Tuesday, August 24, 2010

Installing GAMESS on a linux PC


Probably best viewed in full screen mode

2014.02.18 Update: See this post by +Jimmy Charnley Kromann for more up-to-date instructions

Alchemist requested a post on installing GAMESS on a linux system: after all "I[f] someone can not install a program, how he/she can use it?" Fair enough.

If you have a mac or windows machine, pre-compiled versions of GAMESS is available (see this post on for installing such a version on Macs).  But if you have bought a linux computer, you do have to compile GAMESS yourself.

Three disclaimers:
(1) The post is aimed at people who want to install GAMESS on their personal computer that happens to run linux.
(2) The post is based on installing the March 25, 2010 version of GAMESS and corresponding scripts as they were distributed in mid August, 2010.  If you view this post a few years from now things may have changed.
(3) I don't have a linux PC, so the screencast is made on a shared research computer.  This affects one of the steps as I describe below, and may affect others steps that I don't know about.

The screencast assumes you have already downloaded gamess (gamess-current.tar.Z).  To download GAMESS start here and follow the instructions.  If you have problems watch the first few minutes of the screencast this post.

Here's a summary of the steps in the  screencast:

1. Unpack GAMESS: type "zcat gamess-current.tar.Z | tar -xvf -"
Now you should have a GAMESS directory.  The file gamess/misc/readme.unix has most of the instructions you need.  What follows it basically a condensed version with a few modifications.

2. In the GAMES directory: type "./config".
Follow the instructions and answer the questions.  You need to know whether you have a 32- or 64-bit chip.

3. Type "/sbin/sysctl -w kernel.shmmax=1610612736"
If you are curious about what this does, read section 5 of the file gamess/ddi/readme.ddi.
You need to be logged in as root for this to work.  I don't have root access on the machine I used, so I get an error message in the screencast.  But our system administrator had executed the command previously.

5. Change to the ddi subdirectory (gamess/ddi)Type "./compddi >& compddi.log" and then "mv ddikick.x .."

6. Go back to the gamess directory and type "./compall >& compall.log"
It will take 30-60 minutes to compile GAMESS.

7. Type  "./lked gamess 00 >& lked.log"

8. Edit the file rungms.  Here are the lines I modify or add:
set SCR=./
set USERSCR=./
set GMSPATH=./

setenv ERICFMT ./ericfmt.dat
setenv MCPPATH ./mcpdata

setenv  MAKEFP $USERSCR/$JOB.efp
setenv   GAMMA $USERSCR/$JOB.gamma
setenv TRAJECT $USERSCR/$JOB.trj
setenv RESTART $USERSCR/$JOB.rst
setenv   INPUT $SCR/$JOB.F05
setenv   PUNCH $USERSCR/$JOB.dat

   if ($os == Linux)   set GMSPATH=./

#  if ($NCPUS == 1) then
#     set NNODES=1
#     set HOSTLIST=(`hostname`)
#  endif
#
   set HOSTLIST=(`hostname`:cpus=$NCPUS)
   set NNODES=1 

#           echo I do not know how to run this node in parallel.
#           exit 20

9. Edit one line in the file runall: #chdir /u1/mike/gamess.
Type "./runall >& runall.log"

10. Go to the tools/checktst subdirectory and type "./checktst"
(Update: if the gamess directory is not in your home directory, you need to change this in the checktst file.  See this comment)

Running GAMESS in parallel
If you computer has more than one core, you may want to run GAMESS in parallel. To run exam01 on 2 cores type "./rungms exam01 00 2 >& exam01.log &"


Other useful programs and getting started with GAMESS
Now that you have GAMESS running you may want to install other useful programs such as Avogadro, GAMESSQ, and MacMolplt.
Here are some related blogposts to wet you appetite:
Using GAMESSQ
Building a complicated molecule with Avogadro

And here are a few blogposts on getting started with GAMESS:
Some GAMESS input basics
A typical set of GAMESS calculations

Acknowledgment: Mike Schmidt and Casper Steinmann helped with this post.

August 30, 2010 update: Alchemist has made the following page on installing GAMESS on Ubuntu 64 bit.  Be sure to check out the comments for additional useful links.

October 20, 2010:  Are you using Ubuntu 9.10 and 10.04, Linux Mint 8 and 9, Knoppix 6.2.1 or Suse 11.2? Be sure to check out this comment by Mott.
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