November 17-21:

• Write a script to automate jobs.
  • Update (11/18): Completed.
• Run astrobear in post-processing mode on all of the Beta 10 runs (Shear 0, 15, 30, 60), as well as the convergence tests for Beta 10 Shear 15 (levels 2, 4, 6) for the B vs. n plots. Done twice for the mid-way and end of the simulation. Exception: Beta 10, Shear 60, where we have frames out to 328, and the convergence tests which are at frame 50. This yields 12 simulations in total
  • Update (11/18): Finished shear 0, and 30, and 2/3 of Shear 60. Need to get other chombos for Shear 15.
• Make B vs. n plots for the different runs (convergence tests not necessary), publish on wiki.
  • Update (11/18): See my blog post for the first set: ​madams11182014
• Make B vs. n figures (for the paper).
• Run code for beta maps with projected streamlines, 3 times (10.1, 20.1, 27.2 Myr) for each production run, the final frame of Beta 10 Shear 60 (i.e. frame 328), and all of the convergence tests for Shear 15 at frame 15.
  • Update (11/18): Reservation for tomorrow.
  • Update (11/19): Submitted jobs, waiting in queue for noon to roll around.
• Make plots of the beta maps and the projected streamlines, publish on wiki.
• Make figures for the beta maps.

Waiting on Erica before doing the following:

• Run doe for energy spectra on all the production runs.
• Make plots of spectra, publish on wiki.
• Make figures for paper out of best spectra.

November 24-28:

• Run code for density and velocity spectra on the different runs.
• Make plots of spectra, publish on wiki.
• Make figures for paper out of best spectra.
• Run filament analysis on the 3 or 4 best filaments of each of the runs at end time

Fly Through Movies to Make:

• Movie of camera circling around the collision region for one of the colliding flows cases.
• Make a movie that travels down the barrel of the flow, reaches collision region and circles around.
• Make a movie that travels down the barrel of the flow, reaches the collision region, circles around and then zooms into a smaller region of interest to observe its evolution
• Make a movie that travels down the barrel of the flow, reaches the collision region, circles around, zooms into a smaller region of interest and circles arond to watch its evolution, then pans out to circle around the collision region. Do this for each run.

• Write script to automate analysis of the high resolution colliding flows runs, which will be useful for spectral analysis (see: ​Erica's blog post)
• Run astrobear in post-processing mode on all of the runs (B10 S60, 30, 15, 0) for the B vs. n plots.
• Make B vs. n figures for the paper of the different runs.
• Make column density figures for the paper of each of the different runs stated above including B1S60 and convergence tests.
• Make a movie that travels down the barrel of the flow, reaches the collision region and circles around (i.e. implement the fly through cameras for our colliding flows data)

I'm studying for the physics GRE so I might be locked away in a library for the next week in a half. Wish me luck.

Made some VisIt documentation! Weeeeeeeeeee

• How to make 3D CDM Boxes: ​Check it out!

• Plotting sinks with a script instead of P_mass: ​Check it out!

Working on fly-throughs for the CollidingFlows problem by referencing Jonathan's ​blog post. So far I've implemented his problem.f90 and got the code to make properly. I've got some results to visualize, so I'll post those later when I get around to it.

Managing some jobs on Stampede, however things are ​pretty expensive.

Tasks for this week:

• Particular CDM movies.
• Post Processing for convergence tests on Bluestreak. Encountered the following error on Erica's account:

  2014-09-27 05:11:02.120 (FATAL) [0x40001069280] 22137:ibm.runjob.client.Job: could not start job: job failed to start
  2014-09-27 05:11:02.126 (FATAL) [0x40001069280] 22137:ibm.runjob.client.Job: Load failed on R00-ID-J06: Application executable ELF header contains\
   invalid value, errno 8 Exec format error
  

• Reading Shapes and Shaping of Planetary Nebulas (2002) by Bruce and Adam.
• Attempting to visualize these ascii files in SHAPE.

Last week was spent attempting to construct a quick dirty table of the high res colliding flows runs… however I ran into a plethora of issues regarding visit on BH2. Using x2go is fine and works well. Apparently my account is unable to use public key authentication to use some particular nodes. Talk with Jonathan and this is getting sorted with CIRC.

Visualizing from my own computer while ssh-ing into a local machine painstaking. It takes half a day just to get a movie of a .bov. So now I am working on Erica's computer and it is going quite swimmingly. Also have these simulations with sink particles. There are still some issues regarding particular files, however, that are putting a damper on getting the data out there.

