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   installing tinker on your computer

Tinker


2. Installing TINKER on your Computer

The TINKER package is distributed on the Internet via either the web site or the anonymous ftp account on dasher.wustl.edu with an IP number of 128.252.68.48. This node is an AlphaServer 4100 file server running Compaq Tru64 Unix located in the Ponder lab at Washington University School of Medicine. The package is available via the web and standard browsers from the TINKER home page at http://dasher.wustl.edu/tinker. Alternatively TINKER can be downloaded by logging into dasher.wustl.edu under anonymous ftp (Username: anonymous, Password: "your email address" ) and downloading the software from the /pub/tinker subdirectory. The complete TINKER distribution as well as individual files can be downloaded from this site.

On dasher.wustl.edu, the TINKER package is present as both a compressed Unix tar archive and as a complete set of uncompressed source and data files. Binaries are provided for Intel PCs running Windows 9X/NT/2000, PCs running Linux, and for Apple Power Macintosh. All of these executables are available in standard compressed formats as individual programs or as complete sets of executables. It is expected that other Unix users and PC users who need specially customized versions, will build binaries for their specific system. Sites with access to the Unix tar, compress and uncompress commands should simply obtain the archive file tinker.tar.Z. Alternatively, a file tinker.tar.gz containing a tar archive compressed with GNU gzip is also provided. If you choose to download individual files, you will need at a minimum the contents of the /doc, /source and /params subdirectories. Also required are the compile/build scripts from the subdirectory named for your machine type. Other areas contain test cases and examples, benchmark results, and machine-translated C code. The entire TINKER package, after building the executables, will require from about 40 to over 100 megabytes of disk space depending on the components installed and the use of shared libraries in the executables.

The documentation for the TINKER programs, including the guide you are currently reading, is located in the /pub/tinker/doc subdirectory. The documentation was prepared using the Applixware Words and Graphics programs. Portable versions of the documentation are provided as ascii text in .txt files and in .ps Postscript and .pdf Adobe Acrobat file formats. Please read and return by mail the TINKER license. While the intent is to distribute the TINKER code to anyone who wants it, the authors would like to keep track of the sites using the package. The returned license forms also help us justify further development of TINKER. When new modules and capabilities become available, and when the almost inevitable bugs are uncovered, we will attempt to notify those who have returned a license form. Finally, we remind you that this software is copyrighted, and ask that it not be redistributed in any form.

The compilation and building of the TINKER executables should be easy for most of the common workstation and PC class computers. We provide in the /make area a Unix-style Makefile that with some modification can be used to build TINKER on most Unix machines. As a simpler alternative to Makefiles for the Unix versions, we also provide machine-specific directories with three separate shell scripts to compile the source, build an object library, and link binary executables. Three similar command files are provided for Open VMS, and for PC and Macintosh systems. Compilation on Unix workstations should use the vendor supplied Fortran compiler, if available. The public domain GNU g77 Fortran compiler available from http://gcc.gnu.org is also capable of building TINKER on Unix machines and under Linux. The Linux executables we provide are built with the either the Portland Group (PGI) compiler or the Absoft ProFortran compiler, both of which generate somewhat faster executables than g77. For the Macintosh we have favorable experience with the Absoft ProFortran compiler running under the Macintosh Programmers’ Workbench (MPW). On PC’s running Windows 9X/NT/2000, the distributed TINKER executables are built on an Intel Pentium III CPU under the Compaq Visual Fortran 6.5 compiler. While the CVF 6.5 compiler has Athlon- specific optimizations, we have not yet investigated these options. The Microsoft Fortran Power Station 4.0 and Watcom F77 compilers are also sufficient for building TINKER, and we provide scripts for each of these PC compilers. Alternative Windows compilers such as those from Lahey/Fujitsu and The Portland Group should work as well, but we have not evaluated them yet. Please see the README files in each of the machine-specific areas for further information.

The first step in building TINKER using the script files is to run the appropriate ‘‘compile’’ script. Next you must use the ‘‘library’’ script to create an archive of object code modules. Finally, run the ‘‘link’’ script to produce the complete set of TINKER executables. The executables can be renamed and moved to wherever you like by editing and running the ‘‘rename’’ script.

Regardless of your target machine, only three small pieces of code can possibly require attention prior to building. The first two are the system dependent time and date routines found in clock.f and calendar.f respectively. Please uncomment the sections of these routines needed for your computer type. The final set of source alterations are the master array dimensions found in the include file sizes.i. The most basic limit is on the number of atoms allowed, ‘‘maxatm’’. This parameter can be set to 10000 or more on most workstations. Personal computers with minimal memory may need a lower limit, perhaps 1000 atoms, depending on available memory, swap space and other resources. A description of the other parameter values is contained in the header of the file. Note that in order to keep the code completely transparent, TINKER does not implement any sort of virtual memory or heap data structure. This requires that sizes.i dimensioning values be set at least as large as the biggest problem you intend to run. Obviously, you should not set the array sizes to unnecessarily large values, since this can tax your compute resources and may result in performance degradation. The worst case we know of at present is for some of the Compaq Alpha-based machines, where running a ‘‘small’’ problem with TINKER executables dimensioned to ‘‘large’’ sizes can result in a 25-50% CPU time penalty, especially if only the default compiler options are used.

Specific questions about the building or use of the TINKER package should be directed to ponder@dasher.wustl.edu. TINKER related questions or comments of more general interest can be sent to the Computational Chemistry List (http://www.ccl.net/) run by Jan Labanowski of The Ohio Supercomputer Center. The TINKER developers monitor this list and will respond to the list or the individual poster as appropriate.




© Goodman Group, 2005-2017; privacy; last updated November 16, 2017

department of chemistry University of Cambridge