Linux Desktops Documentation, Slides of Compilers

Download Linux Desktops Documentation and more Slides Compilers in PDF only on Docsity! Linux Desktops Documentation Release RHEL7 University of Southampton Aug 17, 2018 Linux Desktops Documentation, Release RHEL7 Welcome to the documentation for Linux Desktops at the University of Southampton Basics 1 Linux Desktops Documentation, Release RHEL7 2 Basics CHAPTER 1 Desktop Manager You can manage your desktop using the Desktop Manager tool. Log in to your desktop computer, open a web browser and go to the following location: https://deskctl You can also open the Desktop Manager tool within GNOME by press the Start button and searching for “Desktop Manager” and then selecting the resulting entry for the tool. Desktop manager allows you to: • Install software, including University provided software • Manage permissions (change who can do what) • Check the status of backups • Start a backup on demand • Check the software update status • Check the health of the system • View the system hardware information • Open this documentation 3 Linux Desktops Documentation, Release RHEL7 sudo yum remove <package-name> 6 Chapter 2. Installing software CHAPTER 3 Backups Your home directory is backed up automatically at least once a day. 3.1 When are backups taken? Your workstation will attempt to back up all the data in /home between 11pm and 12am. If your computer is switched off at this time do not worry, the next time you start your computer a backup will be attempted then instead. 3.2 Do I need to keep my computer on overnight? You do not need to leave your computer on overnight. If you prefer to keep your computer turned off then backups will still take place. Whenever your computer starts up it determines if a backup should be taken and then initiates a backup if required. 3.3 How long are backups kept for? Backups of each workstation are kept for 30 days after the backup was taken. If your machine is not switched on, or otherwise unavailable, for 30 days, then all backup data will be deleted. To ensure you always have a copy of data in case of hardware failure please ensure your computer takes at least one backup a month. 3.4 How can I check the backups are working? You can use Desktop Manager to check the status of the last backup attempt. You can also run the following command in a terminal: 7 Linux Desktops Documentation, Release RHEL7 sudo drone backup status 3.5 Can I trigger a backup? Yes you can start a backup whenever you need to. This allows you, for example, to take a backup before turning your computer off before leaving the office. You can start a backup using Desktop Manager or if you prefer you can run the following command in a terminal: sudo drone backup now 3.6 Can I use my PC whilst a backup is underway? Yes. The backup system takes a snapshot of the data when the process begins and backs up the data in the snapshot. You can thus carry on using your computer without affecting the backup (or the backup affecting your data). The backup system uses LVM thin snapshots to accomplish this. 3.7 Do backups work when outside the University network? For the backups to work you must connect to the University network via one of these methods: • Connect to the university network via an Ethernet cable • Connect to the eduroam wireless network • Connect to the university virtual private network (VPN) service 3.8 Can backups be disabled? In very rare circumstances iSolutions will disable backups on a workstation. To do this, you need to be a member of iSolutions staff with root access, and you run the following command to do so: sudo drone backup disable Backups can be then enabled again at a later date with: sudo drone backup enable 8 Chapter 3. Backups CHAPTER 5 Network storage 5.1 Available locations There are several storage systems available to connect to on the University network: 5.1.1 Personal Filestore (via SSH) • Location: sftp://ssh.soton.ac.uk/home/$username/ • Protocol: SSH/SFTP • Linux friendly semantics: Yes This is your central university storage or ‘filestore’. Data stored here is backed up and available on Linux, Windows and Mac OS X computers. You can also access data stored here via Filestore Web Access. 5.1.2 Personal Filestore (via SMB) • Location: sftp://ssh.soton.ac.uk/home/$username/ • Protocol: SMB1, SMB2 • Linux friendly semantics: No You can also access your personal filestore via the SMB protocol (the Windows file sharing protocol). If you connect via this method then you will not be able to set or view file/directory permissions, create symbolic links or use any other POSIX (Linux/UNIX) features. Due to this it is strongly recommended that you utilise SSH instead. 5.1.3 Linux Shared Filestore • Location: sftp://ssh.soton.ac.uk/research/$groupname/ • Protocol: SSH/SFTP 11 Linux Desktops Documentation, Release RHEL7 • Linux friendly semantics: Yes Many research groups and departments have access to shared storage locations specifically designed for use from Linux systems. These are available at the above location. Data stored here is backed up. You can also access data stored here via Filestore Web Access. 