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Add python-cairo-devel
 
Add python-cairo-devel
  
Add python-Cython
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Add python-Cython (may need an upgrade later, see below)
  
 
Add python-dateutil
 
Add python-dateutil
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If missing cacert files are reported when running pip or easy_install, be root user to remove the certifi package with the command line "pip uninstall certifi". In Opensuse Leap 42.1 the certifi package modifies the default search paths for cert files, and does not provide the certifi versions  in a location that setup.py will find them.  Removing certifi fixes the issue.
 
If missing cacert files are reported when running pip or easy_install, be root user to remove the certifi package with the command line "pip uninstall certifi". In Opensuse Leap 42.1 the certifi package modifies the default search paths for cert files, and does not provide the certifi versions  in a location that setup.py will find them.  Removing certifi fixes the issue.
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 +
Cython installed in OpenSuse Leap may be outdated.  Some packages (notably pywcs) require a more recent version.  Therefore before installing packages upgrade Cython
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Upgrade Cython (pip  install --upgrade Cython)
  
 
Install pyephem (pip install pyephem)
 
Install pyephem (pip install pyephem)

Revision as of 20:02, 13 August 2016

The observatory's servers and control computers run on the OpenSuse distribution of Linux-based software. Most current systems use the long-term (Evergreen) 13.1 release which is expected to be maintained until late 2016. Our evolving installation notes given below are being rewritten for the latest version With version 13.2 there were major structural changes affecting remote, unattended, computer operation: the full implementation of systemd and the introduction of wicked, a new comprehensive network manager based on dbus, and the use of the BTRFS root file system. Leap 42.1, the current distribution, provides a significantly improved wicked implementation and versatile hardware support. Except for older Nvidia video cards, install an Nvidia driver after the default installation and remove or disable the Nouveau community driver. With that exception, the installation from a USB iso image will work.

The following describes how to build a system with OpenSuse that provides a solid foundation of software for physics and astronomy for real-time control of telescopes and observatories, operating small servers, and processing astronomical data.


Before Installation

Prepare a DVD or a USB memory stick with the ISO image of the 64-bit distribution. OpenSuse's imagewriter is a convenient way to create the correct structure on the USB device.

On a new system not using RAID, deselect RAID in BIOS if it is offered. This will prevent OpenSuse from creating disk partitions with RAID.

For most new machines allow UEFI (custom option, if available) and disable compatibility mode. The installer will identify the system as allowing UEFI and properly select the boot configuration. However, also use the BIOS setup to change the boot priority to the medium reflecting this choice. The boot medium and a UEFI installation must match.

Opensuse will detect and set up a UEFI boot protocol unless this option is turned off in the BIOS. With that selection it will handle and format large disks.


During installation

Insert the medium, reboot the system, and select Installation from the splash screen. If there is a booting problem, use the keyboard to bring up a boot selection screen (often F11 or F12), and check the boot order and if needed also the BIOS setup.

At this point if the system has a recent Nvidia card it also may be best to disable modeset. The symptom this is necessary is that subsequent booting freezes before the installation begins. With Leap 42.1 edit the boot options by pressing "e" before the system tries to start an installation. This will open a simple boot editing screen with instructions.

At the end of the line for linux add "nouveau.nomodeset=0" .

Continue with the installation as instructed on this editing screen. The default settings should work with the following additions and exceptions.

Deselect software by taking the checkmark off with a spacebar press. After installation is complete, return to the software menu of YAST and make sure that those items never to be install (pk-update is the worst of them) are marked "Taboo". For now, just do not install them.

Select a user interface of "Other" rather than KDE or Gnome, and then Xfce as default environment to have a lightweight but fully functional system.

Select almost all packages by group except Apparmor which should be marked "taboo". Include PHP, MySQL, and Apache unless not needed not needed for your use. Decline KDE and Gnome desktop but add their development code. Some KDE and Gnome applications may be loaded individually later. Do not install laptop tools unless you are configuring a laptop. Otherwise network management will default to be selectively controlled by the user rather than by the system at boot time.

Set the computer system clock to use UTC, check the time zone and the local time.

