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Darkmatter Server Info 2013 Rebuild

Pre-2013 configuration here


The server is a Dell PowerEdge T710 with dual 6-core CPUs (Intel® Xeon® X5680, 3.33Ghz, 12M Cache,Turbo, HT, 1333MHz), 60 Gb RAM (6x2Gb 1333MHz, 1Gb/core & 4x12Gb, 4Gbx3, CT1026036 240-pin DIMM from crucial at $345 per kit), 175 Gb boot volume (RAID1) and 7.7Tb data volume (RAID5).

Development Environment

Compilers installed via package build-essential

GNU auto tools installed via packages autoconf automake autotools-dev.

GNU fortran (version 4.6) installed via the gfortran package.

Mercurial (hg) installed via apt-get install mercurial.

Git repository management via Gitolite.


There is no X11 server or window manager installed, but X11 clients can be built and run on the server. See here for rationale and details.

Installed Packages

Installed via ubuntu package manager:

  • libpng 12 (pkg libpng12-dev)

  • lapack 3.3.1 (pkg liblapack-dev)

  • imagemagick
  • csh
  • openmpi-bin openmpi-doc libopenmpi-dev
  • gpicview
  • python-numpy python-matplotlib python-scipy python-pyfits

The following packages were installed to allow ROOT to be built from source. See details here:

  • libx11-dev
  • libxpm-dev
  • libxft-dev
  • libxext-dev

Installing mathematica requires the following additional packages to be installed via apt-get:

  • smbfs (needed for the network install of mathematica)
  • libXmu-dev (needed to run the graphical front-end)
  • libasound2

Mathematica installed into /usr/local/Wolfram/Mathematica/9.0 on 9-Jan-2013 following the instructions How to Install Mathematica on Linux via the Network. The install script reports an error:

$ cat /usr/local/Wolfram/Mathematica/9.0/InstallErrors 
xdg-desktop-menu: No writable system menu directory found.

This doesn't really seem to be problem since we are not running a desktop environment.

To run mathematica on the server, just follow section 5 of the installation instructions. The activation key is common to all users and the name of the network license server is flexlm.oit.uci.edu.

Built from source into /usr/local:

  • boost 1.52.0 (See here for details) Updated to 1.56 on 26-Aug-2014.

  • GSL 1.15

  • cfitsio 3.310

  • SZIP 2.1 and HDF5 5-1.8.10 (using ./configure --prefix /usr/local --enable-cxx for HDF5)

  • FFTW 3.3.3 with the following build configs:

    • float: ./configure --enable-sse --enable-float --enable-shared

    • double: ./configure --enable-sse2 --enable-shared

    • long double: ./configure --enable-long-double --enable-shared

  • ROOT 5.34 (See here for details.)

  • Minuit2 5.28.00 (pkg root-plugin-minuit2 pulls in all of ROOT 5.18)

The following were installed following the Galsim installation: (See here for details.)

  • python-dev
  • scons

To Do

GIT code repository installed via packages git-core, gitosis. See here for details. It appears gitosis is no longer supported.

  • condor 7.2 (Note: condor is not available from the ubuntu repo for 12.04. Also, the software package has been renamed HTCondor)

Built from source into /usr/local:

  • ffmpeg video encoder (See here for details.)


Running MoinMoin served via apache2 with mod-wsgi. Most pages are readonly except for trusted users.

Filesystem Info

Notes on setup of backup and data volumes are here.