5.1.4 Other Shared Filestore • Location: smb://filestore.soton.ac.uk/$sharename/ • Protocol: SMB1, SMB2 • Linux friendly semantics: No Many other shared locations exist, such as the “J: drive” shared storage locations. These are available at the above location. Data stored here is backed up. You can also access data stored here via Filestore Web Access. These locations are unfortunately designed for use by Windows users. You will not be able to set or view file/directory permissions, create symbolic links or use any other POSIX (Linux/UNIX) features. 5.2 How to connect There are various methods of connecting to network storage: 5.2.1 via the file browser If you’re using GNOME (the default), XFCE, MATE or KDE then you can simply open the file browser and enter the location you want to connect to by pressing Ctrl+L or clicking Connect to server in the menu. You will be prompted for a username and password as necessary. We strongly recommend you use this mechanism to connect to network storage. You can also access the connected storage from other applications and the command line. Once connected they are available via the normal file system here: /run/user/$uid/gvfs/ 5.2.2 via FUSE (SSH only) If you prefer to connect to networked storage on the command line only, you can do so using the sshfs command. We strongly recommend you use the above mechanism (the file browser) instead since that can also be accessed from the command line. If you do want to use sshfs directly then run the command like so: sshfs [user@]host:[dir] mountpoint For example, here is how to connect to your personal filestore as testuser: mkdir ~/personalfs sshfs testuser@ssh.soton.ac.uk:/home/testuser/ ~/personalfs You can then later disconnect with: 12 Chapter 5. Network storage Linux Desktops Documentation, Release RHEL7 fusermount -u ~/personalfs 5.2.3 via the mount command You can also instruct the kernel to mount network storage if you desire. This can however be quite complicated and this documentation only covers the basics. You can use the mount command via sudo if you are in the sys group (see Permissions for more information). You can thus use the command like so: sudo mount <options> Here is an example of how to mount personal filestore via the cifs driver with the example username testuser: mkdir ~/personalfs sudo mount -t cifs -o username=testuser,password=<password>,domain=soton.ac.uk // →˓filestore.soton.ac.uk/users/testuser/ /home/testuser/personalfs/ 5.2. How to connect 13 Linux Desktops Documentation, Release RHEL7 9. The printer is now added to the system, and you should now be able to print to it 10. Note that you can’t set a system-wide default printer here as that is managed by system policy (and if you manage to change it, it will get reverted), however you can change the default printer for your account on your desktop using the documentation below. To change the default printer: 1. Open the Print Settings application 2. Right-click the printer you wish to make the default for you 3. Choose Set as Default from the menu 4. Choose Set as my personal default printer 5. Click OK 16 Chapter 6. Printing CHAPTER 7 E-Mail At present, the univerity’s e-mail solution is Microsoft Exchange for most staff and Office 365 for students. 7.1 Using Outlook web access The easiest way to access your e-mail (and calendars and contacts) is to use Outlook web access: • Staff and postgraduates: www.outlook.soton.ac.uk • Students: www.outlook.com/soton.ac.uk 7.2 Using GNOME / Evolution The next easiest way to access your e-mail (and contacts) is to use the e-mail client in GNOME - evolution. The fastest way to set it up is to open Settings and click Online Accounts. • Click “Add an online account” • Choose “Microsoft Exchange” • Enter the E-Mail as yourusername@soton.ac.uk • Enter your normal university password Open Evolution and your e-mail account will have automatically been created. 7.3 Using other clients If you decide to use another e-mail client you’ll likely want to use IMAP and SMTP for sending and receiving e-mails. The support in Microsoft Exchange for IMAP clients is very poor however (performance is appauling and the IMAP server is not very compliant to the RFC - surprising, no?). We thus recommend either using Outlook Web Access or Evolution, but if you really do want to take the plunge, here are the details: 17 Linux Desktops Documentation, Release RHEL7 • IMAP server: imap.exchange.soton.ac.uk • IMAP security: SSL/TLS (port 993) • SMTP server: smtp.soton.ac.uk • SMTP security: STARTTLS (port 25) 18 Chapter 7. E-Mail Linux Desktops Documentation, Release RHEL7 Finally, choose Linux Desktop 7: 8.2. Start the installation 21 Linux Desktops Documentation, Release RHEL7 You will be prompted for the Linux build password: 22 Chapter 8. Installation Linux Desktops Documentation, Release RHEL7 If the build starts you’ll see a loading screen like this one: 8.2. Start the installation 23 Linux Desktops Documentation, Release RHEL7 Press any key to start the installer and then enter the computer name if it was not automatically detected: You then need to enter your university username and password. The account must be within the jfStaff group - so don’t use adm accounts, use your normal account.: 26 Chapter 8. Installation Linux Desktops Documentation, Release RHEL7 The University installer will then complete all its tasks automatically without requiring any further input. It can take between 5 and 15 minutes for this to finish, dependening on the speed of the hard drive: Once complete the installer will show “all done” and