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Installation of deMon2k and running calculations

This guide refers to the installation of the deMon2k master version using the install script based on CREX, shipped with the deMon2k software package. The installation guide is also available for download as a compressed postscript file (53 kb) and as a compressed pdf file (53 kb). For installing of other deMon2k branches see the Program Branches section.

Before installing deMon2k
How to install deMon2k
How to compile deMon2k
How to run deMon2k

1. Before installing deMon2k

FORTRAN90 compiler
To install deMon you will need an Unix or Linux operating system running on your machine and a working FORTRAN90 compiler. If you do not have a FORTRAN90 compiler install it first. You can find different FORTRAN90 compilers in the net. Some are free of charge.

Bourne Again Shell
You will need a Bourne Again Shell (bash) for the installation of deMon. The bash is included in almost all current Linux distributions and installed by default. However, if you are running a Unix system like AIX or IRIX, the bash might be missing. If you are not sure if you have the Bourne Again Shell just type

which bash

in a console. If you have bash you should get a message like

/bin/bash

If not, you have to install bash first. You can check the web for available packages or contact your system administrator.

MPI
The deMon code is parallelized using the MPI (Message Passing Interface) routines. If you want to run deMon in parallel you need to install MPI in your system first (not included in the deMon package).

2. How to install deMon2k

The deMon2k program is shipped as a packed archive deMon2k.sh (For obtaining the installation package see the download section). For the installation unpack the deMon archive deMon2k.sh first by typing

sh ./deMon2k.sh

then change into the unpacked directory deMon.x.y, where x.y corresponds to the version number. Inside this directory you will find the deMon program tree, the LICENSE file, a README file and the install script. If you want to install deMon accessible for all users of a maschine you should become root fist. Then run the installation script by typing

./install

And follow the instructions of the script. The script will first display the license text which you have to confirm. After this you will be asked for the directory, where you want to install deMon.

Where do you want to install deMon [/usr/local]?

The standard directory for installing deMon as root is

$CREX_ROOT=/usr/local

If you accept this just hit < Enter >, otherwise choose another directory by giving the absolute path. The script will check, if the path exists. If not, it will be create automatically. If you have already installed an older version of deMon, the script will ask you, if you want to update the version. If you choose to do so, the script will install the new version and make it the default. The older versions will not be deleted. If you try to install the same version again, you will be asked, if you want to override the version which is already installed. In this case, the old files will be deleted.
The installation script tries now to identify your operating system and the platform you are using. If your system is unknown to the script, you will have to specify compiler and link flags by yourself. For this purpose, you have to edit the file "database.new". Some instructions will be provided by the installation script. For more information see the README file in the directory deMon.x.y, the FAQ section of this web page or the deMon user's guide.
If your system was recognized by the script you will be asked for the type of installation.

    Choose a compilation type:

      1. Standard compilation
      2. Debug compilation
      3. Optimization compilation
      4. Parallel MPI compilation
      5. Parallel MPI debug compilation

    Select a number:

The installation will start. The install script uses CREX to do the compilation. You will see the message

Compiling with CREX

when CREX takes over the control. After the successful installation you will see the message

deMon installation successful

You should modify your profile according to the information provided by the installation script at the end of the installation process. If you are updating your deMon version, you will be asked if some files like AUXIS, BASIS and so on should be updated, too.
If the compilation was not successful the installation script will abort with the message

deMon compilation failed

In this case you should check the README file in the directory deMon.x.y for trouble shooting, the FAQ section of this web page or the deMon user's guide.

3. How to compile deMon2k

Once deMon is installed in your system you might want to recompile an executable because you need to change some parameters or you want to include some modifications. The deMon program is shipped with two compilation scripts called CREX and crex (CReate EXecutable).

