GAMESS Installation Instructions for UnionTech OS GNU/Linux 20

1.Visit the GAMESS homepage and request a copy of the “64 bit x86_64 under Linux using gnu compilers” source code

2.Download the source code file, gamess-current.tar.gz, using the username “source” and the password in the email message that you received.

My UOS example:

3.Make sure you have csh and gfortran and patch installed

sudo yum install csh gcc-gfortran  #for CentOS and Amazon Linux
sudo yum install patch  #for CentOS and Amazon Linux

or

sudo apt-get install csh gfortran  #for Debian, Ubuntu, UOS
sudo apt-get install patch  #for Debian, Ubuntu, UOS​

My UOS example:

4.Uncompress the archive

cd ~
tar xzf ~/Downloads/gamess-current.tar.gz

My UOS example:

5.Install math libraries MKL ( recommendation , not required, it depends on the choice of step 6 )

  •  Download the MKL source file and uncompress
cd ~/Downloads/
curl -O https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/l_mkl_2020.4.304_online.tgz
tar vfx  l_mkl_2020.4.304_online.tgz 

My UOS example:

  • Install MKL with GUI
cd l_mkl_2020.4.304_online/
./install_GUI.sh

My UOS example:

  • Notice:  the default install path is $HOME/intel ,in my example  the path is /home/ditan/intel  Remeber the path,we will use it in step 6.
  • With the GUI click the “Next” ->”Next->”Install ” ,wait till the installation complete.(ps.This will take 5 minitues or more, keep the Internet connected)

6.Configure the GAMESS installation

cd ~/gamess
./config
  • Follow the on screen prompts
  • Set the machine type to linux64
  • Leave the gamess installation directory as the default
  • Leave the gamess build location as the default
  • Leave the gamess version number as 00
  • Enter “gfortran” for your choice of FORTRAN
  • Follow the onscreen instructions to obtain the gfortran version
  • If you have “MKL” math libraries installed, enter “MKL” ,otherwiser enter “none”
  • Use “sockets” rather than MPI
  • Answer “no” to LibXC interface, CCT3 & CCSD3A methods, and LIBCCHEM options

 My UOS example:

(1) please enter your target machine name: linux64

(2)GAMESS directory? [/home/ditan/gamess] Press Enter 

(3)GAMESS build directory? [/home/ditan/gamess] Press Enter 

(4)Version? [00] Press Enter 

(5)Please enter your choice of FORTRAN: gfortran

(6)Please enter only the first decimal place, such as 4.9: 8.3

To check the version of gfortran use commands below:

fortran -v

(7)hit to continue to the math library setup.Press Enter

(8)Enter your choice of ‘mkl’ or ‘atlas’ or ‘acml’ or ‘libflame’ or ‘openblas’ or ‘pgiblas’ or ‘armpl’ or ‘none’: mkl

(9)MKL pathname? /home/ditan/intel/mkl                            # it depends on step 5  path setting.

(10)MKL version (or ‘proceed’)? proceed

(11)please hit to set up your network for Linux clusters.Press Enter

(12)communication library (‘serial’,’sockets’ or ‘mpi’ or ‘mixed’)? sockets

(13)Optional: Build LibXC interface?  (yes/no): no

(14)Optional: Build Michigan State University CCT3 & CCSD3A methods? (yes/no): no

(15)Do you want to try LIBCCHEM? (yes/no): no

(16)the finnal outputs in my exmale:

Your configuration for GAMESS compilation is now in
/home/ditan/gamess/install.info
Now, please follow the directions in
/home/ditan/gamess/machines/readme.unix

7.Compile ddi

cd ~/gamess
make ddi

 My UOS example:

8.Compile modules

cd ~/gamess
make modules
My UOS example:

9.Compile gamess (takes >10 minutes)
cd ~/gamess
make -j 4          #The "-j" specifies the number of jobs (commands) to run, will save your time on compiling.
 My UOS  example:

9.Update the rungms  script

find the lines  :

set SCR=/scr1/$USER
set USERSCR=~/gamess-devv
set GMSPATH=~/gamess-devv

 Edit the following lines to read as follows

set SCR=/tmp
set USERSCR=/tmp
set GMSPATH=~/gamess
Use tool gedit or vim or sed edit the file like below:
gedit ~/gamess/rungms
or
vim ~/gamess/rungms
or
cd ~/gamess
sed -i 's/\/scr1\/$USER/\/tmp/' ./rungms
sed -i 's/USERSCR\=\~\/gamess-devv/USERSCR\=\/tmp/' ./rungms
sed -i 's/GMSPATH\=\~\/gamess-devv/GMSPATH\=\~\/gamess/' ./rungms

10.Update the runall  script,repalce the first the “si.msg.chem.iastate.edu” with your real hostname

check your hostname like this:
$ hostname
My UOS example:

 Replace the hostname in the runall script with  sed( you can also do it with gedit or vim )
sed -i "s/si.msg.chem.iastate.edu/$HOSTNAME/" ~/gamess/runall  
#Notice: You can only exceute it once,or you'll meet the following error: "xgms: Command not found" .
 My UOS example:

ps. only repalce the first “si.msg.chem.iastate.edu” not all in the script file.

11.Test the program by running all of the short tests.

cd ~/gamess
./runall 00
A script to check all test results automatically can be found in the file ~/gamess/tests/standard/checktst.execute it after above commands finished.
~/gamess/tests/standard/checktst
If the finnal output with  “All 48 test results are correct!”, it shows gamess works well!
My UOS example:

12. To make it easy to access the ‘rungms’ script,It’ better to define alias in the .bashrc files such as alias gms ‘$HOME/gamess/rungms’.

echo "alias gms='$HOME/gamess/rungms'" >> ~/.bashrc                #for Debian, Ubuntu, UOS​
or
echo "alias gms='$HOME/gamess/rungms'" >> ~/.bash_profile           #for CentOS and Amazon Linux​

This will allow them to execute their input file xxx.inp using this universal script, by

gms xxx >& xxx.log &​​

When only one argument is given, the version number will be what you customized in ‘rungms’ and the number of processors will default itself to 1.

My UOS example:

13.Erros Workarounds:

ddikick requires significant amounts of shared memory. If your output file contains the error message:

DDI Process 0: error code 911
ddikick.x: application process 0 quit unexpectedly.
ddikick.x: Fatal error detected.
The error is most likely to be in the application, so check for input errors, disk space, memory needs, application bugs, etc.
ddikick.x will now clean up all processes, and exit…

you can try increasing your shared memory. First display the amount of shared memory available (in bytes):

# cat /proc/sys/kernel/shmmax

Then try increasing it to 4GB:

# echo 4294967296 > /proc/sys/kernel/shmmax
# echo "kernel.shmmax=4294967296" >> /etc/sysctl.conf

or try increasing it to 16GB:

# echo 17179869184 > /proc/sys/kernel/shmmax
# echo "kernel.shmmax=17179869184" >> /etc/sysctl.conf

References:

A.source mannul file1:~/gamess/README.md

B.source mannul file2:~/gamess/machines/readme.unix

C.GAMESS Installation Instructions for Linux

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