445. GAMESS US 2013 R1 on Debian (Wheezy) -- w/o GPU

Update 27/6/2013:
Please note that Kirill Berezovsky has published a series of posts on GAMESS US, including how to compile it for both CPU and GPU use. See
http://biochemicalmatters.blogspot.com.au/2013/06/gamess-us-frequently-asked-questions_26.html
http://biochemicalmatters.blogspot.ru/2013/06/gamess-us-frequently-asked-questions_1687.html
http://biochemicalmatters.blogspot.ru/2013/06/gamess-us-frequently-asked-questions_1447.html
http://biochemicalmatters.blogspot.com.au/2013/06/gamess-us-frequently-asked-questions.html


Original post:
A new version of GAMESS is out now (2013 R1): https://groups.google.com/forum/?fromgroups#!topic/gamess-announce/8j1esKifzEo

GPU support will be a later post.

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0. Install a math library
You can use e.g. acml or atlas. See http://verahill.blogspot.com.au/2013/05/422-set-up-acml-on-linux.html for acml (which I've only had luck with on AMD machines).

To get the debian ATLAS libs do

sudo apt-get install libatlas3-base libatlas-dev

If you want to compile your own ATLAS libs, see e.g. http://verahill.blogspot.com.au/2012/09/rocks-543-atlas-and-gromacs-on-xeon.html or http://verahill.blogspot.com.au/2012/09/compile-atlas-gromacs-nwchem-on-amd-fx.html

You can also link to openblas, as shown in this post: http://verahill.blogspot.com.au/2012/09/compiling-and-testing-gamess-us-on.html

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1. Get GAMESS US
Go to http://www.msg.chem.iastate.edu/GAMESS/download/register/
Check the tick boxes next to the architectures you intend to use GAMESS on. Fill out your email address, and hit Submit. You'll receive an email with instructions almost immediately.

The email will contain a URL to an archive with the source code, and a password for downloading it.
I'll presume that you downloaded the file, gamess-current.tar.gz, to ~/Downloads.

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2. Untar and prepare
I'm presuming that you don't already have any /opt/gamess or /opt/gamess/gamess directories. In my earlier write-ups (e.g. this) I put everything in /opt/gamess, which isn't a good long-term strategy since you often want to keep earlier versions of computational software alongside newer ones.

sudo apt-get install build-essential gfortran openmpi-bin libopenmpi-dev libboost-all-dev
sudo mkdir /opt/gamess -p
sudo chown $USER:$USER /opt/gamess
cd /opt/gamess
cp ~/Downloads/gamess-current.tar.gz gamess-2013r1.tar.gz
tar xvf gamess-2013r1.tar.gz
mv gamess gamess-2013r1
cd gamess-2013r1/

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3. Configure
NOTE: Even if you may have gfortran 4.7 (e.g. Wheezy) you should give the version as 4.6 during configure (see below).

./config

please enter your target machine name: linux64
GAMESS directory? [/opt/gamess/gamess-2013r1] 
GAMESS build directory? [/opt/gamess/gamess-2013r1]
Version? [00] 13
Please enter your choice of FORTRAN: gfortran
Please enter only the first decimal place, such as 4.1 or 4.6:  
4.6

ACML:

Enter your choice of 'mkl' or 'atlas' or 'acml' or 'none': acml
enter this full pathname: /opt/acml/acml5.3.1
Math library 'acml' will be taken from /opt/acml/acml5.3.1/gfortran64_int64/lib

Atlas:
I've compiled ATLAS myself in the past, but the libs have not worked with all programs. Here we use the debian libs instead.

Enter your choice of 'mkl' or 'atlas' or 'acml' or 'none': atlas
Please enter the Atlas subdirectory on your system: /usr/lib/atlas-base
Math library 'atlas' will be taken from /usr/lib/atlas-base

mpi:

communication library ('sockets' or 'mpi')? mpi
Enter MPI library (impi, mvapich2, mpt, sockets): openmpi
Please enter your openmpi's location: /usr/lib/openmpi

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4. Build
Edit comp and change

1663 #           -fno-whole-file suppresses argument's data type checking
1664       set OPT='-O2'
1665       if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"

to

1663 #           -fno-whole-file suppresses argument's data type checking
1664       set OPT='-O0'
1665       if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"

or exam44.inp will fail.

cd ddi/
./compddi
cd ../
./compall

If you are building with openmpi, edit lked and change

958             case openmpi:
 959                set MPILIBS="-L$GMS_MPI_PATH/lib64"
 960                set MPILIBS="$MPILIBS -lmpi"
 961                breaksw

to

958             case openmpi:
 959                set MPILIBS="-L$GMS_MPI_PATH/lib"
 960                set MPILIBS="$MPILIBS -lmpi"
 961                breaksw

Make the proper symlinks if you are using ATLAS:

sudo ln -s /usr/lib/atlas-base/libatlas.so.3 /usr/lib/atlas-base/libatlas.so
sudo ln -s /usr/lib/atlas-base/libf77blas.so.3 /usr/lib/atlas-base/libf77blas.so

./lked gamess 13r1 

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I use my own script called gmrun:

#!/bin/csh
set TARGET=mpi
set SCR=$HOME/scratch
set USERSCR=/scratch
set GMSPATH=/opt/gamess/gamess-2013r1
set JOB=$1
set VERNO=$2
set NCPUS=$3

if ( $JOB:r.inp == $JOB ) set JOB=$JOB:r
echo "Copying input file $JOB.inp to your run's scratch directory..."
cp $JOB.inp $SCR/$JOB.F05

setenv TRAJECT $USERSCR/$JOB.trj
setenv RESTART $USERSCR/$JOB.rst
setenv INPUT $SCR/$JOB.F05
setenv PUNCH $USERSCR/$JOB.dat
if ( -e $TRAJECT ) rm $TRAJECT
if ( -e  $PUNCH ) rm $PUNCH
if ( -e  $RESTART ) rm $RESTART
source $GMSPATH/gms-files.csh

setenv LD_LIBRARY_PATH /usr/lib/openmpi/lib:$LD_LIBRARY_PATH
mpiexec -n $NCPUS $GMSPATH/gamess.$VERNO.x|tee $JOB.out
cp $PUNCH .

To run, do e.g.

gmrun exam01.inp 13r1 2