![]() ![]() TheseĪre special commands available in IPython that make doing some common tasksĮasier on the command line. When we use the “%” sign it denotes that the command is an “IPython magic”. Mkdir: cannot create directory `repro_course': File exists A list of files in the current directory. The Jupyter qtconsole A note on the IPython prompt Discuss the difference and edit as needed. Now get with your partner and compare your drawings. Challenge: Draw your stackĮxpandable orange boxes like this one contain challenges for you to try.ĭraw a diagram to illustrate how the programs and computers listed below relate to one another. Teaching you reproducible computing concepts without getting bogged down in the It’s close cousin, tcsh) if you’ve used analysis packages like AFNI, FSL, andįreeSurfer. The Bash shell is anĮxtremely versatile tool designed to allow you to control and interact withįiles and your computer more generally. Leverages the power of the Python programming language. IPython provides an easy way to explore and interact with your data that We’ll be working almost exclusively in the IPython shell in this course. Info that are not essential to the flow of the course. This is the first of many expandable boxes you’ll see in these lesson. It’s named a shell because it stands between the user and the “guts” of the computer system, which is called the kernel. It is designed to allow the user, you, to interact with the computer in an efficient and convenient way. Right side, there is a window running a (Bash) shell. The window on the left of your NX desktop is running an IPython shell. ((VNC) is another common remote desktop program). Remote computer (helix/felix) almost as if you were sitting right in front of ![]() ![]() With the large cluster of computers known as the (Biowulf). This computer (helix or felix) is separate from but closely affiliated That lives over in building 12B at NIH’s high performance computing (HPC)Ĭenter. The desktop you’re looking at inside the NoMachine window is from a computer Understanding this stackĬan help you make your analysis more efficient and secure. Looks like and exactly where everything is happening. It’s worth theĮffort to take some time and understand exactly what your computing (stack) It’s easy and common to click on an icon, open and window and typing, clicking,Īnd analyzing in that window without much thought about how or where thoseĬommands are being executed and where the data is being stored. To run it, type:Īutomagic is OFF, % prefix IS needed for line magics. We’ve setup a short script to get you started quickly in the NIH HPC (felix or helix).Open Terminal from the Application-> System Tools menu.If you work forĪnother institute you can use. Open the NoMachine App and connect toį if you are an NIMH employee or have a temporary course account. You should have already met with the DSST We’ll be conducting this course using a remote desktop utility called Connect to felix or helix using NoMachine.Learn shortcuts and hotkeys to make command line computing fast and efficient Get exposed to IPython and learn it’s strengths. Understand the different ways of interacting with your computer and what the pros and cons areĮxplain when and why command-line interfaces should be used instead of graphical interfaces.Įxplain the advantages of remote computing including cloud and high performance computing.Įxplain how to access the NIMH dedicated computing resources in the most convenient manner. Understand how the components in your computing stack relate to one another ![]()
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