Mod:Hunt Research Group/mac setup

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Revision as of 11:35, 11 March 2011 by Phunt (Talk | contribs) (→‎set-up the terminal)

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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/tricia/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 g03root="/Applications"
# set the default memory
   export GAUSS_MEMDEF="500MB"
# where to put the LARGE temporary files when running gaussian
   export GAUSS_SCRDIR="/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/tricia/Work/tmp
setenv GV_DIR /Applications/gv_5.0
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=6MW
%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
in a terminal window cd /Volumes/CDROM (or name of CD)
read the "readme" file
change to the cshell
csh
tell the script where the cd is mounted
    setenv mntpnt "/Volumes/CDROM"
you can check this has worked by typing echo $mntpnt
tell the script where gaussian (G03) is to be installed
    setenv g03root "/Applications"
now goto the g03root directory
    cd $g03root
read the CD
cat $mntpnt/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 hunt_group g03
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 g03
goto the gaussian directory and run the install script
cd g03
./bsd/install
eject the disk
you are not quite ready to run as the variables g03root, GAUSS_SCRDIR and the g03.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 g03 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 mntpnt "/Volumes/CDROM"
    setenv g09root "/Applications"
    cd $g09root
now read and unpack the CD
cat $mntpnt/tar/*.taz | zcat | tar xvf -
change the group premisions to the same as those for g03
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/yannis/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/g03
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.
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