• GAVO vs. Corona

  2020-04-24 Markus Demleitner

  

  You won't see something like this (the May 2018 Interop group photo) in Spring 2020: The Sidney Interop, planned for early May, is going to take place using remote tools. Some of which I'd rather do without.

  The Corona pandemic, regrettably, has also brought with it a dramatic move to closed, proprietary communication and collaboration platforms: I'm being bombarded by requests to join Zoom meetings, edit Google docs, chat on Slack, “stream” something on any of Youtube, Facebook, Instagram, or Sauron (I've made one of these up).

  Mind you, that's within the Virtual Observatory. Call me pig-headed, but I feel that's a disgrace when we're out to establish Free and open standards (for good reasons). To pick a particularly sad case, Slack right now is my pet peeve because they first had an interface to IRC (which has been doing what they do since the late 80ies, though perhaps not as prettily in a web browser) and then cut it when they had sufficient lock-in. Of course, remembering how Google first had XMPP (that's the interoperable standard for instant messaging) in Google talk and then cut that, too... ah well, going proprietary unfortunately is just good business sense once you have sufficient lock-in.

  Be that as it may, I was finally fed up with all this proprietary tech and set up something suitable for conferecing building on open, self-hostable components. It's on https://telco.g-vo.org, and you're welcome to use it for your telecons (assuming that when you're reading this blog, you have at least some relationship to astronomy and open standards).

  What's in there?

  Unfortunately, there doesn't seem to be an established, Free conferencing system based on SIP/RTP, which I consider the standard for voice communication on the internet (if you've never heard of it: it's what your landline phone uses in all likelihood). That came as a bit of a surprise to me, but the next best thing is a Free and multiply implemented solution, and there's the great mumble system that (at least for me) works so much better than all the browser-based horrors, not to mention it's quite a bit more bandwidth-effective. So: Get a client and connect to telco.g-vo.org. Join one of the two meeting rooms, done.

  Mumble doesn't have video, which, considering I've seen enough of peoples' living rooms (not to mention Zoom's silly bluebox backgrounds) to last a lifetime, counts as an advantage in my book. However, being able to share a view on a document (or slide set) and point around in it is a valid use case. Bonus points if the solution to that does not involve looking at other people's mail, IM notifications, or screen backgrounds.

  Now, a quick web search did not turn up anything acceptable to me, and since I've always wanted to play with websockets, I've created poatmyp: With it, you upload a PDF, distribute the link to your meeting partners, and all participants will see the slides and a shared pointer. And they can move around in the document together.

  What's left is shared editing. I've looked at a few implementations of this, but, frankly, there's too much npm and the related curlbashware in this field to make any of it enjoyable; also, it seems nobody has bothered to provide a Debian package of one of the systems. On the other hand, there are a few trustworthy operators of etherpads out there, so for now we are pointing to them on telco.g-vo.

  Setting up a mumble server and poatmyp isn't much work if you know how to configure an nginx and have a suitable box on the web. So: perhaps you'll use this opportunity to re-gain a bit of self-reliance? You see, there's little point to have your local copy of the Gaia catalogue, and doing that right is hard. Thanks to people writing Free software, running a simple telecon infrastructure, on the other hand, isn't hard any more.

• The Bochum Galactic Disk Survey

  2020-04-01 Markus Demleitner

  

  Fig 1: How our haphazard variability ratio varies over the sky (galactic coordinates). And yes, it's clear that this isn't dominated by physical variability.

  About a year ago, I reported on a workshop on “Large Surveys with Small Telescopes” in Bamberg; at around the same time, I've published an example for those, the Bochum Galactic Disk Survey BGDS, which used a twin 15 cm robotic telescope in some no longer forsaken place in the Andes mountains to monitor the brighter stars in the southern Milky Way. While some tables from an early phase of the survey have been on VizieR for a while, we now publish the source images (also in SIAP and Obscore), the mean photometry (via SCS and TAP) and, perhaps potentially most fun of all, the the lightcurves (via SSAP and TAP) – a whopping 35 million of the latter.

  This means that in tools like Aladin, you can now find such light curves (and images in two bands from a lot of epochs) when you are in the survey's coverage, and you can run TAP queries on GAVO's http://dc.g-vo.org/tap server against the full photometry table and the time series.

