ifpack:BOOL=ON \
-D Trilinos_ENABLE_AztecOO:BOOL=ON \
-D Trilinos_ENABLE_Amesos:BOOL=ON \
-D Trilinos_ENABLE_Anasazi:BOOL=ON \
-D Trilinos_ENABLE_Belos:BOOL=ON \
-D Trilinos_ENABLE_ML:BOOL=ON \
-D Trilinos_ENABLE_Phalanx:BOOL=ON \
-D Trilinos_ENABLE_Intrepid:BOOL=ON \
-D Trilinos_ENABLE_NOX:BOOL=ON \
-D Trilinos_ENABLE_Stratimikos:BOOL=ON \
-D Trilinos_ENABLE_Thyra:BOOL=ON \
-D Trilinos_ENABLE_Rythmos:BOOL=ON \
-D Trilinos_ENABLE_MOOCHO:BOOL=ON \
-D Trilinos_ENABLE_TriKota:BOOL=OFF \
-D Trilinos_ENABLE_Stokhos:BOOL=ON \
-D Trilinos_ENABLE_Zoltan:BOOL=ON \
-D Trilinos_ENABLE_Piro:BOOL=ON \
-D Trilinos_ENABLE_Teko:BOOL=ON \
-D Trilinos_ENABLE_SEACASIoss:BOOL=ON \
-D Trilinos_ENABLE_SEACAS:BOOL=ON \
-D Trilinos_ENABLE_SEACASBlot:BOOL=ON \
-D Trilinos_ENABLE_Pamgen:BOOL=ON \
-D Trilinos_ENABLE_EXAMPLES:BOOL=OFF \
-D Trilinos_ENABLE_TESTS:BOOL=ON \
-D TPL_ENABLE_Matio=OFF \
-D TPL_ENABLE_HDF5:BOOL=ON \
-D TPL_ENABLE_Netcdf:BOOL=ON \
-D TPL_ENABLE_MPI:BOOL=ON \
-D TPL_ENABLE_BLAS:BOOL=ON \
-D TPL_ENABLE_LAPACK:BOOL=ON \
-D TPL_ENABLE_Boost:BOOL=ON \
-D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \
-D Trilinos_VERBOSE_CONFIGURE:BOOL=OFF \
-D Netcdf_INCLUDE_DIRS=/usr/include/mpich-x86_64/ \
-D HDF5_INCLUDE_DIRS=/usr/include/mpich-x86_64/ \
..

It is important that you modify the second line of this file by changing the absolute path to the location where you unpacked Trilinos on your machine. We will then change the authorization of the build.sh file to make it executable by your Linux user by typing chmod a+x build.sh and can configure the compilation of Trilinos by executing this file, just type: ./build.sh The Cmake compiler will now configure Trilinos for compilation, it will take some time…. After that, we can finally install Tirlinos, by typing:

make -j
make install

This is also going to take some time, but after it, Trilinos will be installed on your machine. Congrats! Next, we are going to compile Peridigm. We are directly going to pull the latest release of Peridigm from the Github repository of Peridigm. Go to your home folder by simply typing cd in the terminal, then input line after line:

git clone https://github.com/peridigm/peridigm.git
git fetch
git checkout release-1.4.1

You should now have a folder called peridigm in you home folder. We are now going to create a build folder in it (similar to what we did for Trilinos) to compile Peridigm:

cd peridigm 
mkdir build
cd build

The next step is also similar to what we previously did with Trilinos, you will need to create a build.sh text file in the build folder and paste the following content in it:

cmake \
-D CMAKE_BUILD_TYPE:STRING=Release \
-D Trilinos_DIR:PATH=/home/ilyass/trilinos-12.6.2-source/lib/cmake/Trilinos/ \
-D CMAKE_C_COMPILER:STRING=/usr/lib64/mpich/bin/mpicc \
-D CMAKE_CXX_COMPILER:STRING=/usr/lib64/mpich/bin/mpicxx \
-D CMAKE_CXX_FLAGS:STRING="-O2 -Wall -ansi -pedantic -Wno-long-long -ftrapv -Wno-deprecated -std=gnu++11" \
..