you can restart to use the new Linux desktop by pressing any key: 8.3. University installer 27 Linux Desktops Documentation, Release RHEL7 8.4 Post-installation tasks Once the system has rebooted you might want to grant additional permissions to the user for whom you built the workstation for. To do so, logon to the system and use Desktop Manager to change Permissions. Your account must be within the linuxadm or linuxsys Linux groups to do this. 28 Chapter 8. Installation Linux Desktops Documentation, Release RHEL7 9.6 Secondary hard drives Sometimes a workstation will have a second or even a third physical disk installed. We don’t have to back up this data as the installation for RHEL7 won’t touch these disks - the data will be retained. However, it is best practice to disconnect these drives ‘just in case’. If its easy to open the case and disconnect secondary hard drives, do so (when the power is off of course!) so as to prevent any chance of data on these disks from being lost. Make a note as to how many of these drives there are, and where they are currently mounted. You can get a list of physical drives with lsscsi: lsscsi and you can get a list of mounted partitions with df: df -h This will let you figure out what drives are there, and what mount points to add once you’ve installed RHEL7. Make sure to write down the full path to the disk, e.g. it will probably be /dev/sdb1 for the device path. You’ll also want to make sure you write down the file system type, hopefully it will be ext4. 9.7 Install RHEL7 Once you’ve done the above steps, power the machine off, and unplug the USB hard disk. Then power it back on and follow the Installation guide. 9.8 Reconnect secondary hard drives Once you’ve installed RHEL7 you should power the machine off again and reconnect any hard drives you previously disconnected. You can then power the machine back on and reconnect them. Log in and gain root, and then find a list of the new drives: lsscsi You should then re-create the directories where you want to mount the drives. In nearly all cases this will be /data so just run: mkdir /data Now you’ll need to edit the file system tab (fstab) to add a record so the drive is mounted at startup. Edit /etc/ fstab in the editor of your choice and add the following: /dev/sdb1 /data ext4 defaults 0 0 Change this line to match what you need it to - .e.g change /dev/sdb to be the device path you wrote down in the earlier steps. Change /data to be wherever the disk should be mounted. And change ext4 to whatever file system is in use (and you wrote down earlier). In nearly all cases though you probably won’t need to change anything. Once that is done, save and exit the file, and run: mount -a Now check the disk is mounted: 9.6. Secondary hard drives 31 Linux Desktops Documentation, Release RHEL7 df -h 9.9 Copy data back The last step is to copy data back onto the workstation. You’ll have to plug in the USB drive in again, and then work out what it got attached as: lsscsi And you should get an output somewhat similar to this: [0:0:0:0] disk ATA KINGSTON SA400S3 71E0 /dev/sda [1:0:0:0] cd/dvd TSSTcorp CDDVDW SH-224BB SB00 /dev/sr0 [2:0:0:0] disk Seagate Expansion 9300 /dev/sdb As you can see from the above, the USB drive (in this case a Seagate USB drive) is listed and it is available at the path /dev/sdb. Create the place we’ll mount it: mkdir /mnt/migrate And then mount it: mount /dev/sdb1 /mnt/migrate Now we can copy data back. Start with the /local/scratch/ directory and use rsync again to copy back: rsync -av –progress /mnt/migrate/scratch/ /local/scratch/ You can then recover the /home directory data. You probably should not recover the data directly though. In most cases, users will be moving from GNOME 2 to GNOME 3, and starting with a fresh home directory makes more sense. If a user insists they want their original home directory, feel free to restore it, but it can lead to problems, and so you should recommend that they do not. Either restore the data into /local/scratch/home/ like so: rsync -av --progress /mnt/migrate/home/ /local/scratch/home/ Or restore individual directories for users (not recommended): rsync -av –progress /mnt/migrate/home/<username>/ /home/<username/ 32 Chapter 9. Migration Guide CHAPTER 10 Permissions 10.1 Standard permissions All members of the University of Southampton can log on to any Linux Desktop. Once logged in you are granted all normal Linux account rights, and in addition you may perform the following actions: • Can install software packages via Desktop Manager • Can install software packages via GNOME Software • Can mount and umount file systems via sudo mount (See Network storage) • Mount a file systems via GNOME disk management • Can manage NVIDIA graphics settings via sudo nvidia-settings • Can reboot/poweroff/hibernate/suspend the computer • Can run the following commands: reboot, poweroff, halt • Can start a backup with sudo drone backup now • Can check the backup status with sudo drone backup status 10.2 Additional permissions There are four user groups on each workstation which grant additional privileges: 10.2.1 SSH Access Users in the group users are granted the privilege of being able to logon to the system via SSH from anywhere within the university network. 