  Regular readers of this blog will not be surprised to see me use this as an excuse to show off a bit of ADQL trickery.

  If you have a look at the bgds.phot_all table in your favourite TAP client, you'll see that it has a column amp, giving the difference between the highest and lowest magnitude. The trouble is that amp for almost all objects just reflects the measurement error rather than any intrinsic variability. To get an idea what's “normal” (based on the fact that essentially all stars have essentially constant luminosity on the range and resolution scales considered here), run a query like:

  SELECT ROUND(amp/err_mag*10)/10 AS bin, COUNT(*) AS n
  FROM bgds.phot_all
  WHERE nobs>10
  GROUP BY bin
  

  As this scans the entire 75 million rows of the table, you will probably have to use async mode to run this.

  

  Figure 2: The distribution of amplitude over magnitude error for all BGDS objects with nobs>10 (blue) and the subset with a mean magnitude brighter than 15 (blue).

  When it comes back, you will have, for objects where any sort of statistics make sense at all (hence nobs>10), a histogram (of sorts) of the amplitude in units of upstream's magnitude error estimation. If you log-log-plot this, you'll see something like Figure 2. The curve at least tells you that the magnitude error estimate is not very far off – the peak at about 3 “sigma” is not unreasonable since about half of the objects have nobs of the order of a hundred and thus would likely contain outliers that far out assuming roughly Gaussian errors.

  And if you're doing a rough cutoff at amp/magerr>10, you will get perhaps not necessarily true variables, but, at least potentially interesting objects.

  Let's use this insight to see if we spot any pattern in the distribution of these interesting objects. We'll use the HEALPix technique I've discussed three years ago in this blog, but with a little twist from ADQL 2.1: The Common Table Expressions or CTEs I have already mentioned in my blog post on ADQL 2.1 and then advertised in the piece on the Henry Draper catalogue. The brief idea, again, is that you can write queries and give their results a name that you can use elsewhere in the query as if it were an actual table. It's not much different from normal subqueries, but you can re-use CTEs in multiple places in the query (hence the “common”), and they are usually more readable.

  Here, we first create a version of the photometry table that contains HEALPixes and our variability measure, use that to compute two unsophisticated per-HEALPix statistics and eventually join these two to our observable, the ratio of suspected variables to all stars observed (the multiplication with 1.0 is a cheap way to make a float out of a value, which is necessary here because a/b does integer division in ADQL if a and b are both integers):

  WITH photpoints AS (
    SELECT
      amp/err_mag AS redamp,
      amp,
      ivo_healpix_index(5, ra, dec) AS hpx
    FROM bgds.phot_all
    WHERE
      nobs>10
      AND band_name='SDSS i'
      AND mean_mag<16),
  all_objs AS (
    SELECT count(*) AS ct,
      hpx
      FROM photpoints GROUP BY hpx),
  strong_var AS (
    SELECT COUNT(*) AS ct,
      hpx
      FROM photpoints
      WHERE redamp>4 AND amp>1 GROUP BY hpx)
  SELECT
    strong_var.ct/(1.0*all_objs.ct) AS obs,
    all_objs.ct AS n,
    hpx
  FROM strong_var JOIN all_objs USING (hpx)
  WHERE all_objs.ct>20
  

  If you plot this using TOPCAT's HEALPix thingy and ask it to use Galactic coordinates, you will end up with something like Figure 1.

  There clearly is some structure, but given that the variables ratio reaches up to 0.2, this must be reflecting instrumental or pipeline effects and thus earthly rather than astrophysical causes. And that's going beyond what I wouldd like to talk about on a VO blog, although I'll take any bet that you will see significant structure in the spatial distribution of the variability ratio at about any magnitude cutoff, since there are a lot of different population mixtures in the survey's footprint.

  Before winding down, let's have a quick look at the time series. As with the short spectra from Byurakan use case, we have stored the actual time series as arrays in the database (the mjd and mags columns in bgds.ssa_time_series). Unfortunately, since they are a lot less array-like than homogeneous spectra, it's also a lot harder to do interesting things with them without downloading them (I'm grateful for ideas for ADQL functions that will let you do in-DB analysis for such things). Still, you can at least easily download them in bulk and then process them in, say, python to your heart's content. The Byurakan use case should give you a head start there.