CREX
The CREX script can be used to recompile or create a (new) master version of deMon. This is done also by the installation script. If you have created during the installation e.g. an optimized version "opt" and you want to generate now a debug version "dbg", you can do this by running CREX. The master version is usually installed in a directory accessible for all users of a machine. The standard directory is /usr/local. Therefore, you should do this installation as root. CREX expects the following settings:

    $CREX_ROOT=/usr/local              ! or another directory where 
                                       ! deMon is/will be installed;
                                       ! will be installed; you have 
                                       ! to export this variable 
    $CREX_ROOT/deMon/.default-version  ! contains the version number 
                                       ! x.y of the version to be 
                                       ! compiled
    $CREX_ROOT/deMon/x.y/source/       ! directory for source files
    $CREX_ROOT/deMon/x.y/include/      ! directory for include files
    $CREX_ROOT/deMon/x.y/database/     ! directory for database files

The variable $CREX_ROOT must point to the directory where the master version of deMon is installed, if it is not installed in /usr/local. If all files are there type

    CREX

If you are running on a LINUX system the following menu can appear:

    Select compiler (Linux only).

      1. Portland Group pgf90
      2. Intel Fortran 90

    Enter a number:

Choose your compiler and type < Enter >. Afterward choose which kind of executable should be created.

    Choose a compilation type:

      1. Debug compilation
      2. Standard compilation
      3. Optimization compilation
      4. Parallel MPI compilation
      5. Parallel debug compilation

    Select a number:

CREX will start with the compilation. After successful compilation and linking CREX will terminate with the message

    Executable program deMon.x.y.* created.
  
    Normal termination of crex.

The executable is written to

    $CREX_ROOT/x.y/object.*/object.*/deMon.x.y.*

where the "*" stands for the type of executable, for example "opt" if you have generated an optimized version.
If the compilation was not successful the message

    Abnormal termination of crex.

appears. In this case you should check the README file in the directory deMon.x.y for trouble shooting, the FAQ section of this web page or the deMon user's guide.

crex
The crex script can create a local version of deMon. This is useful e.g. if a user needs to make modifications in some source or include files of deMon. crex will compile only the modified files and link them together with the unchanged files of the master version. Every user can therefore create his or her own version. crex expects the following settings:

    $CREX_ROOT=/usr/local              ! or another directory where 
                                       ! the master version of deMon
                                       ! is installed. The default 
                                       ! is /usr/local
    $CREX_ROOT/deMon/.default-version  ! contains the deMon version x.y
    $CREX_ROOT/deMon/object.*/         ! contains all object files 
                                       ! of the master version. The "*"
                                       ! denotes the kind of version, 
                                       ! e.g. "opt"
    $HOME/demon/                       ! main directory for the local 
                                       ! version (small characters!)
    $HOME/demon/.default-version       ! contains the deMon version x.y 
    $HOME/demon/x.y/source/            ! contains the version number 
                                       ! x.y of the version to be 
                                       ! compiled
    $HOME/demon/x.y/include/           ! contains modified include files 
                                       ! (directory must exist, 
                                       ! but can be empty)

Type

    crex

and follow the instructions which are similar to those of the CREX script (see above). After successful compilation the executable is written to

    $HOME/demon/x.y/object.*/deMon.x.y.*

If the compilation was not successful the message

    Abnormal termination of crex.

appears. In this case you should check the README file in the directory deMon.x.y for trouble shooting, the FAQ section of this web page or the deMon user's guide.

4. How to run deMon2k

To run the deMon program you can use either the deMon script or you can run deMon directly. We recommend to use the deMon script.

Running deMon directly
Generate a working directory, e.g.

mkdir /tmp/job

Copy the executable, the AUXIS, BASIS and if necessary the ECPS and the MCPS file in that directory as well as your input file (note: The name of the input file must be "deMon.inp")

cp deMon.x.y.* /tmp/job/deMon.x.y.*
cp AUXIS /tmp/job/AUXIS
cp BASIS /tmp/job/BASIS
cp ECPS /tmp/job/ECPS
cp MCPS /tmp/job/MCPS
cp your.inp /tmp/job/deMon.inp

The "*" denotes the kind of version, e.g. "opt". Change to the directory

cd /tmp/job

and type

nohup deMon.x.y.* &

Running the deMon script
By default a deMon script for an NQS/PBS queuing system is installed in $CREX_ROOT/deMon/bin. This script is used in our group in CINVESTAV for working with deMon. It is only an example what can be done and it certainly has to be modified for other queuing systems and/or environments.
However, using this script as a template for other systems the modifications should be relatively easy to do. To run a job with the deMon script just type

deMon your.inp

where your.inp denotes the input file which must be in the current directory. You are asked to select an execution modus. If you are running NQS/PBS it could look similar to the following:

    Select an execution modus.

