Upgrading SHARP/autoSHARP
From time to time we will announce upgrades (patch releases) to an
existing SHARP/autoSHARP release (see release notes). Please follow the
instructions very carefully.
It is not recommended to just upgrade your SUSHI 3.4.X to 3.8.0
- instead a fresh installation should be done, following the instructions here.
If you want to carry over some existing configurations, please check
the Notes for users of old versions of SHARP.
The basic, underlying structure hasn't changed that much between 3.2.X
and 3.4.0 - with two exceptions:
- a new external program is being used (SHELXC/SHELXD for
heavy atom detection in autoSHARP): this requires the correct
configuration - using the administrative script
$BDG_home/adm/bin/shelx-setup
- the interface to the submission mechanism has been updated and
slightly altered: if the administrator configured their own submission
mechanims (rsh, DQS, LSF, etc), the local configuration in
$BDG_home/submit.local needs to be updated
- a new script for setting up connection to external
helpers (like O, Xfit, Coot, Plotmtv etc) can simplify setting
these up for the user. This is available in $BDG_home/bin/add2rdf.sh.
Therefore, the recommended upgrade procedure is the following:
- get all new files from the download page into the
SHARP/autoSHARP installation directory ($BDG_home).
- if a local submission mechanism was configured: get the
differences between the previously distributed mechanism and the
locally configured ones:
% cd /where/ever/sharp
% diff -cr submit submit.local > submit.local.diff
- unpack/install SHARP/autoSHARP:
% cd /where/ever/sharp
% ./installSHARP -u # to just unpack new files
- or -
% ./installSHARP -U # to unpack new files and run through
# the whole configuration again (recommended)
- update machine-specific configuration for each
machine (i.e. each machine with its own subdirectory inside the
$BDG_home/machines directory):
% cd /where/ever/sharp
% source ./setup.csh # for csh/tcsh
% foreach m ( `find machines/ -type d | sed "s%machines/%%g"` )
adm/bin/newmachine $m
end
- or -
% . ./setup.sh # for sh/bash/ksh
% for m in `find machines/ -type d | sed "s%machines/%%g"`
do
adm/bin/newmachine $m
done
This will also check the machine-specific configurations for CCP4,
ARP/wARP and MAPMAN (since these might have changed since the last
installation). The relevant configuration files for .e.g CCP4 can
always be found in $BDG_home/machines/*/ccp4.setup - but you
should use the corresponding administrative scripts
(e.g. $BDG_home/adm/bin/ccp4-setup) to update these if
necessary!
- let every user re-run the script useSHARP:
% /where/ever/sharp/useSHARP <SHARP account>
- update your submission system: if you configured your own
submission system (in $BDG_home/submit.local) you might need to adapt
the files in $BDG_home/submit.local to follow the new
format/requirements in $BDG_home/submit.
- It is highly recommended to use the checkBDG.sh
script afterwards to test the new installation/upgrade (and try to
follow the recommendations it might give):
% cd /where/ever/sharp
% source ./setup.csh # for csh/tcsh
- or -
% . ./setup.sh # for sh/bash/ksh
% adm/bin/checkBDG.sh
Since a lot of changes have occured between 3.0.15 and 3.2.0, you
might want to do a fresh installation (following the installation
instructions at the SHARP/autoSHARP installation pages.
It is also possible to upgrade your existing installation (which might
be easier if you have a lot of users and machines or configured your
own submission system). This can be done using
- get all new files from the download page and
unpack/install SHARP/autoSHARP:
% cd /where/ever/sharp
% ./installSHARP -u # to just unpack new files
- or -
% ./installSHARP -U # to unpack new files and run through
# the whole configuration again
- update machine-specific configuration for each machine
(i.e. each machine with its own subdirectory inside the
$BDG_home/machines directory):
% cd /where/ever/sharp
% source ./setup.csh # for csh/tcsh
% foreach m ( `find machines/ -type d | sed "s%machines/%%g"` )
adm/bin/newmachine $m
end
- or -
% . ./setup.sh # for sh/bash/ksh
% for m in `find machines/ -type d | sed "s%machines/%%g"`
do
adm/bin/newmachine $m
done
This will also check the machine-specific configurations for CCP4,
ARP/wARP and MAPMAN (since these might have changed since the last
installation). The relevant configuration files for .e.g CCP4 can
always be found in $BDG_home/machines/*/ccp4.setup - but you
should use the corresponding administrative scripts
(e.g. $BDG_home/adm/bin/ccp4-setup) to update these if
necessary!
