SPIDER Installation on Linux and OSX

Contents

1. LOADING THE DISTRIBUTION
2. INSTALLATION
3. RUNNING SPIDER
4. TESTING SPIDER
5. DOCUMENTATION
6. BUGS

1. LOADING THE SPIDER/WEB DISTRIBUTION

   1. Download SPIDER/Web and place it in an appropriate directory: PARENT-DIR.
      The compressed SPIDER/Web distribution takes about 180 Mb of disk space. The uncompressed whole distribution will take about 850Mb but includes libraries and executables for several different systems some of which can be discarded.
   2. Uncompress the tar archive e.g.
      gunzip spiderweb.tar.gz
   3. Unpack the tar archive e.g.
      tar -xvf spiderweb.tar

   The following SPIDER directories will be created under: PARENT-DIR (along with other directories for Web, etc.):

   Directory	Contents
   spider/src	SPIDER source code, SPIDER libraries
   spider/bin	SPIDER executables
   spider/docs	SPIDER documentation, html pages
   spider/proc	Sample procedure files
   spider/fftw	FFTW code and libraries
   spider/man	Operation manual pages, Nextresults
   spider/pubsub	PubSub scripts, documentation and executables

2. INSTALLATION

   • Executables

     The spider/bin directory should contain the following executable files (as well as others):

     SPIDER	optimal processor	optimal byte order	"Makefile"
     spider_linux_fftw	AMD/Intel 32 (single processor)	SGI	Makefile_linux_fftw
     spider_linux_mpfftw_intel	AMD/Intel 32 (multiple processors)	SGI	Makefile_linux_mpfftw_intel
     spider_linux_mpfftw_opt64	AMD Opteron 64 (multiple processors)	SGI	Makefile_linux_mpfftw_opt64
     spider_osx_mpfftw_xeon	Intel Xeon on Apple (multiple processors)	SGI	Makefile_osx_mpfftw_xeon

   • FFTW Libraries

     The GNU-Linux and OSX SPIDER executables are statically linked with necessary FFTW libraries. You no longer need to have shared run-time FFTW libraries on your system.

   • Compiling and Linking SPIDER.

     If you wish to modify SPIDER source code, link SPIDER with different libraries, or compile SPIDER with different compilation options (e.g. optimize speed for your processors) you will have to have a Fortran 95 compiler on your system. See SPIDER Compilation and Linking on GNU-Linux documentation for further information.

   • Setting "spider" Command

     You can define an alias for your SPIDER executable's location. If you are using the 'C' shell, you would put a line similar to the following in the .cshrc startup file in your home directory:

     alias spider PARENT_DIR/spider/bin/spider_linux_mpfftw_intel

     Alternatively, you can modify your executable search path so that your system can locate the executable file when you type "spider". To alter your path (if you are using the 'C' shell) add the following to the PATH environmental variable in your .cshrc startup file:
     
     

     If PATH is not already set in your startup file add the following line to your .cshrc startup file

     set path= PARENT_DIR/spider/bin

     If PATH is already set in your startup file, add the following line to your .cshrc startup file

     set path=($path PARENT_DIR/spider/bin)

     Then rename the desired spider_linux executable in PARENT_DIR/spider/bin to: spider.

   • Setting environment variables

     You will also need to tell SPIDER the location of your manual pages and SPIDER system procedure files. If you are using the 'C' shell, you should place following lines in your .cshrc startup file:

     setenv SPMAN_DIR "PARENT_DIR/spider/man/"
     setenv SPPROC_DIR "PARENT_DIR/spider/proc/"
     

3. RUNNING SPIDER

   Run SPIDER in a terminal window:

   spider three-character-data-extension

   All SPIDER data files will have the three-character-data-extension (or datacode) added automatically inside SPIDER.

   The SPIDER "RESULTS" files are named results.ext.? where "?" is incremented for existing results file in that directory.

   SPIDER can be run in the background or submitted as a batch using the UNIX "at" command.

   If SPIDER does not run and you get an error message like: command not found see "Setting 'spider' command" above to ensure that your desired executable is accessible.

   If the SPIDER does not start running and you get a error message about a missing library, then you are missing one or more run-time (shared) libraries. Check your LD_LIBRARY_PATH environment variable.

   If SPIDER still does not run please contact us at the address below. Please send complete info on what you are trying to do, error messages, screen dump, etc.

4. DOCUMENTATION

   There is an overview of SPIDER documentation in the file: documents.html in the SPIDER_DIR/docs sub-directory. All SPIDER documentation is included with the distribution and is accessible via your Web browser. Just point your browser at: SPIDER_DIR/docs/spider.html

5. TESTING SPIDER

   Some simple tests are available to see if SPIDER is operating correctly.

6. BUGS, SUGGESTIONS

   In the event that you have questions about methodologies or wish to report bugs please send us complete info on what you are trying to do, including relevant results files, procedure files, and error messages.

   Send this info to:

   ArDean Leith
   Wadsworth Labs, P.O. Box 509, Albany, New York 12201
   Phone: 518-486-5604
   Email: spider@wadsworth.org