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399 |
DM-2277
|
03/05/2015 15:09:34
|
Document HOW-TO setup-up krb5 for easy cluster access
|
{code:bash} su aptitude install krb5-user # edit /etc/krb5.conf w.r.t ccage one # then as desktop user kinit ssh ccqservxxx {code} /etc/krb5.conf {code:bash} [libdefaults] default_realm = IN2P3.FR ... allow_weak_crypto = true ... [realms] IN2P3.FR = { kdc = kerberos-1.in2p3.fr:88 kdc = kerberos-2.in2p3.fr:88 kdc = kerberos-3.in2p3.fr:88 master_kdc = kerberos-admin.in2p3.fr:88 admin_server = kerberos-admin.in2p3.fr kpasswd_server = kerberos-admin.in2p3.fr default_domain = in2p3.fr {code} sshconfig: {code:bash} Host ccqservbuild GSSAPIAuthentication yes GSSAPIDelegateCredentials yes ForwardX11 yes HostName ccqservbuild.in2p3.fr #ProxyCommand ssh -W %h:%p cc Host ccqserv1* GSSAPIAuthentication yes GSSAPIDelegateCredentials yes ForwardX11 yes HostName %h.in2p3.fr ProxyCommand ssh -W %h:%p ccqservbuild {code}
| 2 |
400 |
DM-2279
|
03/05/2015 22:21:00
|
Fix problems with mysql timeout
|
We added some code for supporting reconnecting (see https://dev.lsstcorp.org/trac/ticket/3042) but clearly not enough to recover from connection timeouts. This needs to be addressed.
| 1 |
401 |
DM-2280
|
03/06/2015 09:19:00
|
The TAN_PIXELS cameraGeom coordinate system should be with respect to the center of the focal plane
|
The TAN_PIXELS cameraGeom coordinate system (the position on a detector if there is no optical distortion) is presently defined with respect to the center of the detector -- i.e. a star at the center of the detector will have the same position in PIXELS and TAN_PIXELS coordinates. That is a mistake. TAN_PIXELS should be defined with respect to the center of the focal plane, since it then reflects the effects of having optical distortion or not. Fixing this will help meas_astrom match stars. The effects of not fixing it are making the matcher search farther for a fit. As long as we allow sufficient offset in the matcher config the current system will work, but it is not ideal.
| 2 |
402 |
DM-2281
|
03/06/2015 11:08:04
|
Implement connection pool
|
Implement a class that manages a connection pool, and optionally, if configured, restarts connection as needed in case of timeout.
| 1 |
403 |
DM-2282
|
03/06/2015 11:09:52
|
Switch to using db connection pool
|
Switch to using the db connection pool. Note, in addition to getting auto-reconnect, in metaserv that would handy if we need to talk to multiple database servers simultaneously.
| 1 |
404 |
DM-2294
|
03/09/2015 13:31:01
|
Unable to start cmsd on Qserv worker node
|
Some build issues have qlready been fixed in commit: 9dd378829e8751a6852356967411c20580e2a1c3 Here's the log: {code:bash} [fjammes@ccqserv101 ~]$ cat /qserv/qserv-run/var/log/worker/cmsd.log 150309 21:19:46 9794 Starting on Linux 3.10.0-123.8.1.el7.x86_64 Copr. 2004-2012 Stanford University, xrd version v20140617-203cf45 ++++++ cmsd [email protected] initialization started. Config using configuration file /qserv/qserv-run/etc/lsp.cf =====> all.adminpath /qserv/qserv-run/tmp =====> xrd.port 1094 =====> xrd.network nodnr Config maximum number of connections restricted to 4096 Config maximum number of threads restricted to 2048 Copr. 2007 Stanford University/SLAC cmsd. ++++++ [email protected] phase 1 initialization started. =====> all.role server =====> ofs.osslib libxrdoss.so =====> oss.localroot /qserv/qserv-run/xrootd-run =====> cms.space linger 0 recalc 15 min 10m 11m =====> all.pidpath /qserv/qserv-run/var/run =====> all.adminpath /qserv/qserv-run/tmp =====> all.manager ccqserv100.in2p3.fr:2131 =====> all.export / nolock The following paths are available to the redirector: w / ------ [email protected] phase 1 server initialization completed. ++++++ [email protected] phase 2 server initialization started. Plugin Unable to find required version information for XrdOssGetStorageSystem in osslib libxrdoss.so ------ [email protected] phase 2 server initialization failed. 150309 21:19:46 9794 XrdProtocol: Protocol cmsd could not be loaded ------ cmsd [email protected]:1094 initialization failed {code}
| 2 |
405 |
DM-2305
|
03/11/2015 11:10:03
|
Measurement transforms for Flux
|
Provide calibration transforms for flux measurements to magnitudes.
