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Users which their main field is Computational Chemistry may consult the following Application Database

AppDB at EGI -- EU level -- link to EGI AppDB

AppDB at IGI -- IT level -- link to IGI AppDB

Here an overview of the applications currently ported in the GRID environment is presented.

User Guides for the application porting for specific applications will be ready as soon as possible.

Installation and porting guides

The following best practices document aims to provide some hints and examples on how to configure and compile some Computational Chemistry related applications on a grid based infrastructure.

DL_POLY

Application description

DL_POLY is a package of subroutines, programs and data files, designed to facilitate molecular dynamics simulations of macromolecules, polymers, ionic systems, solutions and other molecular systems on a distributed memory parallel computer. The package was written to support the UK project CCP5 by Bill Smith and Tim Forester under grants from the Engineering and Physical Sciences Research Council and is the property of the Science and Technology Facilities Council (STFC). Two forms of DL_POLY exist. DL_POLY_2 is the earlier version and is based on a replicated data parallelism. It is suitable for simulations of up to 30,000 atoms on up to 100 processors. DL_POLY_3 is a domain decomposition version, written by I.T. Todorov and W. Smith, and is designed for systems beyond the range of DL_POLY_2 - up to 10,000,000 atoms (and beyond) and 1000 processors.

-Scientific Contact: W. Smith, CSE Department, STFC Daresbury Laboratory, UK

-Web Site: http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/

-Name of VO: COMPCHEM

-VO Contact: Pacifici Leonardo, University of Perugia (Italy) – xleo@dyn.unipg.it

DL_POLY 2.20

Sequential executable

Needed for compilation are: 1) a FORTRAN90 compliant compiler (if the PATH to it is not passed to the DEFAULT ENVIRONMENT PATH, then it MUST be supplied in Makefile). Note: Compiler used: native gfortran; composerxe-2011.5.220 2) a MAKE command (Makefile interpreter in the system SHELL). Note: native make (bash shell) used Contact your System Admin if the needed software is missing or not available.

Download or copy the tar file of DL_POLY_2.20 MD package in a machine with the gLite3.2 middleware installed, untar it in an appropriate sub-directory. Copy the file named MakeSEQ and stored in the build directory into the srcmod directory

cp build/MakeSEQ srcmod/Makefile

The file enable to compile the source code to obtain the sequential version of the executable

Edit the Makefile as follow - set EX variable to chose the appropriate name for your executable

Using gfortran compiler - the architecture is already set in the MakePAR file - add “- static” to the the LDFLAGS variable under the gfortran target architecture:

LDFLAGS="-static"

Using ifort compiler - add the specific target architecture #======== ifort (serial) =================================== ifort: $(MAKE) LD="ifort -o " LDFLAGS="-static" FC=ifort FFLAGS="-c -O2" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)

Compile the source code #make Note: for other architectures, please refer to the appropriate OS user guide or contact the System Admin.

After the compiling procedure you should find into the “executable” directory the DL_POLY executable. To be sure that the executable is statically linked, run the following command #ldd “not a dynamic executable should be visualized.

You can use the executable and submit it to the GRID environment.

DL_POLY 3.09

-- AlessandroCostantini - 2011-12-12

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Topic revision: r2 - 2011-12-14 - AlessandroCostantini
 
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