The gparted package may be useful to manage disks larger than 2 TB. As of Opensuse 13.2 with new disks the installer will use BTRFS for the root partition and XFS for the remainder to make full use of large disks on UEFI systems. In the event of a failure, leaving a critical disk formatted in the wrong size or filesystem, add gdisk from a repository and reformat the disk. Reboot, and re-install the operating system on the reformatted disk.

While it would be preferred to use 100 GB for the root directory in a BTRFS, Opensuse by default allocates a marginally large enough 40 GB. It is sufficient for the base system, and if large files are needed in /usr/local/ they can be located in the /home partition with a soft link from /usr/local. The remaining space on the system disk will be formatted as XFS. An advantage to putting locally installed software in /usr/local/ and having that outside of the root partition is that in subsequent upgrades there is less risk of losing special software installations.

Deselect and mark "taboo" Apparmor for systems which do not require its access controls.

Add nano so that you will have a simple terminal-based editor after booting the first time

Delete pk-update to avoid nagware about package updates and mark it for non-installation permanently by selecting "taboo"

Turn off firewall (assuming your system is already behind an institutional or local firewall)

Open port for SSH

Check the boot option for grub2 on a non-UEFI system

Complete the installation from the media (either USB or DVD)

Remove the medium, reset the boot priority to the hard disk, reboot


From OpenSuse using YAST

Start yast from the command line as su with yast --qt

Disable DVD or USB in software respositories

Unless doing GPU development or you have recent nvidia hardware, do not include the repository for nvidia (creates a long term maintenance problem) and use the Nouveau Xorg driver

Perform all updates based on default respositories as needed

Note that in removing packages, as of OpenSuse 13.2, select Options --> Cleanup when deleting packages to prevent their automatic reinstalling though the preselection feature of Yast. Generally it is not necessary to remove packages unless there is something about them that interferes with your use of the system. In most cases they may be disabled in subsequent system configuration.

Remove really annoying pk-update-icon if you missed deleting it initially. You will have to mark it in YAST for permanent deletion.

Add Nvidia respository ftp://download.nvidia.com/opensuse/13.2/ if needed and nvidia graphics/gpu drivers

Add lsb5

Add apache if used as web server

Add php and packages if used as web server

Add gsl and gsl-devel

Add nano

Add timidity

Add audacity

Add audio-recorder

Add celestia (kde-celestia)

Add stellarium

Add galculator

Add gedit

Add gnome-disk-utility (previously palimpsest)

Add gnumeric

Add gtkglext-devel

Add hdf5 (required by Python Pynpoint-exoplanet)

Add hdf5-devel

Add hdf5-devel-static

Add imagewriter

Add libatlas3 (optional required by astromatic software)

Add libatlas3-devel (optional required by astromatic software)

Add lua-devel

Add mlocate

Add nasm (used by openh264)

Add netpbm

Add libnetpbm-devel

Add okular

Add pavucontrol (pulse audio control to work around problems with defaults)

Add plplot

Add plplot-devel (optionally other plplot packages as needed)

Add python-cairo-devel

Add python-Cython (may need an upgrade later, see below)

Add python-dateutil

Add python-distutils-extra

Add python-Distutils2

Add python-idle

Add python-matplotlib and related packages

Add python-numpy

Add python-numpy-devel

Add python-pip

Add python-qt4

Add python-scipy

Add python-scipy-weave

Add libevent-devel

Add fftw3-devel, fftw3-threads, and fftw3-threads-devel

Add xfig

Add ufraw

Add gimp-ufraw

Add gphoto but not gphotofs

Add qiv

Add luvcview

Add motif

Add motif-devel

Add motif-devel-32bit

Add other motif libraries if they are not installed by default

Remove all virtualbox rpm's installed from OpenSuse

Add yasm

Add yasm-devel

Add libpng12-devel

Add libpng16-devel

If using Grace earlier than 5.1.25 deselect libpng16-compat-devel and select libpng12-compat-devel

Add fxload (used by SBIG cameras)


After updates

Disable modemmanager because it interferes with serial ports used for instruments

Disable avahi as unnecessary in our environment

Edit /etc/sysconfig to set locate default search to root

Use YAST to set NTP servers for your domain rather than Opensuse's defaults


From source in /usr/local

For rpm packages use zypper --non-interactive install package.rpm or add --no-gpg-checks if necessary.