33 Linux Desktops Documentation, Release RHEL7 36 Chapter 10. Permissions CHAPTER 11 Remote access 11.1 SSH You can connect to your Linux desktop via the SSH protocol. To do so your user account needs to be in the users group. Read the Permissions page for more details about permissions, or use Desktop Manager to add yourself to the SSH group. The address to connect to will be of the form: uos-NNNNN.clients.soton.ac.uk If you don’t know what your computer’s “UOS” number is, you can find out by either opening Desktop Manager or by opening a terminal and typing: hostname For example if your computers UOS name were uos-57292 you would connect to the address uos-57292. clients.soton.ac.uk. You can then login with your normal university username and password. 37 Linux Desktops Documentation, Release RHEL7 38 Chapter 11. Remote access CHAPTER 13 Virtualisation 13.1 VirtualBox iSolutions recommends the use of VirtualBox for creating and running virtual machines on the linux desktop platform. VirtualBox is designed for a multi user environment, unlike KVM/libvirt which runs everything as root. You can install the latest VirtualBox with the following command: sudo yum install VirtualBox-5.1 Older versions are available but we recommend you install the latest. Once installed you can start VirtualBox and start creating virtual machines straight away! We recommend you store your virtual machine disks in the /local/scratch/<username/ directory - see Local storage for more info. 13.2 Rebuilding the kernel module After a kernel update is installed you might find that VirtualBox no longer works and generates an error similar to Kernel driver not installed. To fix this you must run the following command in a terminal: sudo /usr/lib/virtualbox/vboxdrv.sh setup To run the above command you must be in the sys or vboxusers group. See Permissions for more information. 13.3 VirtualBox user group In previous versions of VirtualBox anybody who wanted to use the software had to be in the vboxusers group. This is no longer the case and membership of this group is only required if: • You want to be able to rebuild the kernel module without being in sys 41 Linux Desktops Documentation, Release RHEL7 • You want to be able to use USB passthrough devices See Permissions for more information. 42 Chapter 13. Virtualisation CHAPTER 14 Firewall From RHEL7 (Red Hat Enterprise Linux Version 7) onwards you can now manage the firewall of your workstation provided you are a member of the sys users group. See Permissions for further information on groups. The firewall is managed by the firewalld utility. To manage the firewall you need to start the graphical tool “Firewall Config”. You can then use this GUI tool to make changes. Please only make changes to the firewall if absolutley necessary. The defaults are probably all you need. 43 Linux Desktops Documentation, Release RHEL7 46 Chapter 15. GNOME Extensions CHAPTER 16 Environment modules system Most of the scientific and research software provided by iSolutions uses the environment modules system. Most if not all of the software on the IRIDIS super computer also uses the environment module system. The modules system is a way to dynamically alter your environment (e.g. variables in your terminal session) in a ‘modular’ way. An application specifies a ‘module file’ which contains code to modify the shell so that the application works. You can then ‘load’ the module which uses the module file. 16.1 How to load a module First you have to install some software which makes use of the modules system, for example you could install PyPy 5.6: sudo yum install pypy256 Once the package is installed you can switch into the module like so: module load pypy/5.6 Once loaded you can use the pypy binary directly. 16.2 How to unload a module Just replace module load with module unload: module unload pypy/5.6 47 Linux Desktops Documentation, Release RHEL7 16.3 List available modules You can list all the modules installed with: module avail 16.4 Show the help for the module Each module should have some help text, use this command to show it: module help pypy/5.6 16.5 List loaded modules You can list the modules in use right now type: module list 48 Chapter 16. Environment modules system CHAPTER 18 Python Python is a popular and versatile programming language used in many scientific disciplines across the university. It is by far the most popular language in use by staff at Southampton and is the most used tool on Windows desktops too! The university Linux desktop platform has a large number of Python implementations for you to choose from. We’ve worked hard to try to provide the options you might need and granted you the privileges needed to install packages as required. Note: To install python modules via sudo pip you need to be in the Administrators group. See Permissions for more information. You don’t need to be in this group to use the conda command. You can also use pip directly, without sudo, and install packages in your home directory. 18.1 List of available implementations • CPython – RHEL system python - 2.7.5 – Miniconda (Anaconda) - 2.7, 3.6 – IUS packages - 3.4.6, 3.5.3, 3.6.0 – SCL packages - 2.7.8, 3.3.2, 3.4.2, 3.5.1 – EPEL package - 3.4.5 • PyPy – PyPy 5.6 - 2.7.12 – PyPy3 5.5-alpha - 3.3 • Jython – SCL Jython 2.7 51 Linux Desktops Documentation, Release RHEL7 You can use Desktop Manager to install the various options, or read below for the yum commands to use instead. 