  For a quick demo, I couldn't resist checking out objects that Simbad classifies as possible long-period variables (you see, as I write this, the public excitement over Betelgeuse's brief waning is just dying down), and so I queried Simbad for:

  SELECT ra, dec, main_id
  FROM basic
  WHERE
    otype='LP?'
    AND 1=CONTAINS(
       POINT('', ra, dec),
       POLYGON('', 127, -30, 112, -30, 272, -30, 258, -30))
  

  (as of this writing, Simbad still needs the ADQL 2.0-compliant first arguments to POINT and POLYGON), where the POLYGON is intended to give the survey's footprint. I obtained that by reading off the coordinates of the corners in my Figure 1 while it was still in TOPCAT. Oh, and I had to shrink it a bit because Simbad (well, the underlying Postgres server, and, more precisely, its pg_sphere extension) doesn't want polygons with edges longer than π. This will soon become less pedestrian: MOCs in relational databases are coming; more on this in a later post.

  

  Fig 3: V566 Pup's BGDS lightcuve in a TOPCAT configured to auto-plot the light curves associated with a row from the bgds.ssa_time_series table on the GAVO DC TAP service.

  If you now do the usual spiel with an upload crossmatch to the bgds.ssa_time_series table and check “Plot Table” in Views/Activation Action, you can quickly page through the light curves (TOPCAT will keep the plot style as you go from dataset to dataset, so it's worth configuring the lines and the error bars). Which could bring you to something like Fig. 3; and that would suggest that V* V566 Pup may be long-period (perhaps we are watching a slow maximium here), but on top of that there probably much faster ripples – unless the errors are grossly off; I am amazed that you can apparently do photometry at error levels of a dozen millimags or so from the ground these days.

• Parallel Queries

  2020-02-14 Markus Demleitner

  

  An experiment with parallel querying of PPMX, going from single-threaded execution to using seven workers.

  Let me start this post with a TL;DR for

  scientists:

  Large analysis queries (like those that contain a GROUP BY clause) profit a lot from parallel execution, and you needn't do a thing for that.

  DaCHS operators:

  When you have large tables, Postgres 11 together with the next DaCHS release may speed up your responses quite dramatically in some cases.

  So, here's the story –

  I've finally overcome my stretch trauma and upgraded the Heidelberg data center's database server to Debian buster. With that, I got Postgres 11, and I finally bothered to look into what it takes to enable parallel execution of database queries.

  Turns out: My Postgres started to do parallel execution right away, but just in case, I went for the following lines in postgresql.conf:

  max_parallel_workers_per_gather = 4
  max_worker_processes = 10
  max_parallel_workers = 10
  

  Don't quote me on this – I frankly admit I haven't really developed a feeling for the consequences of max_parallel_workers_per_gather and instead just did some experiments while the box was loaded otherwise, determining where raising that number has a diminishing return (see below for more on this).

  The max_worker_processes thing, on the other hand, is an educated guess: on my data center, there's essentially never more than one person at a time who's running “interesting”, long-running queries (i.e., async), and that person should get the majority of the execution units (the box has 8 physical CPUs that look like 16 cores due to hyperthreading) because all other operations are just peanuts in comparison. I'll gladly accept advice to the effect that that guess isn't that educated after all.

  Of course, that wasn't nearly enough. You see, since TAP queries can return rather large result sets – on the GAVO data center, the match limit is 16 million rows, which for a moderate row size of 2 kB already translates to 32 GB of memory use if pulled in at once, half the physical memory of that box –, DaCHS uses cursors (if you're a psycopg2 person: named cursors) to stream results and write them out to disk as they come in.

  Sadly, postgres won't do parallel plans if it thinks people will discard a large part of the result anyway, and it thinks that if you're coming through a cursor. So, in SVN revision 7370 of DaCHS (and I'm not sure if I'll release that in this form), I'm introducing a horrible hack that, right now, just checks if there's a literal “group” in the query and doesn't use a cursor if so. The logic is, roughly: With GROUP, the result set probably isn't all that large, so streaming isn't that important. At the same time, this type of query is probably going to profit from parallel execution much more than your boring sequential scan.

