Minimal XSEDE starter scripts

condor.osg-xsede

universe = vanilla
requirements = (FileSystemDomain != "") && (Memory >= 1) && (Arch == "X86_64")

# has to specify project name to get it run on xsede osg cluster
+ProjectName=TG-AST150046

# executeable path is relative to current dir, not InitialDir
executable = ../git/STSP/stsp_todaysdate
# if there is file argument, it must apply based on the remote gw
arguments  = test.in

# input file
transfer_input_files = transit000.txt, test.in
transfer_output_files = test_mcmc.txt, test_lcbest.txt, test_finalparam.txt, tes
t_parambest.txt

# transfer output back
should_transfer_files = YES
when_to_transfer_output = ON_EXIT

# command output and log
output = output/myrun.out
error = output/myrun.err
log = output/myrun.log

notification = never 

# this only affects in/out file path root dir
queue

test.in

#PLANET PROPERTIES
1							; Number of planets -- (if there are more than 1 planet, then the set of 8 planet properties are repeated)
2454605.8915400002					; T0, epoch         (middle of first transit) in days.
4.8878023300				; Planet Period      (days)
0.0034300000				; (Rp/Rs)^2         (Rplanet / Rstar )^ 2
0.0982000000			; Duration (days)   (physical duration of transit, not used)
0.1270000000					; Impact parameter  (0= planet cross over equator)
89.4234790468			; Inclination angle of orbit (90 deg = planet crosses over equator)
103.0000000000					; Lambda of orbit (0 deg = orbital axis along z-axis)
0.2610000000			; ecosw
0.0850000000			; esinw
#STAR PROPERTIES
1.8063440000 			; Mean Stellar density (Msun/Rsun^3)
29.977266532			; Stellar Rotation period (days)
4780					; Stellar Temperature
0.31					; Stellar metallicity
80						; Tilt of the rotation axis of the star down from z-axis (degrees)
0.00000 0.86410 0.00000 -0.15021			; Limb darkening (4 coefficients)
100			; number of rings for limb darkening appoximation
#SPOT PROPERTIES
2						; number of spots
1.0						; fractional lightness of spots (0.0=total dark, 1.0=same as star)
#LIGHT CURVE
transit000.txt		; lightcurve input data file
2454957.7156000002		; start time to start fitting the light curve
0.19548999983817		; duration of light curve to fit (days)
1.0000000000		; real maximum of light curve data (corrected for noise), 0 -> use downfrommax
0						; is light curve flattened (to zero) outside of transits?
#ACTION
M		; M= unseeded mcmc
74384338	; random seed
2.5		; ascale
100		; number of chains
800		; mcmc steps
1		; 0= use downfrommax normalization, 1= calculate brightness factor for every model

transit000.txt

2454957.7156 0.999970773582 8.72544e-05
2454957.71628 1.00001500859 8.72773e-05
2454957.71696 0.999975967878 8.72975e-05
2454957.71764 1.00000337692 8.73178e-05
2454957.71833 0.999916420615 8.73333e-05
2454957.71901 1.00018733647 8.73626e-05
2454957.71969 1.00011942681 8.73753e-05
2454957.72037 1.00010062849 8.73907e-05
2454957.72105 1.0000035937 8.74027e-05
2454957.72173 0.999988809698 8.74147e-05
2454957.72241 1.00011563716 8.74312e-05
2454957.72309 1.00009777836 8.74391e-05
2454957.72377 1.00008752116 8.74456e-05
2454957.72446 1.00015532961 8.74518e-05
2454957.72514 1.00012431752 8.74504e-05
2454957.72582 1.00005879938 8.74459e-05
2454957.7265 0.999897620904 8.74339e-05
2454957.72718 0.999994383689 8.74267e-05
2454957.72786 0.999925449119 8.74086e-05
2454957.72854 0.999929626365 8.73896e-05
2454957.72922 0.999763066996 8.73562e-05
2454957.72991 0.999842576767 8.7336e-05
2454957.73059 0.9999746997 8.73065e-05
2454957.73127 0.999993738462 8.72814e-05
2454957.73195 0.999988264264 8.72466e-05
2454957.73263 1.000005424 8.72124e-05
2454957.73331 1.00032938007 8.71873e-05
2454957.73399 0.999985165798 8.71354e-05
2454957.73467 0.999966452904 8.71022e-05
2454957.73535 1.0000268306 8.70675e-05
2454957.73604 0.99998198191 8.70318e-05
2454957.73672 1.00004338455 8.6999e-05
2454957.7374 0.999976414419 8.69631e-05
2454957.73808 0.999888774826 8.69288e-05
2454957.73876 1.0000954616 8.69057e-05
2454957.73944 0.999986127606 8.68722e-05
2454957.74012 1.0001239731 8.68503e-05
2454957.7408 0.999834507282 8.68128e-05
2454957.74148 1.00006323007 8.67929e-05
2454957.74217 0.999922208594 8.67676e-05
2454957.74285 0.999968835125 8.67456e-05
2454957.74353 1.00000546856 8.67258e-05
2454957.74421 0.999922953635 8.66998e-05
2454957.74489 0.999938490546 8.66756e-05
2454957.74557 0.999784999062 8.66468e-05
2454957.74625 1.00004139504 8.66372e-05
2454957.74693 0.999937612756 8.66098e-05
2454957.74761 1.00011133086 8.65918e-05
2454957.7483 0.999974067483 8.65614e-05
2454957.74898 0.999938016142 8.65329e-05
2454957.74966 0.999901708568 8.65026e-05
2454957.75034 1.0000095748 8.64762e-05
2454957.75102 1.00005816577 8.64484e-05
2454957.7517 0.999894083319 8.64118e-05
2454957.75238 0.9999062892 8.63832e-05
2454957.75306 0.99998161382 8.63561e-05
2454957.75375 1.00002123664 8.63279e-05
2454957.75443 1.00001926429 8.62987e-05
2454957.75511 0.99993094142 8.6268e-05
2454957.75579 0.999945795043 8.62411e-05
2454957.75647 1.00008509251 8.62208e-05
2454957.75715 1.00006074249 8.6197e-05
2454957.75783 0.999845328023 8.61691e-05
2454957.75851 1.00002630605 8.61502e-05
2454957.75919 0.99986094244 8.61313e-05
2454957.75988 0.999987855323 8.61205e-05
2454957.76056 0.999933526025 8.61036e-05
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2454957.76192 1.00004078648 8.60855e-05
2454957.7626 0.999862013338 8.60632e-05
2454957.76328 1.00005511976 8.6061e-05
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2454957.90632 1.00006542014 8.80972e-05
2454957.907 0.999897237961 8.82573e-05
2454957.90768 0.999921230562 8.84211e-05
2454957.90837 0.999847512964 8.85775e-05
2454957.90905 0.999951962752 8.87283e-05
2454957.90973 1.00003557224 8.88655e-05
2454957.91041 0.999923932152 8.89804e-05
2454957.91109 0.999980978816 8.90833e-05