Install nedit from rpm to /usr/bin and link to /usr/local/bin

Add lame and lame library packages for mp3 audio

Build and install ffmpeg from source using ./configure --enable-pic

Build and install vlc from source (VLC) using ./configure --disable-mad --disable-a52

Install mplayer through the command line svn checkout svn://svn.mplayerhq.hu/mplayer/trunk mplayer

Install ds9

Install xpa

Install cfitsio and manually copy lib64 and include installation directories to /usr/local/lib64 and /usr/local/include

Install grace (build from source with local FFT modifications for normalization)

Install ImageJ (separately from AstroImageJ below if needed for other features)

Install Aladin

Install xephem

Install astrometry.net

Install swarp

Install sextractor

Install psfex (current release does not build in Opensuse 13.2 due to plplot differences)

Install cinepaint if available or if it will build from sources

Install moodle (depends on mysql, apache, and php) on educational servers

Install mediawiki on servers as needed


Python

For OpenSuse Leap both Python-2.7 and Python-3.4 are installed. By default /usr/bin/python points to Python-2.7, but pip and easy_install will have softlinks in /etc/alternatives pointing to Python-3. Since we still work in Python-2.7, remove the softlinks in /etc/alternatives and redefine them to point to /usr/bin/pip2.7 and /usr/bin/easy_install-2.7 so that these commands will work in our environment. This has to be redone whenever there is a software upgrade too.

If missing cacert files are reported when running pip or easy_install, be root user to remove the certifi package with the command line "pip uninstall certifi". In Opensuse Leap 42.1 the certifi package modifies the default search paths for cert files, and does not provide the certifi versions in a location that setup.py will find them. Removing certifi fixes the issue.

Cython installed in OpenSuse Leap may be outdated. Some packages (notably pywcs) require a more recent version. Therefore before installing packages upgrade Cython

Upgrade Cython (pip install --upgrade Cython)

Install pyephem (pip install pyephem)

Install stscipython with astropy using pip install stsci.distutils then pip install stscipython or

Alternatively install pyfits and pywcs using pip install pyfits and pip install pywcs

Install healpy (healpix)

Install reproject (image reprojection for fits conversion)

Install quantities (physical constants)

Install emcee (MCMC)

Install pyastronomy (pip install pyastronomy) or from source on github pyastronomy

Upgrade cython to the current release (pip install --upgrade cython)

Install scikit-image (pip install scikit-image). With OpenSuse Leap 42.1 the version of Cython installed is Cython-0.19.2. However scikit-image requires a more recent version. The Cython upgrade is required to install scikit-image.

Optionally install Pynpoint-exoplanet (pip install Pynpoint-exoplanet)

Configure matplotlibrc in /usr/lib64/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc for the GTK3Cairo backend. Since this default configuration may change on upgrades, each user should also have a copy of their preferred configuration in their .config/matplotlib/matplotlilbrc . The GTK3Cairo backend is compatible with the Xfwm and IceWm window managers and with the Xfce desktop that is on most of our systems.


From local software in /usr/local

Install AstroImageJ

Install AstroCC

Install Alsvid

Install sidereal

Install xmtel (if needed)

Install xmccd (provides libcfitso and xpa if needed)


Update /etc

Copy motd

Edit HOSTNAME

Add entries to /etc/rc.d/boot.local

Add profile.local

Edit /etc/dnsmasq.conf as needed



Settings for the network

Configure network as needed for additional cards defined for internal zone

Configure dnsmasq as needed to service one or more cards

Add masquerade to firewall settings if internal zone present (required for dnsmasq ip forwarding)

Start the firewall if using dnsmasq or needing the security it provides

Start dnsmasq

Run services manager and turn off unused services

Run lsof -i to confirm there are no insecure open ports

Reboot the system

With Opensuse 13.2's use of the wicked network daemon, a configured network device will not show its IP until it is physically connected to an active network. The yast configuration option "at boot time" for network configuration means that these ports must see a live connection when the system is booted to find their configuration. This is not a bug, it is a "feature". The alternative option "on cable connection" is not useful for a fixed instrument controller. If a device is physically connected and does not show its IP in ifconfig, try "systemctl restart network.service" or a reboot.