18.2 Which implementation should I use? • If you want to use Python 2, and you don’t need conda packages, then use the RHEL system Python, and use pip to install packages. • If you want to use Python 3, and you don’t need conda pacakges, then use the IUS Python 3.6 package and use pip3.6m to install pacakges • If you need conda packages (Anaconda Python packages) then use miniconda 18.3 RHEL system Python Unless you need Python 3 or conda packages then we recommend you use the system python in /usr/bin/ python. This is supported by Red Hat and kept up to date with security and bug fixes. You can install packages by running sudo pip eg: sudo pip install numpy 18.4 IUS Python The IUS repository provides Python 3 packages for Red Hat Enterprise Linux. If you need to use Python 3 then we recommend you use the IUS Python packages. Several versions are available for install: • Python 3.4 - sudo yum install python34u python34u-pip • Python 3.5 - sudo yum install python35u python35u-pip • Python 3.6 - sudo yum install python36u python36u-pip You can then use Python via the following paths to the binary: • Python 3.4 - /usr/bin/python3.4 • Python 3.5 - /usr/bin/python3.5 • Python 3.6 - /usr/bin/python3.6 The version of Python in /usr/bin/python3 depends on the order the IUS packages are installed, so we don’t recommend you use that path. You can install packages via sudo pip: • Python 3.4 - sudo pip3.4 • Python 3.5 - sudo pip3.5 • Python 3.6 - sudo pip3.6 For example, to install numpy on IUS Python 3.6: sudo pip3.6 install numpy 52 Chapter 18. Python Linux Desktops Documentation, Release RHEL7 18.5 PyPy PyPy is a just-in-time (JIT) compiler for Python which aims to be compatible with the standard CPython implementa- tion. Using PyPy often yields significant performance benefits. To install PyPy run the following command: sudo yum install pypy256 This installs PyPy 5.6 which is compatible with CPython 2.7.12. To install PyPy3 run the following command: sudo yum install pypy3355 This installs PyPy3 5.5-alpha which is compatible with CPython 3.3.5. To run PyPy you can either use the following paths: • /usr/bin/pypy56 - PyPy 5.6 (Python 2.7.12) • /usr/bin/pypy3355 - PyPy 5.5-alpha (Python 3.3.5) Or you can use the module system: • module load pypy/5.6 - PyPy 5.6 (Python 2.7.12) • module load pypy/3.3-5.5 - PyPy 5.5-alpha (Python 3.3.5) Once you’ve loaded the module you can use the pypy command directly and it will correspond to the version of pypy you chose to load. You can install packages with pip: • sudo /local/software/pypy/5.6/bin/pip - PyPy 5.6 (Python 2.7.12) • sudo /local/software/pypy/3.3-5.5/bin/pip3 - PyPy 5.5-alpha (Python 3.3.5) For example, to install numpy on PyPy 5.6: sudo /local/software/pypy/5.6/bin/pip install numpy 18.6 Miniconda (Anaconda) Anaconda, and its conda package manager, is an alternative to the pip package manager (although the developers insist it complements pip and solves different problems). Anaconda, conda and miniconda are not designed for “system-wide” use, they are intended for individual users to download and install for just that one user. Better multi user support is planned, but as of March 2017, is not yet available. To use conda you don’t need to download and install Anaconda or miniconda yourself, instead you can get started by installing miniconda which just contains conda and python: sudo yum install miniconda Once installed you can use conda to create a new environment within your home directory with whatever version of Python and whichever Python packages you need. You should start by creating an environment, e.g: 18.5. PyPy 53 Linux Desktops Documentation, Release RHEL7 56 Chapter 18. Python CHAPTER 19 C and C++ C is a general-purpose, low level, imperative computer programming language, supporting structured programming, lexical variable scope and recursion, while a static type system prevents many unintended operations. C++ is an extension of C with object-oriented features and a much larger standard library. 19.1 List of compilers Several C and C++ compilers are available on the Linux desktop platform: • GCC (GNU compiler collection) – v4.8 - Red Hat’s built in GCC – v4.9 - part of RHDT 3 – v5.3 - part of RHDT 4 – v6.2 - part of RHDT 6 • ICC/ICPC (Intel compiler suite) – 2017 Update 2 • Clang (LLVM C/C++ compiler) – v4.0.0 – v3.9.1 – v3.4.2 from the EPEL project • PGI (NVIDIA Portland Group Compiler Suite) – 17.1 57 Linux Desktops Documentation, Release RHEL7 19.2 GCC Several versions of GCC are available. The system gcc - the one used to build Red Hat Enterprise Linux 7 - is version 4.8. You can install it like so: sudo yum install gcc gcc-c++ Later versions are available as part of the RHDT bundles: • v4.9: sudo yum install devtoolset-3-gcc devtoolset-3-gcc-c++ • v5.3: sudo yum install devtoolset-4-gcc devtoolset-4-gcc-c++ • v6.2: sudo yum install devtoolset-6-gcc devtoolset-6-gcc-c++ Once you have installed the packages you need to use SCL to use the updated version of gcc like so: * v4.9: ``scl enable devtoolset-3 bash`` * v5.3: ``scl enable devtoolset-4 bash`` * v6.2: ``scl enable devtoolset-6 bash`` Once those commands are run then running ‘gcc’ will run the version you requested. See the Software collections (SCL) document for more information on using SCL. 19.3 Intel Intel’s C and C++ compiler is part of the Intel Parallel Studio XE product. This is available to you as a member of the University. At the time of writing the latest version - 2017 Update 2 - is available. To install it you can use the following command: sudo yum install intel-parallel-studio-2017u2 This installs all of the components of the Cluster Edition of the Intel Parallel Studio. To use the Parallel Suite you must first load the environment module: module load intel/2017u2 Once loaded all of the environment modules are set such that you should be able to run the configure script (or similar mechanism) and it should use the Intel compilers. You can also use icc, icpc and ifort directly. See Environment modules system for more information on using the module system. 