      1. Interactive job (background)
      2. Interactive job (foreground)
      3. NQS/PBS batch job in queue e at cobre
      4. NQS/PBS batch job in queue l at cobre
      5. NQS/PBS batch job in queue md at oro
      6. NQS/PBS batch job in queue md at plata
      7. NQS/PBS batch job in queue xl at uranio
      8. NQS/PBS batch job in queue xxl at uranio

    Enter a number:

Afterward, the script checks which deMon versions are available. The script tries to read first the version number in your home directory $HOME/demon/.default-version. If this file is not available, it will take the version which is specified in the $CREX_ROOT/deMon/.default-version file. You can choose then between the available executables, e.g.:

    The following program versions are available:

      1. /usr/local/deMon/x.y/object.opt/deMon.x.y.opt
      2. /usr/local/deMon/x.y/object.dbg/deMon.x.y.dbg
      3. /home/florian/demon/x.y/object.opt/deMon.x.y.opt
      4. /home/florian/demon/x.y/object.dbg/deMon.x.y.dbg

    Enter a number:

After choosing the executable the calculation is started. The output files will be written to $HOME/demon/x.y/outputs after the calculation is finished. You can also specify a different output directory. See the man page for the deMon script or type

deMon -h

to get further information.

The deMon user's guide

The deMon user's guide can be downloaded as a compressed postscript file (86 Mb), as a pdf file (18 Mb) or in HTML format. The current guide covers the basic input structure of deMon2k and gives an overview and a description of the keywords which are available. Furthermore, the output files generated by deMon2k are described and a list of user adjustable parameters (e.g. maximum number of atoms/orbitals, maximum RAM etc.) is given.
For the installation of deMon2k, please see the installation guide on this web page.

Frequently asked questions

In this section answers are provided to questions which often occur when installing or running the deMon2k program.

Getting the program
Installation of deMon2k
Running deMon2k

1. Getting the program

Q: Which versions of deMon can be obtained?
A: You can obtain the latest master version of deMon2k from this site. For other branches of deMon2k or programs related to deMon2k see the Program Branches section.

Q: How do I get the deMon program?
A: To get the deMon2k source code you have to sign and submit a license agreement first. Then you can download the code. Or you can download binary versions of deMon2k. In this case no license agreement is required.

Q: Do I have to pay a license fee?
A: In general, the deMon2k source code is free of charge for an academic license. For a non-academic license you have to pay a fee. Please, see the license section for details concerning the academic and non-academic license.

Q: Can I get a free trial version of deMon?
A: Yes, you can download binary versions of deMon2k. There are no restrictions concerning the functionality of the program.

2. Installation of deMon2k

Q: What hardware/software is required to install and run deMon?
A: deMon runs on a variety of UNIX/Linux based platforms. Currently compilations on the following systems are supported by the deMon package:
- IBM AIX: AIX 4.3, AIX 5.1
- SGI IRIX: 6.5 (IP27, IP35)
- Alpha: OSF1 4.0, OSF1 5.1
- Mac: Mac OS X (Darwin Kernel Version 7.9.0)
- Linux: AMD/Intel i686, Intel Itanium2, x86_64 (AMD Athlon 64 bit/AMD Opteron 64 bit/Intel Xeon 64 bit)
Other platforms require adjustment of the compilation parameters.

Minimum requirements (installation): 256MB RAM, 50MB disk space (full installation: 100MB)
Software requirements (installation): FORTRAN90 compiler, Bourne-Again-Shell (bash), MPI for parallel version

The amount of RAM and disk space necessary to run deMon2k depends on the size of the system and on the type of calculation you want to run. 1GB RAM and disk space is recommended.

Q: I have downloaded a binary version of deMon2k. How do I install it?
A: Just unpack the deMon2k directory by typing tar -xvf deMon2k.*.tar.gz where * stands for the platform, e.g. x86_linux. Change into the new directory, typ ./install and follow the installation steps.

Q: I have obtained the deMon source code. How do I install it?
A: Unpack the deMon2k package by typing ./deMon2k.sh. Change into the directory deMon.x.y and run the installation script by typing ./install. For further reference see the installation guide on this web page.

