Mod:Hunt Research Group/mac setup

make a group

open accounts in system prefs

click on the + button

choose groups on pulldown menu

type in a name and add those users you want to belong to the group

in this case call the group "hunt_group"

exit

set-up the terminal

create the file ".bash_profile"

copy and paste the following into it

#echo "bash_profile"
. ~/.bashrc

create the file ".bashrc"

copy and paste the following into it

# .bashrc
# WARNING: had to make .bash_profile and added  execute to this file
#
#  important stuff
#
# tells the computer where to look for personal scripts
   export PATH=$PATH:/Users/$USER/bin:/usr/local/bin
#
# change the prompt
   export PS1="[\$USER@\h]\$PWD \$ "
#
# control-R lets you search backward through history
   HISTSIZE=100
   EDITOR=vi
   export EDITOR
#
#  gaussian
#
# where to fine the executable
   export g09root="/Applications"
# set the default memory
   export GAUSS_MEMDEF="500MB"
# where to put the LARGE temporary files when running gaussian
   export GAUSS_SCRDIR="/Users/$USER/Work/Jobs/tmp"
# script which sets many variables for gaussian
   source $g09root/g09/bsd/g09.profile
#
#   gaussview
#
# where to find gaussview
   export GV_DIR="/Applications/gv"
# libraries 
   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${GV_DIR}/lib
# allow start from the comand line in mac terminal
   alias gv="open $GV_DIR/gview.app"
#  
#  alias definitions            
#
   alias home="cd"
   alias force="grep -i 'Maximum Force'"
   alias dist="grep -i 'Maximum Disp'"
#

create the file ".login"

this is needed because gaussview looks for csh stuff

copy and paste the following into it

setenv g09root /Applications
source $g09root/g09/bsd/g09.login
setenv GAUSS_SCRDIR /Users/$USER/Work/Jobs/tmp
setenv GV_DIR /Applications/gv

of course replace my name with your name (or directory structure)

and the directory tmp should exist before you run any jobs.

set-up working directories

make a directory called "work", keep ALL your files here

inside work make a directory called "jobs", keep all your gaussian jobs here

inside work make a directory called "testing" ie full path is /Users/name/work/jobs/testing

vi a file "test.com" and copy and paste the following into it

ps don't forget the last line must be blank

%chk=test.chk
%mem=500MB
%nproc=1
# hf/3-21g geom=connectivity

Title Card Required

0 1
 C
 H                  1              B1
 H                  1              B2    2              A1
 H                  1              B3    3              A2    2              D1
 H                  1              B4    3              A3    2              D2

   B1             1.07000000
   B2             1.07000000
   B3             1.07000000
   B4             1.07000000
   A1           109.47120255
   A2           109.47125080
   A3           109.47121829
   D1          -119.99998525
   D2           120.00000060

 1 2 1.0 3 1.0 4 1.0 5 1.0
 2
 3
 4
 5

install gaussian

insert the CD

double click on the .dmg file

a CDROM disk icon will appear

in a terminal window cd /Volumes/CDROM (or name of CD)

read the "readme" file

change to the cshell

csh

tell the script where gaussian (G09) is to be installed

    setenv g09root "/Applications"

now goto the g03root directory

    cd $g09root

read the CD

cat /Volumes/CDROM/tar/*.tgz | zcat | tar xvf -

this will unpack and copy the contents of the CD, you should see a stream of file names, when this stops and the prompt returns

ensure that the group permissions are set

chgrp -R gaussian g09 

check this has worked, type "ls -al"

you should see a list with the following

drwxr-x---  154 name  hunt_group   5236  1 Nov  2007 g09

goto the gaussian directory and run the install script

cd g09
./bsd/install

eject the disk

you are not quite ready to run as the variables g09root, GAUSS_SCRDIR and the g09.login script need to be set in your .bashrc file ... this was done in the terminal instructions above

you may also want to get rid of the pesky error "-bash: ulimit: open files: cannot modify limit: Invalid argument" which shows up because you have asked "source $g09root/g09/bsd/g09.profile" in your .bashrc

goto the direcotry g09/bsd

edit the file g09.profile, goto the end and hash out the following command

#turned off by tricia to stop error message
#ulimit -n hard

now you are ready to run a test job

nohup means don't stop if you logout

the trailing & means run in the background

cd work/jobs/testing
nohup g09 test & 

ls to see that the job is running and that test.chk and test.log files are being generated.

check that the job finishes ok

install gaussview

getting ready

insert the CD

double click on the .dmg file

a CDROM disk icon will appear

in a terminal window cd /Volumes/CDROM (or name of CD)

read the "readme" file

do the install

change to the cshell

tell the script where the cd is mounted

    csh
    setenv g09root "/Applications"
    cd $g09root

now read and unpack the CD

cat /Volumes/CDROM/tar/*.tgz | zcat | tar xvf -

change the group premisions to the same as those for g09

chgrp -R hunt_group gv 

eject the disk

gaussview uses csh, so you need to have a .login if you want to run from the launcher

check that you have the following in your .login

setenv g09root /Applications
source $g09root/g09/bsd/g09.login
setenv GAUSS_SCRDIR /Users/tricia/Work/tmp
setenv GV_DIR /Applications/gv_5.0
setenv GAUSS_EXEDIR /Applications/g09

set-up quick starting of gaussview

goto the Applications folder and click on the gv folder

drag the gaussview icon into the launcher

double click to start gaussview

if you get an error saying that it cannot find gaussian directories then

cd to the gv directory

cd into the data directory

edit the gpath.txt file (and give the correct path to the g03 application)

/Applications/g09

quit gaussview and then restart it, your problem should be fixed

set-up preferences

now we need to set some directories in the preferences of gaussview

click on preferences

choose the "File?Directory" option

under the starting directory, choose Specify, click on the "..." button and pick your work/jobs directory

under the scratch directory, choose "Use GAUSS_SCRDIR"

test run a job

start X11 (this is in Applications/Utilities folder, drag the X11 app to a launcher)

type "gv" in the window (and press return)

choose "open" and goto your /work/jobs/testing directory, open your test.com file

submit it to run (save as test_1.com) so that you don't overwrite the other test job

check that it finishes OK

open your test molecule's com file

set-up easy remote connections

create the file "config" in your home/.ssh directory

see heiko's notes for what to put in it.