19.4 LLVM Clang Clang is the compiler from the LLVM project. To use it first install the latest version: sudo yum install llvm400 The LLVM package includes: • LLVM core libraries • Clang • compiler-rt 58 Chapter 19. C and C++ CHAPTER 20 Fortran Fortran is a general-purpose, imperative programming language that is especially suited to numeric computation and scientific computing. FORTRAN was developed in the 1950s making it one of the oldest languages still in use. It is often use for computational chemistry and fluid dynamics. 20.1 List of compilers Several different compilers are available: • gFortran (Part of the GNU compiler collection) – v4.8 - Red Hat’s built in gFortran – v4.9 - part of RHDT 3 – v5.3 - part of RHDT 4 – v6.2 - part of RHDT 6 • NVIDIA Portland Group (PGI) Fortran – 17.1 • Intel Parallel Studio XE: – 2017 Update 2 20.2 GCC Several versions of gFortran are available. The standard version, tied to the system GCC version, is v4.8 You can install it like so: sudo yum install gcc-gfortran Later versions are available as part of the RHDT bundles: 61 Linux Desktops Documentation, Release RHEL7 • v4.9: sudo yum install devtoolset-3-gcc-gfortran • v5.3: sudo yum install devtoolset-4-gcc-gfortran • v6.2: sudo yum install devtoolset-6-gcc-gfortran Once you have installed the packages you need to use SCL to use the updated version of gfortran like so: • v4.9: scl enable devtoolset-3 bash • v5.3: scl enable devtoolset-4 bash • v6.2: scl enable devtoolset-6 bash Once those commands are run then running ‘gfortran’ will run the version you requested. See the Software collections (SCL) document for more information on using SCL. 20.3 PGI Fortran The portland group (PGI) compilers, now owned by NVIDIA, are a series of high performance C, C++ and Fortran compilers which are heavily used within high performance computiing. To use the PGI compilers first install the latest version: sudo yum install pgi171 Once installed you should use the Environment modules system to use the compilers: module load pgi/17.1 You can then use pgfortran (the Fortran compiler) directly, or one of the several version specific binaries: • pgf77 • pgf90 • pgf95 See Environment modules system for more information on using the module system. 20.4 Intel Intel’s Fortran compiler - ifort - is part of the Intel Parallel Studio XE product. This is available to you as a member of the University. At the time of writing the latest version - 2017 Update 2 - is available. To install it you can use the following command: sudo yum install intel-parallel-studio-2017u2 This installs all of the components of the Cluster Edition of the Intel Parallel Studio. To use the Parallel Suite you must first load the environment module: module load intel/2017u2 Once loaded all of the environment modules are set such that you should be able to run the configure script (or similar mechanism) and it should use the Intel compiler. You can also use ifort directly. See Environment modules system for more information on using the module system. 62 Chapter 20. Fortran CHAPTER 21 Java Java is a general purpose object oriented programming language and runtime. It is intended to let application devel- opers “write once, run anywhere” through compiling Java code to ‘byte code’ which is then run on the Java virtual machine. 21.1 Java implementations There are several implementations of Java available on the Linux desktop platform: • Oracle - v1.6, v1.7, v1.8 • OpenJDK - v1.6, v1.7, v1.8 • IBM - v1.7, v1.8 We strongly recommend the use of either Oracle Java 1.8 or OpenJDK Java 1.8. You can install the different versions via Desktop Manager or if you prefer here are the commands to run in a terminal to install them instead: Oracle Java 1.6 sudo yum install java-1.6.0-sun-devel Oracle Java 1.7 sudo yum install java-1.7.0-oracle-devel Oracle Java 1.8 sudo yum install java-1.8.0-oracle-devel OpenJDK Java 1.6 sudo yum install java-1.6.0-openjdk-devel OpenJDK Java 1.7 sudo yum install java-1.7.0-openjdk-devel OpenJDK Java 1.8 sudo yum install java-1.8.0-openjdk-devel IBM Java 1.7 sudo yum install java-1.7.1-ibm-devel IBM Java 1.8 sudo yum install java-1.8.0-ibm-devel Sadly the Java packages do not use the Environment modules system or the SCL system, so you will have to use the full path to the java or javac binaries: 63 Linux Desktops Documentation, Release RHEL7 Note: To install TeX modules via sudo tlmgr you need to be in the Administrators group. See Permissions for more information. You can also install modules in your home directory if you prefer. TeX Live 2016 comes with a package manager called tlmgr. You can install modules like so: sudo tlmgr