- update your submission system: if you configured your own
submission system (in $BDG_home/submit.local) you will need to adapt
the files in $BDG_home/submit.local to follow the new
format/requirements in $BDG_home/submit (since the various scripts for
e.g. dqs, lsf, rsh etc have changed).
- It is highly recommended to use the checkBDG.sh
script afterwards to test the new installation/upgrade (and try to
follow the recommendations it might give):
% cd /where/ever/sharp
% source ./setup.csh # for csh/tcsh
- or -
% . ./setup.sh # for sh/bash/ksh
% adm/bin/checkBDG.sh
If you're running SUSHI 3.0.X and want to upgrade to the latest SUSHI
3.0.15:
- download all necessary
new files into your current $BDG_home directory
(i.e. where you installed SHARP/autoSHARP in - it should contain
a .licence and .bdgrc file). The files you need are usually
- architecture independent files: installSHARP,
sushi.tar.gz, sharp_tutorials.tar.gz
- architecture dependent file(s): sharp.linux.tar.gz and/or
sharp.irixn32.tar.gz and/or sharp.alpha.tar.gz
- run the update procedure (see also the Sushi 3.0.15 Release
notes on the download page)
% cd $BDG_home
% chmod +x installSHARP
% ./installSHARP -U
- that should be it
- if you have trouble: please have a look at notes
If you're running SUSHI 3.0.X and want to upgrade to the latest SUSHI
3.0.14:
- download all necessary
new files into your current $BDG_home directory
(i.e. where you installed SHARP/autoSHARP in - it should contain
a .licence and .bdgrc file). The files you need are usually
- architecture independent files: installSHARP,
sushi.tar.gz, sharp_tutorials.tar.gz
- architecture dependent file(s): sharp.linux.tar.gz and/or
sharp.irixn32.tar.gz and/or sharp.alpha.tar.gz
- run the update procedure (see also the Sushi 3.0.14 Release
notes on the download page)
% cd $BDG_home
% chmod +x installSHARP
% ./installSHARP -u
- that should be it
- if you have trouble: please have a look at notes
If you're running SUSHI 3.0.0 or 3.0.1 you should upgrade to the
latest bug fix release. You can find your SUSHI version at the top of
the "SHARP Control Panel" or in the file
$BDG_home/sushi/.version.
Note : this procedure will overwrite any changes that you've
done in directory $BDG_home/submit. If you've followed the
recommendations in the "BDG Installation manual" (Chapter 5
: Submission mechanisms and queuing systems) you will have all your
local configuration in directory $BDG_home/submit.local and
nothing will get overwritten.
Here are the steps that should get your SUSHI version up-to-date
- Download the latest versions of
the following files to your existing SHARP/autoSHARP
installation directory ($BDG_home):
installSHARP
sushi.tar.gz
sharp_tutorials.tar.gz
Note : you can of course also download additional files
(but these are the necessary ones).
- Then run the following commands:
% adm/bin/kill_server
% chmod +x installSHARP
% ./installSHARP -f
When asked about "Copy configuration from previous SHARP
installation" you should answer "no".
- The sample files contain two new SHARP input files
(samples/sharp/cardfiles/IF3-C.1.sin and
samples/sharp/cardfiles/KrEl.1.sin) that users might
want to fetch.
Last modified:
20.07.2009