Again, do not forget to change the absolute path on the third line of the previous script to the location where you installed Trilinos on your machine. We can now configure the Cmake compiler by executing the build.sh file:

chmod a+x build.sh
./build.sh

Wait for it…. And you can then install Peridigm:

make  -j

You should be done ! To execute Peridigm, you will need to type in your Terminal ./src/Peridigm when you are in the peridigm folder. And that’s it !

Now if you want to be able to run Peridigm from any folder in your machine, you need to modify your .bashrc to tell it where the Peridigm executable is:

cd
nano .bashrc

And add the following line at the end of the file:

export PATH=$PATH:/home/ilyass/peridigm/src/

Restart your terminal, and you’re done ! You can now type the Peridigm command anywhere in your temrinal and it will call out the software.

Many thanks to Patrick Diehl :)

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Just sharing a timelapse of a 18 hours print. The part is the Bird Feeder v4, designed by Printed nest. The print was done on a Leapfrog Creatr, with a layer height of 0.3mm and 80% infill. The Printed Nest team recommends a 100% infill but I try to avoid printing solid parts on printers that are not equipped with an active cooling system (which is the case of the Leapfrog Creatr). Else it is necessary to print very slowly in order to let the previous solid layer cool down before laying the next one on it.

The filament I used is from the PLA Opaque Series. Affordable, no knots in the spool, it flows great, the color is good enough an they have several afety certificatons on their Material Saety Data Sheet. If you woul like t get some, take a look at 3D-TRIP or even more intereting prices around the Montreal area.

Link to the video
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Last September, the jessie update for the Raspbian OS got out. It included a few updates that changes the way you have to set up your network. A clear method to setup a Raspberry Pi with a static IP on wifi is given here. The goal is to have a headless Raspberry Pi that automatically connects to one or several known WiFi networks.

In the previous version, most of the changes to the network configuration had to be done in the interfaces file, you can check its content:

pi@raspberrypi:~ $ cd /etc/network
pi@raspberrypi:~ $ cat interfaces

Which shows you the content:

# interfaces(5) file used by ifup(8) and ifdown(8)

# Please note that this file is written to be used with dhcpcd
# For static IP, consult /etc/dhcpcd.conf and 'man dhcpcd.conf'

# Include files from /etc/network/interfaces.d:
source-directory /etc/network/interfaces.d

auto lo
iface lo inet loopback

iface eth0 inet manual

allow-hotplug wlan0
iface wlan0 inet manual
    wpa-conf /etc/wpa_supplicant/wpa_supplicant.conf

allow-hotplug wlan1
iface wlan1 inet manual
    wpa-conf /etc/wpa_supplicant/wpa_supplicant.conf

You do not need to modify this file anymore. In order to get Wifi on your Raspberry Pi, you need a wireless USB adapter. Once you have one, just plug it and reboot your RPi. (I use this one)

You still need to provide the system with the SSID of your network and the password. You can do that here:

pi@raspberrypi:~ $ cd /etc/wpa_supplicant
pi@raspberrypi:~ $ sudo nano wpa_supplicant.conf

You need to add the following lines:

network={
    ssid="ESSID"
    psk="Your_wifi_password"
    key_mgmt=WPA-PSK
}

The real novelty is the use of dhcpcd to manage static connection. To set up a static IP for your Raspberry Pi, you need to modify the following file:

pi@raspberrypi:~ $ sudo nano /etc/dhcpcd.conf

Add the following lines, after adapting them to your network:

interface wlan0
     static ip_address=192.168.0.XXX
     static routers=192.168.0.1
     static domain_name_servers=192.168.0.1

If you do not have the information about your network, you can always check an already connected device’s settings (smartphone or laptop). You can now reboot your Raspberry Pi. It should automatically connect to the configured network, and reconnect (as soons as it is available again) if the connection is lost for any reason.

The next thing you should do is enable the SSH server in the Advanced settings of sudo raspi-config and you’re good to go !

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