Single Tilt Backprojection using PubSub
- Login to master node of cluster, where PubSub has been
installed and is running, e.g.:
rlogin patroon
- Access your working_dir, e.g.:
cd /usr1/user/bp
- Create input and output sub-directories, e.g.:
mkdir input output
- 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
- 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)
- 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.
- 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
- Start Master SPIDER process bpw2_pub.spi, e.g.
spider spi/dat bpw2_pub 0 &
- 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