Q: The operating system on the computer where I want to install deMon is unknown to the installation script/CREX/crex script. What should I do?
A: You have to edit the file database.new which is located in the directory deMon.x.y/x.y/database, where x.y is the version number of deMon (two or three digits, separated by dots). If you open that file you should see the following:
```
    F90     edit
    FFLAGS  edit
    LFLAGS  edit

    LIBS
    EXCLUDE
  
```
Replace the edit in the first line by the name of your FORTRAN90 compiler. For example, if you have installed the Intel fortran compiler the first line should be:
```
    F90     ifort
  
```
The edit in the second line must be replaced by the compilation flags. You must have at least a flag for double precision padding. Many (but not all!) compilers have for this the -r8 flag. You can add more flags separated by space (e.g. flags for code optimizations). The third line should contain the linking flags. As first try use the same flags as for the FFLAGS. Try then to compile again. For additional information see the README file which is located in deMon.x.y/x.y/database.

Q: I have followed the installation instructions but the installation script finished with the message deMon installation failed. What can be the reason?
A: You should check the following points:
- Access rights
  If you want to install deMon globally e.g. in /usr/local you have to become root first.
- Compiler
  Make sure you have chosen a compiler which you have installed on yourmachine. Check also the name of your compiler. It must match the entry F90 in the corresponding database file. For example
```
       F90      NAME
    
```
  where NAME is you compiler. Then the command
```
       which NAME
    
```
  should give you the location of the compiler.
- Linking
  deMon needs to be linked together with certain libraries. These are specified in the corresponding database file after the entry LIBS. The location of these libraries have to be given after the entry LFLAGS, e.g.
```
       LFLAGS -L/usr/lib/gcc-lib/i386-redhat-linux/2.96
       LIBS   -lg2c
    
```
  expects the library libg2c.a (LIBS) in the directory /usr/lib/gcc-lib/i386-redhat-linux/2.96 (LFLAGS). Check that all the libraries you need are in the locations which are specified after LFLAGS or add the corresponding paths to your LD_LIBRARY_PATH variable.
- Database file
  If you run the installation on a system for which no corresponding database file is available, the installation script will use the file database.new. See how to edit this file.

Q: I have tried to compile a master version of deMon using CREX but I got the message Abnormal termination of CREX. What can be the reason?
A: You should check the following points:
- Directory tree
  Make sure your directory tree is installed correctly. This is done automatically by the installation script for the master version. See the installation guide for details on the directory tree.
- Access rights
  If you want to compile deMon globally e.g. in /usr/local you have to become root first.
- Version
  Make sure you have the .default-version file with the correct deMon version you want to compile in $CREX_ROOT/deMon where $CREX_ROOT is a variable which contains the installation directory of the deMon tree. If you have installed deMon in another location as the default /usr/local this variable must point to the directory where deMon was installed. If you want to compile the version x.y the file .default-version must contain x.y in its first line.
Check also the installation failed FAQ.

Q: I have tried to compile a user version of deMon using crex but I got the message Abnormal termination of crex. What can be the reason?
A: You should check the following points:
- Directory tree
  Make sure your directory tree is installed correctly. See the installation guide for details on the directory tree.
- Version
  Make sure you have the .default-version file with the correct deMon version you want to compile in $CREX_HOME/demon (small "m" for user version !) where $CREX_HOME is a variable which contains the installation directory of the demon tree (user version). If you have installed the user version of deMon in another location as the default $HOME this variable must point to the directory where deMon was installed. If you want to compile the version x.y the file .default-version must contain x.y in its first line.
Check also the installation failed FAQ.

3. Running deMon2k

Q: How do I run the deMon program?
A: You can run deMon either interactively or as a batch job. See the How to run deMon2k section of the installation guide on this web page.

Questions and Remarks

Please, send any question/remark concerning deMon2k to the following e-mail: demon2k-l@mailman.ucalgary.ca

Contact

For issues concerning the installation and running of deMon2k please send an email to Dr. Gerald Geudtner (email: speedy at cinvestav.mx).
For issues concerning the web page, please send an email to Dr. Patrizia Calaminici (email: pcalamin at cinvestav.mx).

Last Update: 28th April 2021

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