Desktop

Run nvidia-settings to set display for a system with Nvidia hardware if the Nvidia drivers are installed. The latest community Nvidia support is adequate for most purposes without installing the proprietary Nvidia driver and kernel module. The system is more easily maintained if it runs using the community supported package which is improving quickly.


OpenGL with Nvidia

Users should be members of the video group to have access to opengl applications. If they are not, the application may run slowly (glxgears) or crash (celestia). For some applications with older hardware the Nouveau open source driver will suffice and be less likely to interfere with system updates later. This driver is compatible with randr and allows command line setting of multiple displays. For example if there are two displays on the graphics card, a command line such as

  • xrandr -q

will list the available displays and their capabilities, while one such as

  • xrandr --output DVI-I-2 --right-of DVI-I-1

will configure them as one screen providing acceleration across the desktop.

Newer Nvidia cards and all of the Quadro family require loading the lastest nvidia driver and the kernel modification. Add Nvidia as a repository and use YAST to manage the updates. Reboot the system afterwards.


Flash and Freshplayer

Do not install the proprietary and outdated Adobe Flash that is offered in the distribution. Remove it if it has already been installed before doing a system update.

Flash is now blocked by default in Firefox and will be deprecated and blocked in Google Chrome by the end of 2016. For those websites still using Flash, install Google Chrome for web browsing. It supports remaining non-complaint web flash usages and defaults to HTML5 when possible. Chrome has its own version of the Flash library for this purpose that Google keeps up to date.

Install the Freshplayer plugin (available from the distribution) to provide Flash support for Firefox. When Firefox is started it will find the version of Flash installed by Chrome and provide the translation for Firefox.


gPhoto2

The gphoto2 application runs Nikon DSLR cameras for real-time observing, scripted imaging, and called by cgi routines from a web server. To give the USB device the proper permissions without invoking unwanted software (the default for a Gnome installation in OpenSuse), we make sure that libgphoto2 is installed, but not the file system. In OpenSuse 13.2 there will not be a udev rules file installed by default.

As root user,

cd /etc/udev/rules.d

/usr/lib64/libgphoto2/print-camera-list udev-rules version 175 group video mode 0666 > 90-gphoto.rules

where the version given has to be high enough to work with udev and still be recognized by libgphoto2.

Add the video group to users who will be observers, and to the user wwwrun by editing /etc/group or by using YAST.

When a camera is connected or turned on, it will accessible by any user in the video group, including the cgi applications used for remote operations.


exFAT

Add fuse-exfat from OpenSuse package search, currently version 1.1.0

  • zypper --non-interactive install fuse-exfat-1.1.0-2.1.x86_64.rpm

This provides support where needed for SDXC memory cards through the Microsoft exfat filesystem.


VLC

The version of VLC that can be installed with Yast lacks all proprietary codecs necessary for many common uses. The OpenSuse version should not be installed. To build from source --

  • Install lua and lua-devel if not already installed
  • Download the latest source tarball from VLC (currently 2.2.1)
  • Use the latest openh264 source tar file, compile, and install
  • Use the latest ffmpeg source tar file, compile, and install
  • Untar ffmpeg
  • ./configure --enable-pic --libdir=/usr/local/lib64 --enable-libmp3lame --enable-libopenh264
  • make
  • make install
  • ldconfig
  • Untar vlc
  • ./configure --disable-mad --disable-a52
  • make
  • make install


Mplayer

  • Install the source code in /usr/local/src/ --
  • svn checkout svn://svn.mplayerhq.hu/mplayer/trunk mplayer
  • Untar the codecs and skin files into /usr/local . We use a collection saved in mplayer_codecs.tar.gz that installs into share/mplayer and lib/codecs
  • In the source directory, ./configure --enable-gui then make, make install



VirtualBox

VirtualBox as supplied by OpenSuse cannot be updated using the Oracle site. Instead of installing their version, we use the latest Oracle RPM which is currently version 5.0.14. Version 5.0 and higher supports USB3 in the host OS, and is therefore advisable for camera or storage drive use.