  This gives rather impressive speed gains. Consider this example (of course, it's selected to be extreme):

  import contextlib
  import pyvo
  import time
  
  @contextlib.contextmanager
  def timeit(activity):
    start_time = time.time()
    yield
    end_time = time.time()
    print("Time spent on {}: {} s".format(activity, end_time-start_time))
  
  
  svc = pyvo.tap.TAPService("http://dc.g-vo.org/tap")
  with timeit("Cold (?) run"):
    svc.run_sync("select round(Rmag) as bin, count(*) as n"
      " from ppmx.data group by bin")
  with timeit("Warm run"):
    svc.run_sync("select round(Rmag) as bin, count(*) as n"
      " from ppmx.data group by bin")
  

  (if you run it yourself and you get warnings about VOTable versions from astropy, ignore them; I'm right and astropy is wrong).

  Before enabling parallel execution, this was 14.5 seconds on a warm run, after, it was 2.5 seconds. That's an almost than a 6-fold speedup. Nice!

  Indeed, that holds beyond toy examples. The showcase Gaia density plot:

  SELECT
          count(*) AS obs,
          source_id/140737488355328 AS hpx
  FROM gaia.dr2light
  GROUP BY hpx
  

  (the long odd number is 2³⁵4^16-6, which turns source_ids into level 6-HEALPixes as per Gaia footnote id; please note that Postgres right now isn't smart enough to parallelise ivo_healpix), which traditionally ran for about an hour is now done in less than 10 minutes.

  In case you'd like to try things out on your postgres, here's what I've done to establish the max_parallel_workers_per_gather value above.

  1. Find a table with a few 1e7 rows. Think of a query that will return a small result set in order to not confuse the measurements by excessive client I/O. In my case, that's a magnitude histogram, and the query would be:

     select round(Rmag) as bin, count(*) as n from ppmx.data group by bin;

     Run this query once so the data is in the disk cache (the query is “warm”).

  2. Establish a non-parallel baseline. That's easy to do:

     set max_parallel_workers_per_gather=0;
     

  3. Then run:

     explain analyze select round(Rmag) as bin, count(*) as n from ppmx.data group by bin;
     

     You should see a simple query plan with the runtime for the non-parallel execution – in my case, a bit more than 12 seconds.

  4. Then raise the number of max_parallel_workers_per_gatherer successively. Make sure the query plan has lines of the form “Workers Planned” or so. You should see that the execution time falls with the number of workers you give it, up to the value of max_worker_processes – or until postgres decides your table is too small to warrant further parallelisation, which for my settings happened at 7.

  Note, though, that in realistic, more complex queries, there will probably be multiple operations that will profit from parallelisation in a single query. So, if in this trivial example you can go to 15 gatherers and still see an improvement, this could actually make things slower for complex queries. But as I said above: I have no instinct yet for how things will actually work out. If you have experiences to share: I'm sure I'm not the only person on dachs-users who't be interested.

  Update 2022-05-17: In Postgres 13, I found that the planner disfavours parallel plans a lot stronger than I think it has in Postgres 11. To make up for that, I've amended my postgres configuration (in /etc/postgresql/13/main/postgresql.conf) with the slightly bizarre:

  parallel_tuple_cost = 0.001
  parallel_setup_cost = 3
  

  This is certainly not ideal for every workload, but given the queries I see in the VO I want to give Postgres no excuse not to parallelise when there is at least the shard of a chance it'll help; given I'll never execute more than very few queries per second, the extra overhead for parallelising queries that would be faster sequentially will never really bite me.

• LAMOST5 meets Datalink

  2019-12-11 Markus Demleitner

  One of the busiest spectral survey instruments operated right now is the Large Sky Area Multi-Object Fiber Spectrograph Telescope (LAMOST). And its data in the VO, more or less: DR2 and DR3 have been brought into the VO by our Czech colleagues, but since they currently lack resources to update their services to the latest releases, they have kindly given me their DaCHS resource descriptor, and so I had a head start for publishing DR5 in Heidelberg.

