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Neil Voss, 05/13/2010 09:16 AM


Install SPIDER

Install documentation at wadsworth.org

the Wadsworth Institute provides detailed documentation on how to install SPIDER on various systems. Below we cover a 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.18.10.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 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
    
  • 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/

Set environmental variables

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

export SPIDER=/usr/local/spider
export SPMAN_DIR=${SPIDER}/man
export SPPROC_DIR=${SPIDER}/proc
export SPRGB_DIR=${SPIDER}/rgb

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

setenv SPIDER /usr/local/spider
setenv SPMAN_DIR ${SPIDER}/man
setenv SPPROC_DIR ${SPIDER}/proc
setenv SPRGB_DIR ${SPIDER}/rgb

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

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Updated by Neil Voss over 14 years ago · 19 revisions