Install SPIDER¶

Install documentation at wadsworth.org¶

The Wadsworth Institute provides detailed documentation on how to install SPIDER on various systems. Below we cover our way to get it working on your system.

Download SPIDER binary from wadsworth.org (250 MiB)¶

Most of our SPIDER scripts were originally designed around SPIDER v14 and v15, but we are diligently working toward compatibility with SPIDER v18. That said you are probably best off using the newest version of SPIDER (v18.10 as of May 2010) and then reporting any bugs to us.

Extract the archive¶

tar -zxvf spiderweb.20.16.tar.gz

The archive will create 3 folders: spider, spire, and web. At this time only the spider program is used within Appion, you can safely ignore web and spire.

Install SPIDER¶

• Copy the spider folder to global directory:
  

  sudo mv -v spider /usr/local/

• Next, you need to determine which version of the spider binary you need to use on your system.
  

  cd /usr/local/spider/bin
  ls spider*
    spider_linux           spider_linux_mp_intel64  spider_linux_mp_opt64  spider_osx_64_pgi
    spider_linux_mp_intel  spider_linux_mpi_opt64   spider_osx_32_pgi
  

• From the wadsworth.org site:

  binary file	system information
  spider_linux	AMD/Intel 32 (single processor)
  spider_linux_mp_intel	AMD/Intel 32 (multiple processors)
  spider_linux_mp_opt64	AMD Opteron 64 (multiple processors)
  spider_linux_mp_intel64	Intel xeon 64 (multiple processors)
  spider_linux_mpi_opt64	AMD Opteron 64 (for MPI use)
  spider_osx_32_pgi	Intel Apple 32 bit (multiple processors)
  spider_osx_64_pgi	Intel Apple 64 bit (multiple processors)

• Additionally you may run the UNIX file command on an individual program to determine its type
  

  file spider_linux_mp_intel64
    spider_linux_mp_intel64: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.4, 
    statically linked, for GNU/Linux 2.6.4, not stripped
  

• If you are unsure, use:
  • spider_linux_mp_intel for 32bit Intel/AMD systems
  • spider_linux_mp_opt64 for 64bit Intel/AMD systems

• After you determine which spider to use create a link to that file in /usr/local/bin:
  

  sudo ln -sv /usr/local/spider/bin/spider_xxxxx /usr/local/bin/spider

Set environmental variables¶

For BASH, create an spider.sh and add the following lines:¶

export SPIDERDIR=/usr/local/spider
export SPMAN_DIR=${SPIDERDIR}/man/
export SPPROC_DIR=${SPIDERDIR}/proc/
export SPBIN_DIR=${SPIDERDIR}/bin/
export PATH=$PATH:${SPIDERDIR}/bin

For C shell, create an spider.csh and add the following lines:¶

setenv SPIDERDIR /usr/local/spider
setenv SPMAN_DIR ${SPIDERDIR}/man/
setenv SPPROC_DIR ${SPIDERDIR}/proc/
setenv SPBIN_DIR ${SPIDERDIR}/bin/
setenv PATH $PATH:${SPIDERDIR}/bin

And then add it to the global /etc/profile.d/ folder¶

sudo cp -v spider.sh /etc/profile.d/spider.sh
sudo chmod 755 /etc/profile.d/spider.sh

-or-

sudo cp -v spider.csh /etc/profile.d/spider.csh
sudo chmod 755 /etc/profile.d/spider.csh

You may need to log out and log back in for these changes to take place.

Test SPIDER¶

• Execute the program:
  • input:
    

    spider bat/spi

  • output:
    

    
     \__`O O'__/        SPIDER  --  COPYRIGHT
     ,__xXXXx___        HEALTH RESEARCH INC., ALBANY, NY.
      __xXXXx__
     /  /xxx\  \        VERSION:  UNIX  18.10 ISSUED: 03/23/2010
       /     \          DATE:     13-MAY-2010    AT  09:32:42
    
     Results file: results.bat.0
     Running: spider
    
     .OPERATION:

  • input:
    

    EN D

  • output:
    

     **** SPIDER NORMAL STOP ****

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