SPIDER Installation on SGI Irix

Contents

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

1. LOADING THE 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/man	Operation manual pages, Nextresults
   spider/pubsub	PubSub scripts & documentation

2. INSTALLATION

   • Installation of Executables.

     • Using Precompiled and Linked Executables.
       The spider/bin directory will contain the following executable binary files spider3, spider4ns, spider4mp, & spider5mp for use as follows.

       SPIDER	processor	Irix
       ----------	----------------------	----
       spider5mp	R8K,R10K,R12K	6.*
       spider4mp	R5K,R8K,R10K	6.*
       spider3	R4K	6.*

       If you are confused which SPIDER to use I suggest you just start at the top of the above list and use the first executable that successfully runs on your machine. It should be good.

       In the following commands substitute the desired SPIDER version (3, 4, 4ns, etc) for the "?".
       Use the following commands to run SPIDER in a terminal window:

       cd PARENT_DIR/spider/bin
       spider?
       

       If SPIDER does not run and you get an error message like: command not found see " Other Installation Tasks" below 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. The current SGI SPIDER distribution requires the following libraries: libfortran.so, libffio.so, libftn.so, libm.so, & libc.so
       which come from the SGI Software package currently called either: ftn_eoe.sw.lib or ftn_eoe.sw64.lib . These packages should be in the standard software distribution that comes with all SGI computers. Most of the SPIDER executables use the SGI Complib run-time library: libcomplib.sgimath.so for Fourier operations. The SGI Complib library contains an SGI tuned version of the Blas libraries. These libraries are preferred for Fourier operations since their code runs 3X faster than the native SPIDER Fourier code. The library is from a package which is called either ftn_eoe.sw64.libblas or ftn_eoe.sw.libblas These packages should be in the standard software distribution that comes with all SGI computers. If these software packages are already loaded, then the SGI operation: versions should list them. If not, you will need to load the missing packages from the correct CDROM. Once you have loaded this software you should not have to relink your SPIDER system.

       If you do not have access to the SGI Complib library you may choose to use the slower native SPIDER code. This is available in the spider4ns executable contined in the distribution. If the appropriate SPIDER executable 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.

     • 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. use native SPIDER fft code instead of SGI's fft code or change optimization levels) you may have to compile and the source code on your computer.
       See SPIDER Compilation and Linking for information on compilation of SPIDER.

   • Other Installation Tasks.
     • Setting "spider" Command. You can define an alias for your SPIDER location. If you are using the 'C' shell, you would put a line similar to the following in your .cshrc startup file, depending on the version of SPIDER you intend to use:

       alias spider PARENT_DIR/spider/bin/spider?
       

       Alternatively, you can modify your path so that your your system can locate the executable file when you type "spider". To alter your path add the following directory to the PATH environmental variable in your startup file:

       PARENT_DIR/spider/bin/bin
       

       then rename the spider? executable in PARENT_DIR/spider/bin to: spider.

     • Setting environment variables.
       Set environment variables for the location of your *.sys, *.man, and "Nextresult" files. (Nextresult is a shell command file which increments the version number on the RESULTS file created by Unix SPIDER). If you are using the 'C' shell, you should put lines similar to the following in your .cshrc startup file:

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

       You may need to set the following environment variable for location of run-time libraries if you use spider3, spider4, or spider4mp :
       

       setenv LD_LIBRARYN32_PATH=/usr/lib32:/usr/lib32/X11

     • Memory allocation.
       The main memory allocation for the SPIDER system is in the unlabeled common. This is defined by the size of MAXDI in spider.f. If your system complains about a lack of swap space, then you will have to increase the swap space on your computer. A less satisfactory alternative is to edit spider.f to decrease MAXDI, and remake your SPIDER system. SPIDER is distributed with a unlabeled common size of 28 Mb. Many SPIDER subroutines now allocate their own memory at runtime and no longer use large amounts of space from the unlabeled common.

   • Installation on non-SGI Unix computers.
     See spider-inst-linux.html for installation on computers running a Linux operating system.
     See spider-inst-dec.html for installation on DEC Unix computers. For installation on other Unix based computers, such as SUNs, the FORTRAN code which we supply will have to be compiled and linked on those computers. Such compilation will require familiarity with your operating system to set the necessary flags for compilation and linking. You may also have to change the coding of the Makefile. Please understand that due to limited staff and equipment we may not be able to assist with some problems you may encounter porting SPIDER to other computers. We offer a sample Makefile for Sun-Sparc called Makefile_sunsparc in the SPIDER_DIR/src directory.

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.

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
   fax: 518-486-2192
   email: spider@wadsworth.org