Program installation and setup page


This page is devoted to the different problems arising during configuring, installation, setup and use of different programs of mutual interest.

General software



Simulation software


General software


FireFox and Thunderbird Troubleshooting


There can be several problems after the killing the firefox (rebooting without logout)

1. Firefox does not start and writes: "Another copy of firefox is running but not responding"


cd ~/.mozilla/firefox/<random string>.default/
rm -f .parentlock # note, this file is invisible, but you shoul delete it

2. The same about the thunderbird


cd ~/.mozilla-thunderbird/<random string>.default/
rm -f .parentlock

3. After the rebooting the forward/backward surfing in firefox did not work


cd ~/.mozilla/firefox/<random string>.default/
rm -f places.sqlite
rm -f places.sqlite-journal


---

Ubuntu: Save Dialog causes delays, hangs and crashes of the system


I have experienced, that from time to time on my Ubuntu system the opening of Open/Save dialog (e.g in gedit, or while taking the screenshot) cause the hanging of the system.

Some people blame the tracker application for this. See more details on:
https://bugs.launchpad.net/ubuntu/+source/tracker/+bug/229539


svn problem after installing ubuntu 10.3


Problem:

When i type:

Solution:

add

password-stores =

in the "[auth]" section of your ~/.subversion/config file.


Simulation software


Schrodinger Suite 2010

  • Help does not work

If there are any problems with Acroread 8 or 9, the work-around is to install a copy of Adobe Reader 7 and point SCHRODINGER_PDF_VIEWER to it. This way you still have Reader 8 for regular use while forcing Maestro to use Reader 7 to search through manuals.
The same can be considered for Python links from Help; if they are not opening for some reason, you can set the MAESTRO_HELP_BROWSER environment variable to point to Firefox.
Maestro does not work neither with Konqueror nor with Epiphany.
Note: "on-line" help opens local files. In my case it was:
file: /opt/local/schrodinger/docs/python_api/overview.html - Python module
~/.schrodinger/help/2010/maestro/load_help.html - getting help
~/.schrodinger/help/2010/maestro/load_python_api.html - Python API references


  • Desmond

Running Desmond in parallel with SGE system


Desmond should NOT be submitted with manually prepared SGE-batch script. It has sophisticated algorithm for creating such a scripts. All specification are made in QUARGS line of schrodinger.host file
User has to define:

#schrodinger.host(schrodinger or .schrodinger directory)name: host_name #should be diggerent from defined in 'host' line
queue: SGE
qargs: -q long.q -l long -pe smp %NPROC% # this commands are in SGE original documentation, they are varyable...so...feel free to improove them
host: hydra # ip adress or any other name recognised with DNS server of the LOCAL network
processors: N # this number can not exceed the real number.
schrodinger: path/to/schrodinger/directory
tmpdir: path/to/scratch/directory

#queue/SGE/config
QPATH=path/to/SGE/system
QPROFILE=path/to/settings.sh
QSUB=qsub
QARGS=
QDEL=qdel
QSTAT=qstat
LICENSE_CHECKING=

Submission script is generated automatically (even via GUI).
Submission command line looks like:

$SCHRODINGER/application [options] (!!!) -HOST /hostNAME /(!!!)/ /-in *.cms -c *.cfg


ADF software


ADF is available on the Hydra cluster. You have
to request the resource "adf" while submitting your job,
e.g. interactively via

    • qlogin -l adf=TRUE

or in a script

    • #$ -l adf=TRUE

(ADF is restricted to a single computer, hence, this setup).

Afterwards, you have to set up the environment for ADF, e.g.

    • source /opt/local/scm/adf2010.01/adfrc.csh

and can then start your computations. ADF is installed in /opt/local/scm/adf2010.01

While testing the installation, I noticed a strange behaviour
of ADF when not defining the number of CPUs to use, which resulted
in an error. If I used the switch "-n 1" (for 1 CPU), everything
worked fine. When using more CPUs, do not forget the "-pe smp"
switch (see http://hydra.mis.mpg.de).