install <modulename> If you prefer to install a module just for yourself, or if you don’t have permission to use sudo tlmgr, run: tlmgr --usermode install <modulename> 66 Chapter 22. TeX Live (LaTeX) CHAPTER 23 R R is an open source programming language intended for use within statistical computing and data analysis. It is not installed by default on the Linux desktop platform but it can be installed easily via the following command in a terminal: sudo yum install R 23.1 Installing R packages There are two methods to installing R packages. Either install them via yum or via CRAN within R itself. Only a limited number of packages are available via yum so we recommend using R itself. To find the list of R packages you can install via yum run this command: sudo yum list R-\* Since very few packages are available its best to install packages via CRAN from within R. First start R in a terminal: R then enter the following command: install.packages("pkgname") Replace pkgname with the package to install, e.g. for Bio3D: install.packages("bio3D") You can install multiple packages like this: install.packages(c("bio3D","devtools")) 67 Linux Desktops Documentation, Release RHEL7 The first time you try to install packages R will prompt you to install into your home directory and create a library there, do so and you will be able to install R packages. Note: If you wish to install the devtools package you should first run the command sudo yum install openssl-devel libcurl-devel libssh2-devel so that the prerequisite development files are available. Sadly there is no easy way to allow via sudo the ability for you to install R packages system wide so any user can use them. This is because you must first start R as root and execute a specific command. We’ll keep working on a way to solve this but as for now you’ll need to install R packages in your home directory - sorry about that! 68 Chapter 23. R CHAPTER 25 OpenMPI OpenMPI is the defacto standard implementation of the Message Passing Interface system. OpenMPI allows develop- ers to create programs that scale across multiple machines. 25.1 Available versions Several versions of OpenMPI are available for use: • Compiled by gcc 4.8 – 1.10.3 (Red Hat package) – 1.10.6 – 2.0.2 • Compiled by gcc 6.2 – 1.10.6 – 2.0.2 – 2.1.0 • Compiled by icc (Intel) – 1.10.6 – 2.0.2 • Compiled by PGI – 1.10.6 – 2.0.2 The implementations are either compiled with the GNU Compiler Collection (GCC), the Intel C/C++ compiler (icc) or the PGI C/C++ compiler. You can use the implementation and version based on the C/C++ compiler you’ve chosen 71 Linux Desktops Documentation, Release RHEL7 to use. All of the GCC versions have been compiled with the RHEL7 default GCC (GCC 4.8). On request we will compile additional versions with newer versions of GCC. 25.2 Installing OpenMPI Select a version and then run the command for that version listed below. You can install all of the different versions at the same time: • 1.10.3 (gcc 4.8): sudo yum install openmpi • 1.10.6 (gcc 4.8): sudo yum install openmpi1106 • 1.10.6 (gcc 6.2): sudo yum install openmpi1106-gcc62 • 1.10.6 (icc): sudo yum install openmpi1106-intel • 1.10.6 (pgi): sudo yum install openmpi1106-pgi • 2.0.2 (gcc 4.8): sudo yum install openmpi202 • 2.0.2 (gcc 6.2): sudo yum install openmpi202-gcc62 • 2.0.2 (icc): sudo yum install openmpi202-intel • 2.0.2 (pgi): sudo yum install openmpi202-pgi • 2.1.0 (gcc 6.2): sudo yum install openmpi210-gcc62 25.3 Using OpenMPI All of the OpenMPI implementations use the Environment modules system. Thus to use an implementation simply module load the version you prefer: • 1.10.3 (gcc 4.8): module load mpi/openmpi-x86_64 • 1.10.6 (gcc 4.8): module load openmpi/1.10.6 • 1.10.6 (gcc 6.2): module load openmpi/1.10.6-gcc62 • 1.10.6 (icc): module load openmpi/1.10.6-intel • 1.10.6 (pgi): module load openmpi/1.10.6-pgi • 2.0.2 (gcc 4.8): module load openmpi/2.0.2 • 2.0.2 (gcc 6.2): module load openmpi/2.0.2-gcc62 • 2.0.2 (icc): module load openmpi/2.0.2-intel • 2.0.2 (pgi): module load openmpi/2.0.2-pgi • 2.1.0 (gcc 6.2): module load openmpi/2.1.0-gcc62 72 Chapter 25. OpenMPI CHAPTER 26 Ruby Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. According to its developers it it has an elegant syntax that is natural to read and easy to write. 26.1 Installing Ruby Red Hat Enterprise Linux 7 includes Ruby version 2.0 and can be installed like this in a terminal: sudo yum install ruby rubygems ruby-devel Other versions are also available as part of SCL: • Ruby 1.9.3: sudo yum install ruby193 ruby193-ruby-devel • Ruby 2.2: sudo yum install rh-ruby22 rh-ruby22-ruby-devel • Ruby 2.3: sudo yum install rh-ruby23 rh-ruby23-ruby-devel To use the other versions of Ruby you must first ‘enable’ them like so: • Ruby 1.9.3: scl enable ruby193 bash • Ruby 2.2: scl enable rh-ruby22 bash • Ruby 2.3: scl enable rh-ruby23 bash For more information see Software collections (SCL) 26.2 Installing gems (packages) Note: To install Ruby gems via sudo gem you need to be in the Administrators group. See Permissions for more information. You can also use gem without sudo to install gems in your home directory. 