SPIDER Installation

Contents

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

1. LOADING THE SPIDER DISTRIBUTION

   1. Download SPIDER from Github and place it in an appropriate directory: PARENT-DIR.
      (If you also wish to install Web download it from Github and place it in the same directory: PARENT-DIR.)
   2. Uncompress and unpack the SPIDER tar archive e.g.
      tar -xzvf spider.27.01.tar.gz

   The following SPIDER directories will be created under: PARENT-DIR):

   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

2. INSTALLATION

   • Executables

     The SPIDER distribution should contain the following executable files in the spider/bin directory and Makefiles in the spider/src directory. In addition the spider/src/Makefile_samples directory contains a number of other sample Makefiles for AIX, legacy systems, and alternative compilers.

     SPIDER	Optimal processor	Optimal byte order	"Makefile"	Compiler
     spider_linux_mp_intel	Intel Xeon 32 bit OS (1+ processors)	Big endian	Makefile_linux_mp_intel	PGI Fortran compiler
     spider_linux_mp_intel64	Intel Xeon 64 bit OS (1+ processors)	Big endian	Makefile_linux_mp_intel64.ifort	Intel ifort compiler
     spider_linux_mp_opt64	AMD Opteron 64 bit OS (1+ processors)	Big endian	Makefile_linux_mp_opt64	PGI Fortran compiler

   • 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  "$SPIDER_DIR/bin/"
     setenv SPPROC_DIR "$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="$SPIDER_DIR/bin/"
     export SPPROC_DIR="$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 SPIDER executables are statically linked with necessary FFTW libraries. You do not need to have shared run-time FFTW libraries on your system when using SPIDER's supplied binaries. These are supplied in case you compile/link your own SPIDER.

   • Compiling and Linking SPIDER.

     If you wish to use SPIDER with MPI you will have to compile and link SPIDER on your system. This is necessary due to the tight coupling of the MPI library within the compilation and large differences among MPI distributions.

     If you wish to use MPI, or modify SPIDER source code, or 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 2003+ 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: spiderem.software@gmail.com. (Is anybody still alive to read this email?)