  With some minor updates, here it is now: Over nine million medium-resolution spectra covering large parts of the northen sky – the spatial coverage is like this:

  

  There's lots of fun to be had with this; of course, there's an SSA service, so when you point Aladin or Splat at some part of the covered sky and look for spectra, chances are you'll see LAMOST spectra, and when working on some of our tutorials (this one, for example), it happened that LAMOST actually had what I was looking for when writing them.

  But I'd like to use the opportunity to mention two other modes of accessing the data.

  

  Tablesample and TOPCAT's Plot Table activation action

  Say you'd like to look at spectra of M stars and would like to have some sample from across the sky, fire up TOPCAT, point its TAP client the GAVO DC TAP service (http://dc.g-vo.org/tap) and run something like:

  select
    ssa_pubDID, accref, raj2000, dej2000, ssa_targsubclass
  from lamost5.data tablesample(1)
  where
    ssa_targsubclass like 'M%'
  

  This is using the TABLESAMPLE modifier in the from clause, which isn't standard ADQL yet. As mentioned in the DaCHS 1.4 announcement, DaCHS has a prototype implementation of what's been discussed on the IVOA's DAL mailing list: pick a part of a table rather than the full one. It takes a percentage as an argument, and tells the server to choose about this percentage of the table's records using a reasonable and fast heuristic. Note that this won't give you perfect statistical sampling, but if it's not “good enough” for some purpose, I'd like to learn about that purpose.

  Drawing a proper statistical sample, on the other hand, would take minutes on the GAVO database server – with tablesample, I had the roughly 6000 spectra the above query returns essentially instantaneously, and from eyeballing a sky plot of them, I'd say their distribution is close enough to that of the full DR5. So: tablesample is your friend.

  For a quick look at the spectra themselves, in TOPCAT click Views/Activation Actions, check “Plot Table” and make sure TOPCAT proposes the accref column as “Table Location” (if you don't see these items, update your TOPCAT – it's worth it). Now click on a row or perhaps a dot on a plot and behold an M spectrum.

  Cutouts via Datalink

  LAMOST releases spectra in FITS format pretty much like the ones you may know from SDSS. The trick above works because we instead hand out proper, IVOA Spectral Data Model-compliant spectra through SSA and TAP. However, if you need to go back to the original files, you can, using Datalink. If you're unsure what this Datalink thing is: call me vain, but I still like my 2015 ADASS poster explaining that. In TOPCAT, you'd be using the “Invoke Service” activation action to get to the datalinks.

  If you have actual work to do, offloading repetetive work to the computer is what you want, and fortunately, pyVO knows about datalink, too. I give you this is hard to discover so far, and the interface is... a tiny bit clunky. Until some kind soul cleans up the pyVO datalink act, a poster Stefan and I showed at the 2017 ADASS might give you an idea which buttons to press. Or read on and see how things work for LAMOST5.

  The shortest way to datalinks is a TAP query that at least retrieves the ssa_pubdid column (that's a must; Datalink can't work without it) and, on the result, run the iter_datalinks method. This returns an object in which you can find the associated data items (in this case, a preview and the original FITS with the #progenitor semantics), plus the cutout service.

  Hence, a minimal example for pulling the legacy FITS links out of the first three items in lamost5.data would look like this:

  import pyvo
  
  svc = pyvo.dal.TAPService("http://dc.g-vo.org/tap")
  for dl in svc.run_sync("select top 3 ssa_pubdid"
          " from lamost5.data").iter_datalinks():
      print(next(dl.bysemantics("#progenitor")
          )["access_url"].decode("ascii"))
  

  This is a bit different from listing 2 in the poster linked above because it's python3, so getting the first element from iterator an iterator looks a bit different, and (curse astropy.votable for returning VOTable chars as bytes rather than strings!) you'll want to turn the URL into a proper string manually.

  Another, actually more interesting, thing you can do with Datalink is cut out regions of interest. The LAMOST spectra are fairly long (though of course still small by image standards), so if you're only interested in a single line, you can save a bit of storage and bandwidth over blindly pulling the whole thing.

  For instance, if you wanted to pull the vicinity of the H and K Fraunhofer lines from the matches in the loop in the snippet above, you could say:

  from astropy import units as u
  proc = next(dl.iter_procs())
  cutout = proc.processed(band=(392*u.nm,398*u.nm))
  

  And this is what I've done for the decorative left border above: it's the H and K line profiles for 0.1% of the stars LAMOST has classified as G8. Building the image didn't take more than a few seconds (where I'd like the cutouts to be faster by a factor of 10; I guess that's about an afternoon of work for me, so if it'd save you more than that afternoon, poke me to do it).