XSEDE-starter.md

Getting Started with XSEDE/OSG

Logging in

Login to the XSEDE login node with:

ssh [email protected]

Login to the Open Science Grid:

gsissh submit-1.osg.xsede.org

Build STSP

Make a directory to store git repositories in:

mkdir git
cd git

Clone the STSP repository there:

git clone https://github.com/lesliehebb/STSP.git
cd STSP

Build STSP (after tweaking appropriate #define settings)

gcc -lm stsp.c -o stsp_todaysdate

where stsp_todaysdate is the name of the new STSP executable. I like to build each one with a date so that you remind yourself which version you're using each time you look at its name.

Create an example HTCondor job

Create a directory for our STSP demo, and create a directory for outputs within the demo directory

mkdir osg_demo
cd osg_demo
mkdir output

Copy the condor.osg-xsede, transit000.txt and test.in files into this directory via scp or copy/paste.

In condor.osg-xsede, you must edit these arguments:

• ProjectName: the allocation which should be charged for this job. This gets printed to the terminal when you log in.
• executable: the path to the stsp_todaysdate executable file
• arguments: the arguments that stsp_todaysdate will expect. For all runs, this will begin with the .in file. For runs seeded from previous runs, you must also enter the path to the _finalparam.txt file, separated from the .in file with a comma.
• transfer_input_files: Since nodes on the OSG don't share a common file system, any files that are needed by your job must be transfered to the node when the job begins. Here, make a comma-separated list of the paths of files that must be present to start your job
• transfer_output_files: Similar to above, list the files that you want returned to your OSG home account.
• output, error, log: Paths for where to place the HTCondor output (stdout), error (stderr) and log files.
• notification: Sets whether or not you'd like to receive email notifications about job initialization/termination

Run an example HTCondor job

Once your condor.osg-xsede file is ready to go, submit it to the condor queue with:

condor_submit condor.osg-xsede

To see your job in the queue, you can use the condor_q command. Typically the outputs are so long, that you'll want to pipe that output into a grep for your username. So, for example, I would do this:

$ whoami
bmorris
$ condor_q -sub bmorris
 ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD               
5712791.0   bmorris         1/26 05:15   0+00:00:15 R  0   0.1  stsp_todaysdate test.in
...
1 jobs; 0 completed, 0 removed, 0 idle, 1 running, 0 held, 0 suspended

If the ST (status) column says I, your job is idle -- likely waiting for its turn in the queue. If ST=R and RUN_TIME is non-zero, your job is running.

If you need to kill your job, you can pass the ID number returned by the condor_q command above to the condor_rm command:

condor_rm 5695989.0

When your job is finished, it will no longer show in the queue, and the files you specified with transfer_output_files will be transferred back to the directory where you submitted the job (osg_demo/).