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	Optima byte order	"Makefile"
     spider_linux	AMD/Intel 32 (single processor)	Big endian	Makefile_linux
     spider_linux_mp_intel	AMD/Intel 32 (multiple processors)	Big endian	Makefile_linux_mp_intel
     spider_linux_mp_opt64	AMD Opteron 64 (multiple processors)	Big endian	Makefile_linux_mp_opt64
     spider_linux_mp_intel64	Intel xeon 64 (multiple processors)	Big endian	Makefile_linux_mp_intel64
     spider_linux_mpi_opt64	AMD Opteron 64 (for MPI use)	Big endian	Makefile_linux_mpi_opt64
     spider_osx_32_pgi	Intel Apple 32 bit (multiple processors)	Big endian	Makefile_osx_x32_pgi
     spider_osx_64_pgi	Intel Apple 64 bit (multiple processors)	Big endian	Makefile_osx_64_pgi

   • Setting "spider" Command and Environment variables

     You will need to tell your system the location of your executables, and other SPIDER system files. You should edit PARENT_DIR in the following lines to point to the location of the SPIDER installation on your system. Then place all of the following set of lines in your .cshrc or .bashrc startup file. (If you do not have such a startup file in your home directory you can create it with any text editor.)

     Using the 'C' shell:

     setenv SPIDER_DIR "PARENT_DIR/spider"
     setenv SPBIN_DIR  "$SPIDER_DIR/bin/"
     setenv SPMAN_DIR  "$SPIDER_DIR/man/"
     setenv SPPROC_DIR "$SPIDER_DIR/proc/"
     if ( $?path ) then
       set path=($path $SPBIN_DIR)
     else
       set path=($SPBIN_DIR)
     endif
     

     Using the 'bash' shell:

     export SPIDER_DIR= "PARENT_DIR/spider"
     export SPBIN_DIR=  "$SPIDER_DIR/bin/"
     export SPMAN_DIR=  "$SPIDER_DIR/man/"
     export SPPROC_DIR= "$SPIDER_DIR/proc/"
     export PATH=       "${SPIDER_DIR}/bin:${PATH}"
     

     Note: Do not use a ~username construct in the SPIDER_DIR path or SPIDER will be unable to find the Results file naming script.

     Finally rename the desired spider_linux executable in PARENT_DIR/spider/bin to: spider for easy access.

   • FFTW Libraries

     The 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 when using SPIDER's supplied binaries.

   • 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 Linux documentation for further information.

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 (called a datacode within SPIDER) added automatically inside SPIDER.

   The SPIDER "RESULTS" files are named results.ext.? where ext is the datacode and "?" is a version number which is incremented over any existing results file version in that directory.

4. TESTING SPIDER

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

   If SPIDER does not run:

   • If you get an error message like: command not found

     See "Setting 'spider' command" above to ensure that your desired executable is accessible.

   • If you get a error message about a missing library:

     The executables distributed with SPIDER are mostly statically linked so this should not be a problem. Any missing libraries are probably system libraries (unless you are trying to use the MPI version of SPIDER). You can use: ldd your-spider-executable to investigate missing libraries.

   • If SPIDER runs but complains about the 'Nextresults' script which increments the Results file version number

     Your Linux distribution (e.g. Ubuntu) may have a non-standard sort operation.

     Edit: spider/bin/Nextresults and replace:

     lastfi=`(\ls $1.[0-9]* | sort -t. +2n | tail -1)`

     with

     lastfi=`(\ls $1.[0-9]* | sort -t. -k2 -n | tail -1)`

   • If SPIDER still does not run

     Please contact us at the address below.

5. 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

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 the operating system, SPIDER executable, relevant results files, procedure files, and error messages. The more complete the info the faster the response.

   Send this info to:

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