Program+installation+and+setup

=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

 * =FireFox and Thunderbird Troubleshooting=
 * =Ubuntu: Save Dialog causes delays, hangs and crashes of the system=
 * =svn problem after installing ubuntu 10.3=

Simulation software

 * =Schrodinger Suite 2010=
 * =Desmond=
 * =ADF 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/ .default/ rm -f .parentlock # note, this file is invisible, but you shoul delete it

2. The same about the thunderbird
cd ~/.mozilla-thunderbird/ .default/ rm -f .parentlock

3. After the rebooting the forward/backward surfing in firefox did not work
cd ~/.mozilla/firefox/ .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: []

=svn problem after installing ubuntu 10.3=


 * Problem:**

When i type: > >     svn export http://sergiiev@triton.mis.mpg.de/svn/fedorov/Main/Bibliography/bibtexfilegeneral.bib > > it writes: > >   Password for '(null)' GNOME keyring: > > When i type ENTER the answer is: > >   svn: OPTIONS of 'http://sergiiev@triton.mis.mpg.de/svn/fedorov/Main/Bibliography/bibtexfilegeneral.bib': > authorization failed: Could not authenticate to server: rejected > Basic challenge (http://triton.mis.mpg.de)


 * Solution:**

add password-stores = in the "[auth]" section of your ~/.subversion/config file.

=Simulation software=

Schrodinger Suite 2010
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
 * ===Help does not work===

===Running Desmond in parallel with SGE system===
 * ==Desmond==

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:

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
 * 1) schrodinger.host(schrodinger or .schrodinger directory)name: host_name #should be diggerent from defined in 'host' line

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

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).