Single Tilt Backprojection using PubSub

  1. Login to master node of cluster, where PubSub has been installed and is running, e.g.:
    rlogin   patroon
  2. Access your working_dir, e.g.:
    cd   /usr1/user/bp
  3. Create input and output sub-directories, e.g.:
    mkdir   input   output
  4. Copy all the necessary input data files, i.e.: Image selection doc. file, Projection angles doc. file, and Aligned projections to the input directory e.g.:
    scp    'user@sylt.wadsworth.org:/usr1/user/bp/angles.dat'   input
    scp    'user@sylt.wadsworth.org:/usr1/user/bp/sel003.dat'     input
    scp    'user@sylt.wadsworth.org:/usr1/user/bp/k35_rtsq_*.dat'   input
  5. Copy bpw2_pub.spi procedure file to the working directory, e.g.:
    scp -v    '/net/bali/usr1/spider/proc/bpw2_pub.spi'    .
    (Note: /net/bali/usr1 is mounted on patroon)
  6. Edit bpw2_pub.spi to set necessary values for input parameters and input file names, e.g.
    xedit   bpw2.spi
    The number of OMP threads should be 2, Number of partitions/nodes = 1...15, and the dimensions are determined by input image dimensions.
  7. Create link in your working directory for a specific SPIDER (ensures that same SPIDER executable is used throughout whole run), e.g.:
    ln -s /usr/local/spider/bin/spider_linux_mpfftw.40    spider
  8. Start Master SPIDER process bpw2_pub.spi, e.g.
    spider spi/dat    bpw2_pub 0 &
  9. Master SPIDER refinement process will create and publish new SPIDER jobs as necessary.


Source file: /net/bali/usr1/spider/pubsub/bpw2_pub.html     Updated: 6/18/03     ArDean Leith