73 Linux Desktops Documentation, Release RHEL7 76 Chapter 27. Perl CHAPTER 28 Index of specialist software 28.1 Amber Assisted Model Building with Energy Refinement (AMBER) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman’s group at the University of California, San Francisco. • sudo yum install amber16 28.2 autodock AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. • sudo yum install autodock426 28.3 Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. • sudo yum install avogadro120 28.4 BIOVIA Discovery Studio Built on the BIOVIA Foundation, Discovery Studio is BIOVIA’s comprehensive predictive science application for the Life Sciences. • sudo yum install biovia-discovery-studio-2016 77 Linux Desktops Documentation, Release RHEL7 28.5 CCDC CSD System For chemists in academia and industry wanting to discover, access and visualise crystal structures easily to support their research. The CSD-System brings you the essential crystallographic and structural chemistry capabilities to deliver knowledge from the CSD. • sudo yum install ccdc2017 28.6 CUDA See CUDA 28.7 DL_POLY DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Lab- oratory by I.T. Todorov and W. Smith. • sudo yum install dlpoly408 28.8 Dropbox Dropbox is the gold standard file hosting and synchronisation solution for modern operating systems. Although we provide this package we offer no support for Dropbox and please do not store any university data within your Dropbox account. • sudo yum install nautilus-dropbox 28.9 FFTW FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of both real and complex data, and of arbitrary input size. • sudo yum install fftw fftw-devel 28.10 gcc See C and C++ and Fortran 28.11 GNU Plot Gnuplot is a command-line driven, interactive function plotting program especially suited for scientific data represen- tation. Gnuplot can be used to plot functions and data points in both two and three dimensions and in many different formats. • sudo yum install gnuplot501 78 Chapter 28. Index of specialist software Linux Desktops Documentation, Release RHEL7 28.26 Mercury Crystal Structure Visualisation, Exploration and Analysis Made Easy. Mercury offers a comprehensive range of tools for 3D structure visualization and the exploration of crystal packing. • sudo yum install mercury39 28.27 MOE Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. • sudo yum install moe20160802 28.28 netcdf A set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. • sudo yum install netcdf 28.29 NWChem NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. • sudo yum install nwchem nwchem-openmpi 28.30 Octave GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient com- mand line interface for solving linear and nonlinear problems numerically, and for performing other numerical exper- iments using a language that is mostly compatible with Matlab. • sudo yum install octave420 28.31 OpenMPI See OpenMPI 28.32 Perl See Perl 28.26. Mercury 81 Linux Desktops Documentation, Release RHEL7 28.33 PGI Compilers See C and C++ and Fortran 28.34 Povray The Persistence of Vision Ray Tracer, or PoV-Ray is a ray-tracing program which generates images from a text-based description of a scene. • sudo yum install povray37 28.35 PyMol PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. • sudo yum install pymol1840 28.36 Python See Python 28.37 R, RStudio and RStudio Server See R RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax- highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace manage- ment. • sudo yum install rstudio • sudo yum install rstudio-server 28.38 SageMath SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. • sudo yum install sagemath751 28.39 Team Viewer TeamViewer is a proprietary computer software package for remote control, desktop sharing, online meetings, web conferencing and file transfer between computers. • sudo yum install teamviewer 82 Chapter 28. Index of specialist software Linux Desktops Documentation, Release RHEL7 28.40 texlive See TeX Live (LaTeX) 28.41 USCF Chimera UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. • sudo yum install chimera1112 28.42 VirtualBox VirtualBox is a powerful PC virtualization solution allowing you to run a wide range of PC operating systems on your Linux system. This includes Windows, Linux, FreeBSD, DOS, OpenBSD and others. • sudo yum install VirtualBox-5.1 28.43 VisIT VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. • sudo yum install visit2121 28.44 VMD VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. • sudo yum install vmd193 28.45 VTK VTK is an open-source software system for image processing, 3D graphics, volume rendering and visualization. VTK includes many advanced algorithms (e.g., surface reconstruction, implicit modeling, decimation) and rendering techniques (e.g., hardware-accelerated volume rendering, LOD control). • sudo yum install vtk vtk-qt 28.46 xdvi A legacy previewer for DVI files within the X Window System. • sudo yum install texlive-xdvi 28.40. texlive 83 Linux Desktops Documentation, Release RHEL7 86 Chapter 29. EPEL CHAPTER 30 IUS 30.1 Inline with Upstream Stable IUS is a repository of add on software for Red Hat Enterprise Linux. It provides up to date copies of important tools like Python, PHP and Git. Although it is intended primarily for use on servers IUS provided packages for Python and PHP offer the latest stable releases and are thus excellent for desktop users of those programming languages too. A complete list of IUS packages is available here. 87 Linux Desktops Documentation, Release RHEL7 88 Chapter 30. IUS