FAHMunge

How to use

0. Install FAHMunge via setup.py using anaconda (not system) python
1. Login to work server using the usual FAH login
2. Check if script is running (screen -r -d). If True, stop here.
3. Start a screen session
4. cd /data/choderalab/fah/Software/FAHMunge
5. /data/choderalab/anaconda/bin/python scripts/munge_fah_data.py
6. To stop, control c when the script is in the "sleep" phase

The metadata for FAH is a CSV file located here:

/data/choderalab/fah/Software/FAHMunge/projects.csv

###Example CSV

project,location,pdb
"10491","/home/server.140.163.4.245/server2/data/SVR2359493877/PROJ10491/","/home/server.140.163.4.245/server2/projects/GPU/p10491/topol-renumbered-explicit.pdb"
"10492","/home/server.140.163.4.245/server2/data/SVR2359493877/PROJ10492/","/home/server.140.163.4.245/server2/projects/GPU/p10492/topol-renumbered-explicit.pdb"
"10495","/home/server.140.163.4.245/server2/data/SVR2359493877/PROJ10492/","/home/server.140.163.4.245/server2/projects/GPU/p10495/MTOR_HUMAN_D0/RUN%(run)d/system.pdb"

pdb points pipeline towards pdb to look at for numbering atoms in the munged data. The top two lines are eamples of using a single pdb for the munging pipeline. The third line shows how to use a different pdb for each run. %(run)d is substituted by the run number via filename % vars() in Python, whic allows run numbers or other variables to be substituted. This is done on a per-run basis, not per-clone.

Single vs. multi process

There is also a multiprocessing version in the scripts/ folder. However, the scripts generate potentially large temporary files. The single process version seems to put less strain on the /tmp filesystem, so we prefer that right now.

More description

Overall Pipeline (Core17/18):

1. Extract XTC data from bzips
2. Append allatom coordinates and filenames to HDF5 file
3. Extract protein coordinates and filenames into a second HDF5 file

General instructions:

1. Run FAH servers
2. Edit scripts/munge_fah_data.py to load your FAH data.
3. Run scripts/munge_fah_data.py in a screen session
4. rsync your stripped data to analysis machines periodically.

Note: the rate limiting step appears to be bunzip.

Sync to hal.cbio.mskcc.org

Munged no-solvent data is rsynced nightly from plfah1 and plfah2 to hal.cbio.mskcc.org via the choderalab robot user account to:

/cbio/jclab/projects/fah/fah-data/munged

This is done via a crontab:

04 01 * * * rsync -av --chmod=g-w,g+r,o-w,o+r [email protected]:/data/choderalab/fah/munged/no-solvent /cbio/jclab/projects/fah/fah-data/munged >> $HOME/plfah1-rsync-no-solvent.log 2>&1
39 01 * * * rsync -av --chmod=g-w,g+r,o-w,o+r [email protected]:/data/choderalab/fah/munged/no-solvent /cbio/jclab/projects/fah/fah-data/munged >> $HOME/plfah2-rsync-no-solvent.log 2>&1
34 03 * * * rsync -av --chmod=g-w,g+r,o-w,o+r [email protected]:/data/choderalab/fah/munged/all-atoms /cbio/jclab/projects/fah/fah-data/munged >> $HOME/plfah1-rsync-all-atoms.log 2>&1
50 03 * * * rsync -av --chmod=g-w,g+r,o-w,o+r [email protected]:/data/choderalab/fah/munged/all-atoms /cbio/jclab/projects/fah/fah-data/munged >> $HOME/plfah2-rsync-all-atoms.log 2>&1

To install this crontab as the choderalab user:

crontab ~/crontab

To list the active crontab:

crontab -l

Transfers are logged in the choderalab account:

plfah1-rsync-all-atoms.log
plfah1-rsync-no-solvent.log
plfah2-rsync-all-atoms.log
plfah2-rsync-no-solvent.log