Molecular Dynamics Simulations with Applications in Soft Matter Handout 1 Outfitting Your PC for Scientific Computing
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1 Dr. Martin O. Steinhauser University of Basel Graduate Lecture Spring Semester 2014 Molecular Dynamics Simulations with Applications in Soft Matter Handout 1 Outfitting Your PC for Scientific Computing Friday, 21 st February Introduction To understand molecular dynamics simulation you have to work with simulation code. This means reading it, modifying it, maybe writing it from scratch. It also means compiling it, running it, and analyzing the results. You will probably be provided with some example codes during the lecture. Some code is just for illustration and practicing certain techniques, some code performs simulations and some of it performs analysis of results. Hence, you need a way to 1. Look at the code, 2. edit it, 3. compile and run it. 1.1 Outfitting your PC / Laptop It is assumed in this course that all students have access to at least a Windows PC (better: a Linux- System) and some familiarity with Windows. If you don t have a PC or laptop on your own you need to get a student account at university. Some students may already have some Unix experience. I feel that it is important for every student of this class to learn at least a minimum about coding in a Unix-like environment. Probably there is no estimate for such a number, but nearly 100% of serious research using molecular dynamics is conducted and tested under Unix (which nowadays is mostly Linux). If you have access to a Linux PC, you needn t do anything more; you are likely ready to begin running code. For all others, we provide here, in a nutshell, what you can do to set-up your Windows PC or laptop for running simulation code during this course: 1. Install a free Linux distribution. Most popular are probably (a) Suse Linux ( (b) Ubuntu ( and (c) Fedora ( 1
2 You find installation instructions for all of these packages on the corresponding websites. Therefore, we do not give explicit installation instructions for installing native Linux distributions but we do note that sometimes considerable administration experience with Unix/Linux environments is necessary to really get things running. On the other hand, in recent years, many distributions have become very user-friendly and provide installer packages that take care of (almost) all administration necessary to obtain a running Linux system, including network settings for internet connection. For preparing software in this course, I use the UNIX-environment provided with the MAC OS X system (Mavericks, Version at the time of writing). Any other Linux system will do equally well for programming, with slight differences in handling and managing the system, also depending on your experience as a system administrator. If you are experienced in installing Linux distributions you can also consider using the free Vmware Player ( as a virtual machine on your Windows PC or laptop, and have running native Linux in a virtual machine on top of Windows. For good performance, this requires a well-equipped PC or laptop in terms of hardware. For installing Vmware Player, we don t provide any detailed instructions. 2. Install Cygwin ( on Windows. Cygwin is freely available. This provides a Linux-like environment on top of Windows. It is relatively small, easy to manage, and can be simply uninstalled later, if you wish, like any other Windows application. It will give you almost all the functionality of a full Linux PC right in Windows, and it is certainly adequate for this course. Cygwin is a port of POSIX (a Unix standard for commands and parameters) compatible software to the Windows system. Cygwin has been designed as dynamic library which ports from POSIX-API to Windows API. Besides a number of developer tools, there is a variety of software available which can be run under windows, e.g. a full X-Windows server which allows for running graphic applications from the Unix world. As I feel that some of the students might opt for this second choice, because it requires minimal effort for a spectacular amount of functionality, we give here a very brief description of the download procedure Installing Cygwin Download setup.exe from This program is used for both, downloading and set-up as well as for updating the Cygwin environment. Execute this file after download. A wizard appears which leads you through the rest of the installation process with the following screens: Cygwin Net Release Setup Program: Click the Next button. Choose A Download Source: Select Install from Internet (first choice); click Next button. Select Root Install Directory: Use the default choice C:\cygwin or pick your own directory. Note, that you should avoid blanks within directory install paths, e.g. you should avoid something like C:\\Program Files (x86) and rather use an install path without blanks. This avoids problems as in Unix paths which are used by Cygwin, no blanks are allowed, or rather have to be masked using the backslash, like in 2
3 C:\\Program\ Files\ (x86) which makes things rather awkward. Under Cygwin, when typing the command cd /cygwin, the directory /cygwin (please note the slash here vs. backslash in Windows directory structures) allows you to access all Windows directories in a Unix-like fashion by e.g. typing cd /cygwin/c/windows which takes you to the directory C:\Windows Select Your Internet Connection: Should be direct if you are on campus but you can also choose a proxy server here. Choose a Download Site: Select a server close to your location, i.e. one within Europe or Germany. You can also add servers to this list by entering a new server into the field User URL and pressing Add. Select Local Package Directory: Use e.g. C:\temp Select Packages: Here is where you get to choose what package to include in the Cygwin installation. There are hundreds if not thousands of packages, so they are grouped in categories. Each category has the word Default next to it. That means you will be given the default set of packages from each category, which corresponds to a minimal installation. We will need more than that so you should always select a full installation with the following categories by clicking directly on the word Default next to each category, changing it to the word Install: Devel Doc Editors Graphics Math Publishing Shells Text X11 The only crucial category is Devel, because this contains the compiler gcc. The others will give you some nice functionality. If you don t want to bother with selecting packages you can simply select everything for full installation by clicking on Default next to the category All, right on top of the list. In this case, when you click Next, the download of packages starts and can take up to an hour depending on the speed of your internet connection. Finalize: Here you select whether an icon is put on the desktop and/or the Windows Start menu. Note, that under the Windows operating system, you may need administrator privileges to install software. 3
4 2 The GNU Scientific Library GSL For some programs later in the course we might need this library primarily for its high-quality pseudorandom number generators. To learn more about GSL and its other useful features, visit To install this library do the following steps: 1. Download the GSL source code package, currently (Feb. 2014) gsl-1.16.tar.gz (released on 19 July 2013) from ftp://ftp.gnu.org/gnu/gsl/. 2. Unpack it. Open a Cygwin terminal and enter the following command: tar zvxf gsl-1.16.tar.gz A large number of files will be extracted into the directory called gsl Change into this new directory by typing: cd gsl If you like, you can follow the install instructions in the file INSTALL. You can browse to this file with Windows Explorer to read it, or read it from the terminal with the command more INSTALL 5. If you don t understand the file INSTALL, just type the following commands:./configure make make install You are done! 4
5 GSL has extensive extensive documentation available both online and as part of the distribution. The command info gsl-ref will display a text-only hyperlinked manual with which you can learn about using the GSL in standard C programs. Even if you choose not to write in C for now, it is useful to have this library installed for a few of the programs I might be giving you during this course. 3 Summary checklist for setting up your PC / Laptop I provide here a checklist to help you get your PC or laptop ready for this course. Everything you do can be easily undone. If you already have access to a Linux PC, MAC computer or Unix workstation, you of course do not need to install Cygwin. Please note that, under Windows, you need administrator access on your PC to install software. For Windows Users: Download and install Cygwin from Detailed instructions are above. Download, compile and install the GNU Scientific Library GSL, according to the instructions above. For Linux / Unix users: Download, compile and install the GNU Scientific Library GSL, according to the instructions above. During the course, I may decide to convince you to install some other free programs, mostly for visualization purposes, but the above suggestions are enough to get you started. 5
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