As I've tried to go about visualizing the runs, noticed some issues with the files other than data endians. A few are missing or have gotten lost/deleted during our move around.

Last week I accomplished the following:

• Using sed I changed the data endians and variable names.
• Wrote a script to change the name of the files so they are all the same and we can efficiently access them with the "smart" grouping in visit. Did this for both BS and local sets of the data.
• Finished the NoShear data set (now we have all hist and pdfs — transferred between local and BS).
• Cherry picking sections of missing data or areas where visit doesn't like the files. Still working on this actually…

Over the past few weeks I've spent my time shuffling around data and organizing things to make visualization not… impossible? So now we have all of the data together in their respective directories, shared between bamboodata and grassdata. Although one can use Erica's directories in grassdata as "home base" as I made sym-links to the bamboodata directories. So everything seems like it is stored with its applicable files on grassdata.

Current Disk Usage:

Now we're doing post processing on the data, along with resolution testing. We have updated our wikipage (see: ​CFRunStatsHighRes).

I am also studying for the physics GRE, and given my study/work schedule I might not show up for group meetings. I'll still post updates.

Running Jobs

• Currently:
  1. Bluestreak (BS):
     • Post processing (PP) on our chombos (reservation, for B1S60 and B10S15 256 nodes). Once those two runs are done, we'll do the other two. Eventually we'll need to throw the NoShear case into the mix (see 2.).
     • Convergence testing at AMR level 3 (pending in Standard queue for both shear 60 cases). Once these jobs are done, we'll do the other two if necessary.
  2. Stampede:
     • Running the NoShear case on there. Have done approximately 3 restarts. Current restart began 187, so this should be the last restart there. After each restart completes and I restart the next one, I tranfer files back to our local directories. Once we have all the files, I'll transfer them to BS to do PP.

• Future:
  1. PP on BS of NoShear data.
  2. PP for B10S30 and B10S60 on BS.
  3. Convergence Tests for the rest of the data sets.

Tranferring Files

• Once all PP on BS is done, transfer everything back to local directories.
• Tranferring NoShear to BS and local machines.

Visualization

• Erica submitted the proposal to the Vista Collaboratory Contest this past Friday.
• Visualization on BS using x2go.

No science this week for me. Still working on Erica's runs, and starting to delve into more development related topics.

On High Res Runs

• Transferring materials currently to Stampede, about to start submitting jobs today (beta 1, shear 60 & beta 10, shear 15). The other two will run on Bluestreak.
• Submitting jobs to Bluestreak. Waiting on Carl to respond to renew reservation, having beta 10 shear 60 running in standard queue at 128 nodes.
• Aiming to update the CF Production Runs Page. Some of our runs are almost done. For instance beta 10 shear 60 is nearly to chombo 190.

Computing Resources

See previous post.

Development

Had a meeting with Jonathan last Friday to start working on development projects.

• Once I am done working with Erica's data I am going to focus on creating a nap sack algorithm (which Eddie kindly gave to me ). Jonathan and I took a look at the current algorithm we use (see: (17) ​http://arxiv.org/pdf/1112.1710.pdf). Found this thesis by Pierre Schaus (see: ​http://becool.info.ucl.ac.be/pub/theses/thesis-pschaus.pdf). Planning to contact both Pierre Schaus (nurse - patient algorithm) and Mark Kremholtz (about load balancing on the accretion module for Orion (astrophysical AMR)). We also came across this Zoltan code which might be useful to look at?
• Cleaning up unused variables in the code.
• Implementing hydrostatic equilibrium in the disk module. For which I assume I'll have to consider:

We know hydrostatic equilibrium is defined generally to be

\frac{1}{\rho}\frac{d P}{d z} = - g_{z}

which I'll define to be g_{z} = - \frac{\partial \Phi}{\partial z} = \frac{G M}{R^{3}} z for some cylindrical coordinate system (with a distance R from the disk axis, and height z above the plane). Then balancing with the ideal gas law and isothermal sound speed, we can integrate our equation, yielding:

\rho(z) = \rho_{0} e^{- \frac{z^2}{2 H}}, \quad H \propto R^{3/2}.

If anyone wants to go over the derivation with me, that is fine, I just included some highlights here. It is a pretty standard derivation, I think it can be found in some books. Given this would be implemented for the disk module, I just assumed a central mass M and an infinitesimal chunk of mass at (R,z) for a cylindrical coordinate system.

However for now I'll be focusing primarily on the napsack problem since it'll be more beneficial for the code.

SHAPE

Downloaded the software. It looks pretty neat. Haven't had any creative ideas of what to do with it yet in order to understand its capabilities.