Difference: CCPorting (2 vs. 3)

Revision 32012-12-06 - EmidioGiorgio

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META TOPICPARENT name="UserSupportCompchem"
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Users which their main field is Computational Chemistry may consult the following Application Database
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Computational Chemistry users may also consult the EGI.EU Application Database
 
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Here an overview of the applications currently ported in the GRID environment is presented.

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

Installation and porting guides

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

DL_POLY

Application description

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

DL_POLY 2.20

Sequential executable
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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.
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To compile it, it's required :
  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.
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A. 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.
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A. Download or copy the tar file of DL_POLY_2.20 MD package in a machine with the gLite3.2 middleware installed, and untar the package 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.
  B. Edit the Makefile as follow
  • set EX variable to chose the appropriate name for your executable.
Line: 57 to 55
 After the compile 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 < executable_name > 
" not a dynamic executable " should be visualized.
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You can use the executable and submit it to the GRID environment.
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You can now use the executable and submit it to the GRID environment.
 
Parallel executable
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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. MPI libraries COMPILED for the architecture and the compiler to be used (if the PATH to them is not passed to the DEFAULT ENVIRONMENT PATH, then it MUST be supplied in Makefile). Note: MPI library used: mpich2-1.4.1.
  3. a MAKE command (Makefile interpreter in the system SHELL). Note: native make (bash shell) used
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It's needed
  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. MPI libraries COMPLIANT with the architecture and the compiler to be used (if the PATH to them is not passed to the DEFAULT ENVIRONMENT PATH, then it MUST be supplied in Makefile). Note: MPI library used: mpich2-1.4.1.
  3. a MAKE command (Makefile interpreter in the system SHELL). Note: native make (bash shell) used
  Contact your Admin if the needed software is missing or not available.
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A. 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.
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A. Download or copy the tar file of DL_POLY_2.20 MD package in a machine with the gLite3.2 middleware installed, and untar it in an appropriate sub-directory.
 Copy the file named MakePAR and stored in the build directory into the srcmod directory
 # cp build/MakePAR srcmod/Makefile 
The file enable to compile the source code to obtain the parallel version of the executable
Line: 103 to 101
 
Sequential executable

Needed for compilation are:

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  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.
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  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.
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A. Download or copy the tar file of DL_POLY_4.02 MD package in a machine with the EMI1 middleware installed, untar it in an appropriate sub-directory. Copy the file named Makefile_SRL1 and stored in the build directory into the source directory
 # cp build/Makefile_SRL1 srcmod/Makefile 
The file enable to compile the source code to obtain the sequential version of the executable.
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A. Download or copy the tar file of DL_POLY_4.02 MD package in a machine with the EMI middleware installed, and untar it in an appropriate sub-directory. Copy the file named Makefile_SRL1 and stored in the build directory into the source directory
 # cp build/Makefile_SRL1 srcmod/Makefile 
The file enable to compile the source code to obtain the sequential version of the executable.
  B. Edit the Makefile as follow
  • set EX variable to chose the appropriate name for your executable.
Line: 137 to 135
 
Parallel executable

Needed for compilation are:

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  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. MPI libraries COMPILED for the architecture and the compiler to be used (if the PATH to them is not passed to the DEFAULT ENVIRONMENT PATH, then it MUST be supplied in Makefile). Note: MPI library used: mpich2-1.4.1.
  3. a MAKE command (Makefile interpreter in the system SHELL). Note: native make (bash shell) used
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  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. MPI libraries COMPLIANT with the architecture and the compiler to be used (if the PATH to them is not passed to the DEFAULT ENVIRONMENT PATH, then it MUST be supplied in Makefile). Note: MPI library used: mpich2-1.4.1.
  3. a MAKE command (Makefile interpreter in the system SHELL). Note: native make (bash shell) used
  Contact your Admin if the needed software is missing or not available.
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A. Download or copy the tar file of DL_POLY_4.02 MD package in a machine with the EMI1 middleware installed, untar it in an appropriate sub-directory.
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A. Download or copy the tar file of DL_POLY_4.02 MD package in a machine with the EMI1 middleware installed, and untar it in an appropriate sub-directory.
 Copy the file named Makefile_MPI and stored in the build directory into the source directory
 # cp build/Makefile_MPI srcmod/Makefile 
The file enable to compile the source code to obtain the parallel version of the executable
Line: 171 to 169
 
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GROMCAS

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GROMACS

 

Application description

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details).
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<-- VO Contact: Alessandro Costantini, University of Perugia (Italy)  alessandro.costantini@dmi.unipg.it -->
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Sequential executable
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Needed for compilation are:
  1. a FORTRAN90 compliant compiler (the PATH has to be passed setting the variable F77). Note: Compiler used: composerxe-2011.5.220.
  2. a MAKE command (Makefile interpreter in the system SHELL). Note: native make (bash shell) used.
  3. FFT libraries (see http://www.fftw.org/)
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To compile it, It is needed for compilation:
  1. a FORTRAN90 compliant compiler (the PATH has to be passed setting the variable F77). Note: Compiler used: composerxe-2011.5.220.
  2. a MAKE command (Makefile interpreter in the system SHELL). Note: native make (bash shell) used.
  3. FFT libraries (see http://www.fftw.org/)
 Contact your System Admin if the needed software is missing or not available.

A. Download or copy the tar file of gromacs-4.5.5.tar.gz MD package in a machine with the gLite3.2 middleware installed, untar it in an appropriate sub-directory.

 
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