  What's coming back is tables. By the time python has digested these, they're numpy record arrays. Thus, you can immediately bring in your beloved scipy (or whatever). For instance, if for some reason you're convinced that the H and K lines should be fit by identical Gaussians in the boring case and would like find objects for which that's patently untrue and that hence could be un-boring, here's how you could do that:

  def spectral_model(wl, c1, c2, depth, width):
      return (1
          -depth*numpy.exp(-numpy.square(wl-c1)
              /numpy.square(width))
          -depth*numpy.exp(-numpy.square(wl-c2)
              /numpy.square(width)))
  
  for pubdid, prof in get_profiles(
          "G8", (392*u.nm,398*u.nm), 0.01, 4):
      prof["flux"] /= max(prof["flux"])
      popt, pcov = curve_fit(
          spectral_model, prof["spectral"], prof["flux"],
          sigma=prof["flux_error"],
          p0=[3968, 3934, 1, 1])
      if pcov[3][3]>1:
          break
  

  – where get_profiles is essentially doing the TAP plus datalink routine above, except I'm swallowing spectra with too much noise and I have the function transform the spectral coordinate into the objects' rest frames. If you're curious how I'm doing this just based on the IVOA Spectral Data Model, check the source linked at the bottom of this post.

  I've just run this, and the first spectrum that the machinery flagged as suspicious was this:

  

  – which doesn't look like I've made a discovery just yet. But that doesn't mean there's not a lot to find within LAMOST5's lines...

  To get you up to speed quickly: here's the actual python3 code I ran for the “analysis” and the plot.

• DaCHS 1.4 is out

  2019-10-15 Markus Demleitner

  

  Since the Groningen Interop is over, it's time for a DaCHS release, and so, roughly half a year after the release of DaCHS 1.3, today I've pushed DaCHS 1.4 into our Debian repository.

  As usual, you should upgrade as soon as you find time to do so, because upgrades become more difficult if they span large version gaps; and one of these days you will need some new feature or run into one of the odd bugs. Upgrading is a good opportunity to also get your DaCHS ready for buster by adding the repos mentioned there.

  The list of new features is rather short this time around. Here are some noteworthy ones:

  • There's now an XML grammar that can be used when you have to parse smallish snippets of XML as, for instance, in VOEvent.
  • You can now use TABLESAMPLE(1) after a table specification in DaCHS' ADQL to tell the database engine to just use 1% of a table for a query. While this isn't a precise way to sample tables, it's great when developing queries.
  • Also among new features I'd like to see in ADQL and have therefore put into DaCHS is GENERATE_SERIES(a,b), which is what is known as table-generating function in SQL . If you know SDSS CasJobs, you'll have seen lots of those already. GENERATE_SERIES, however, is really plain: it just spits out a table with a column with integers between a and b. For an example of why one might what to have that, check out the poster I'm linking to in my ADASS report.
  • If you have an updating data descriptor (usually, because you keep feeding data into a data collection), DaCHS will no longer automatically re-make its dependencies (like, say, views). That's because that's not necessary in general, and it's a pain if every update on an obscore-published table tears down and rebuilds the obscore view. For the rare cases when you do need to rebuild dependencies, there's now a remakeOnDataChange attribute on data.
  • At the interop, I've mentioned a few use cases for knowing which server software you're talking to, and I've said that people should set their server headers to informative values. DaCHS does that now.

  To conclude on a low note: This is probably going to be the last release of DaCHS for python 2. Even though we will have to shed a dependency or two that simply will not be ported to python 3, and even though I'm rather unhappy with a few properties of the python 3 port of twisted, there's probably no way to escape this, given that Debian is purging out python 2 packages quickly already.

  So, when we meet again for the next release, you'll probably be looking at DaCHS 2.0, and where you have custom code in your RDs, it's rather likely that you'll see a minor amount of breakage. I promise I'll do everything I can to make the migration easy for deployers, but I can't do higher magic, so: If there's ever been a time to add regression tests to your RDs, it's now.

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