SL6 Reinstallation Checklist

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Revision as of 22:26, 3 April 2014 by Elke (talk | contribs) (→‎PACKAGES)
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This page lists all publicly used programmes that need to be reinstalled following the upgrade from Scientific Linux 5 to 6. As can be seen here, installation of our software on the original SL6 testbed system went smoothly, so I don't anticipate any significant problems in reinstalling (famous last words…).


Most of our public code is in on AFS at


with less-used or untested packages in the subdirectory


To keep the process from being too disruptive I suggest we create temporary directories in which to reinstall everything, mirroring the above, namely:


Once everything is in place we can then simply replace the existing PACKAGES directory with the new one (and retain the old one for a while for reference).

Temporary copy of SL5 install directories

Most of our PACKAGES don't "install" anywhere; all the build products are located only in their source directory (PACKAGES/blah/). However some of our PACKAGES (e.g. LHAPDF) and many of our TOOLS install under


To minimise disruption while recompiling everything, I have duplicated all the install directories (e.g. bin, lib) under


and modified the eic_cshrc logon script to refer to these instead. If you are building anything that needs to install under the top directory (e.g. anything with a make install step) you can and should install it under


For now, if you need to test the results, you should change your logon script to source


instead of the default


which will continue to point to the SL5 versions until everything is reinstalled.


The table below contains a list of all programmes currently in the PACKAGES directory, though there are a number we likely no longer need. I also included EicRoot, though it is not located in the same directory. Please observe the following:

  • Once an package is reinstalled change the "✔" column from "N(o)" to "Y(es)", to make it easy to see what still needs to be done.
  • I have assigned someone to reinstall each package, typically the person who originally installed it. Feel free to change this if you want to reassign responsibility from (or to!) yourself (but of course, please tell the other person affected!).
  • If there is a newer version of the programme available that could be installed instead of the original, I have noted it in the Upgrade column. If you do install this (or another) later version, please enter the version you use there; if not (i.e. you reinstall exactly the same version), delete the upgrade entry.
  • If a package is no longer needed then mention it in the Notes, but don't delete it from the list .
  • Enter any other miscellaneous notes you want to leave in the Notes column.


Name Assigned Upgrade Notes
Y DJANGOH-4.6.10 Tom B./Elke Pythia 6.4.28, LHAPDF 5.9.1 and jetset-7.4.10
N DPMJetHybrid Liang
Y eicplot Tom B. Installed for ROOT 5.28.00c, 5.30.01 and 5.34.18
N EicRoot Alexander
Y eic-smear Tom B. Multiple versions: 0.0.0, 1.0.0, 1.0.1, 1.0.2, 1.0.3, trunk. 1.0.3 and trunk are installed against ROOT 5.34.18, as opposed to 5.34.05 under SL5. The others are unchanged from SL5.
N FASTJET Matt 2.4.5
Y fastjet-3.0.6 Tom B.
Y flair Tom B. Not installed; FLUKA only currently used for linking by other packages, not used directly
Y fluka Tom B. Made 2 installations: 32bit with g77 (fluka-32) and 64bit with gfortran (fluka-64)
Y gmc_trans Tom B.
Y LEPTO-PHI-32BIT Mark/Elke LHAPDF-5.9.1, letset-7410
Y LHAPDF-5.8.6 Elke 5.9.1 5.9.1 installed, also 6.0.5. See also here.
Y milou32 Sal
N Opera_14R1 Oleg
Y PYTHIA-64BIT Tom B. Not installed (was just a test directory under SL5)
Y PYTHIA-PP Elke 6.4.28
Y PYTHIA-RAD-CORR-32BIT Elke 6.4.28 latest Pythia-6 version installed 6.4.28 all updates I and Mark did to pythia included.
N RAPGAP-3.2 Matt
Y root_v5.28.00c Tom B. For backward compatibility with older Monte Carlo trees
Y root_v5.30.01 Tom B. For backward compatibility with older Monte Carlo trees
Y root_v5.34.05 Tom B. 5.34.18 Installed both 5.34.05 and 5.34.18 for now, but maybe best to just go with 5.34.18
N sartre Tobias


A number of these were installed by me originally at the request of Tobias (because computers hate him), so I have assigned them to him :D

Name Assigned Upgrade Notes
N cascade-2.2.06 Tobias
Y CASCADE-2.2.06 Elke Duplicate of cascade-2.2.06, not compiled
N FLmrst2002 Ramiro Not compiled
N GiBUU Matt
N herafitter-0.2.0 Tobias
N herafitter-0.3.0 Tobias
N herafitter-1.0.0 Tobias
N hztool-4.2 Tobias 4.3
N hztool-4.2-32bit Tobias 4.3
N jimmy-4.31 Tobias
N jimmy-4.31-32bit Tobias
N mcatnlo_hadr Tobias 4.10?
N mcatnlo_point Tobias 4.10?
N mcatnlo_point64 Tobias 4.10?
Y pythiaeRHIC Tom B. Both 1.0.0 (first stable release) and svn trunk
N qcdnum-17-00-06 Tobias
N smartre Tom B.
Y torino32 Tom B. Renamed to just "torino" as it is actually a 64-bit build


These are general (non-physics) software utilities. I will take care of installing all of them, but everyone should check whether the packages they are installing have dependencies here.

Most of these will be installed under the main EIC AFS area, so they will need to go there directly, not first to a temporary directory like PACKAGES-SL6, to make sure any install paths they record are correct.

Name Assigned Upgrade Notes
N boost Tom B. Symlink to Boost in FAIRROOT, will be updated automatically when that is reinstalled
Y boost_1_53_0 Tom B. 1.55.0
Y cmake- Tom B.
Y cmake-2.8.9 Tom B. See above
Y git- Tom B. 1.9.1
Y gnuplot Tom B. 4.6.5
Y graphviz-2.36.0 Tom B.
Y gsl Tom B. See below
Y gsl-1.14 Tom B. 1.16 gsl is a symlink to this
Y gsl-1.14-32bit Tom B. Not installed. AFAIK we do not need an additional 32-bit install
Y kcachegrind-0.7.4 Tom B. Not installed as our system is missing some KDE developer packages and I don't know where to find them. It wasn't actually installed under SL5 either - just the source code was there. It's not very important, so forget it.
Y LHAPDF-6.0.4 Tom B. 6.0.5 Moved to PACKAGES, see notes there
Y matplotlib-1.3.1 Tom B.
Y mercurial-2.8-rc Tom B. 2.9.1
Y numpy-1.7.1 Tom B. 1.8.0
Y Python-2.7 Tom B. 2.7.6 Priority - a dependence for a number of others (inc. ROOT)
Y scons-2.3.0 Tom B. 2.3.1
Y yaml-cpp Tom B. 0.5.1 Not sure which version is installed

New additions:

Name Assigned Upgrade Notes
Y docutils-0.11 Tom B. Python module required by Mercurial
Y scipy Tom B. 0.14.0b1
Y vim Tom B. 7.4 Fix error messages with system vim because of clash between system and our Python

Outstanding Issues

  • pythiaeRHIC should have a new stable release 1.0.1 to include Elke and Mark's PYTHIA updates.
  • LHAPDF 6 needs to be checked for compatibility with our Fortran codes. The authors claim 6 is backward-compatible with Fortran, but I encountered problems with an undefined symbol (structa_) when I attempted to link PYTHIA against version 6 libLHAPDF.