  • Set the BIOS to allow virtualization technology and to allow advanced I/O for sharing resources.
  • Retrieve the packages from https://www.virtualbox.org/wiki/Linux_Downloads .
  • zypper --non-interactive install -no-gpg-checks install VirtualBox-5.0-5.0.14_105127_openSUSE132-1.x86_64.rpm .
  • Retrieve the extension pack from Oracle's download site.
  • VBoxManage extpack install Oracle_VM_VirtualBox_Extension_Pack-5.0.14-105127.vbox-extpack.
  • In Opensuse YAST, add the Virtualbox guest kernel modules and guest tools, or use the guest additions from Oracle.
  • As root run /etc/vboxadd-service .
  • Create a directory that will be shared with the guest OS and set this up in virtualbox when building a virtual machine .
  • Once the guest OS is installed, add the guest additions to it also, to enable the shared directory and mouse/pointer integration .
  • Add the virtualbox group to the user(s) who will run it .
  • Start the qt interface from the command line with virtualbox .
  • Lastly, read the Virtualbox on-line manual .

For access to the USB system the guest OS must have a driver installed. Virtualbox presents a virtual xHCI USB3 device to the guest. The driver provided by Intel has worked for us in a Windows 7 installation.


OpenGL

Users must belong to the video group to have access to OpenGL when NVidia drivers are in use.


Skype

Skype is supported on Linux through its new Alpha version under rapid development. It integrates with the web version of Skype, and should soon allow the same features as the older obsolete Skype. Alternatives which are very good and also cross platform for video conferencing are Ezuce and Zoom. All of them offer a selection of audio devices within the application, but pavucontrol is also useful when the applications fail to detect the preferred hardware.


Wireless

Laptops by default will have networkmanager running their hardware and wireless connections. Desktops will not. To enable desktop wireless with minimal need for configuration, use Yast, Network Settings, and Global Settings to select networkmanager rather than wickedd. With that change, there will be a desktop icon in the system tray and the interface may be selected by the user.

Few USB network adapters work with the Linux kernel in OpenSuse 13.1 . Only one we have found readily available new is the Buffalo Nfinity Wireless-N compact USB 2.0 adapter. It is recognized immediately and requires no additional configuration, other than the selection of networkmanager, and the user's choice of connection.


Static LAN and dnsmasq

We use dnsmasq to manage local area networks (LAN) from a second network device on telescope computers. Typically the device address is set to 192.168.0.1/24, or to 1.1/24 if there is another LAN operating. The configuration file for dnsmasq is set to point to the device, i.e. eth1, to which the switch is attached.

This works well if (a) there is a switch attached and turned on, and (b) the computer is running the wickedd manager which is the default in current Opensuse releases based on systemd. It is seeming not possible, or certainly not straightforward, to run a lan from a laptop which is configured with networkmanager.

To attach a networked instrument such as a camera to a laptop that by default is configured with network manager the options are

  • Attach the device to a switch which itself is integrated into a LAN with DHCP provided by another computer system
  • Change the laptop networking to run wickedd instead of networkmanager.

The disadvantage to the second option in the laptop world is that wickedd does not have the end-user support for wireless networking that networkmanager provides. Further, when switching from one system to another, there are inevitable configuration issues, particularly with the management of host resolution and the file /etc/resolv.conf.

The basic process is to use yast or yast2, select network device configuration, and change the manager to wickedd. This will allow editing the individual network devices. Set the static ip address for the device that will handle the LAN, edit the device entry, change it to "internal", and set it to activate on boot through the setting in the Global tab. Shutdown and reboot the system. The ethernet adapter must be inserted at boot time.

As superuser use "wicked show all" to see the status of the devices, or "wicked ifstatus eth1" to see the status of one network device. Each device has a configuration file in /etc/sysconfig/network/, such as ifcfg-eth1 for eth1. Within that file there should be a line which says

LINK_REQUIRED=no

As of Opensuse 42.1, this line is not inserted by the yast2 configurator, and consequently the network device will stall and wickedd will report "setup-in-progress". The simple solution is to enter this by hand if you see this error and need a second network active on power up.