| 3 |
406 |
DM-2306
|
03/11/2015 11:10:56
|
Measurement transforms for centroids
|
Provide calibration transforms for all algorithms measuring centroids.
| 5 |
407 |
DM-2307
|
03/11/2015 11:11:34
|
Measurement transforms for shapes
|
Provide calibration transforms for algorithms measuring shapes.
| 2 |
408 |
DM-2309
|
03/11/2015 15:12:51
|
Update dev quick-start guide to new git repositories
|
The quick-start documentation for developers still points to the old git repositories. The RST document needs to be updated to the GitHub repos.
| 0.5 |
409 |
DM-2312
|
03/12/2015 12:19:41
|
obs_test's table file is out of date
|
obs_test's table file is somewhat out of date. Problems include: - afw is required but missing - meas_algorithms and skypix are used by bin/genInputRegistry.py, which is only used to create the input repo so these can be optional - daf_persistence is not used - daf_base is only used by bin/genInputRegistry.py, so it can be optional (though it is presumably setup by daf_butlerUtils in any case)
| 1 |
410 |
DM-2316
|
03/12/2015 19:47:27
|
Clarify expectations for unauthenticated user data access
|
h4. Short version: Clarify what existing community practices, notably including VO interfaces, appear to rely on the availability of unauthenticated access to information in astronomical archives. h4. Details: At the February DM All Hands, [~frossie] raised an objection when it was mentioned that there is a presumption that all user access to LSST data through the DM interfaces (as opposed to through EPO) will be authenticated. We don't appear to have ever documented an explicit requirement that all access be authenticated. The basic controlling requirement is OSS-REQ-0176, "The LSST Data Management System shall provide open access to all LSST Level 1 and Level 2 Data Products, as defined in the LSST System Requirements and herein, in accordance with LSSTC Board approved policies. ...", which was a carefully crafted indirection at a time when the policy for non-US/Chile access was still being developed. However, this presumption has been around for a long time. It is inherent to the project policy that access to the non-Alert data will be limited to individuals who are entitled to it. No matter what we think the final policy might be, we do have to design a system that can be consistent with this policy. [~frossie] stated that the astronomical community relies on certain types of data and metadata - she mentioned coverage maps, among others - being available through unauthenticated interfaces. This ticket is to ask her (and others) to collect documentation of those existing practices, so that we can figure out what the expectations may be and how to respond to them in our design.
| 2 |
411 |
DM-2334
|
03/16/2015 09:28:21
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Simplify interactions with XrdOss
|
The qserv code is still using the old ssi scheme for the cmsd, this needs to be rewritten. For details, see https://listserv.slac.stanford.edu/cgi-bin/wa?A1=ind1503&L=QSERV-L#3
| 5 |
412 |
DM-2340
|
03/16/2015 11:08:46
|
Reprise SDRP processing metrics
|
In support of an SDRP-based science talk of Yusra AlSayyad, we spent some cycles gathering/summarizing processing middleware results and metrics from the US side of processing of the Split DRP. This information from notes, logs, databases, etc provided contextual information on the processing campaign that produced the SDRP science results.
| 2 |
413 |
DM-2341
|
03/16/2015 11:24:43
|
Use parallel ssh to manage Qserv on IN2P3 cluster
|
IN2P3 sysadmin won't manage Qserv through puppet. So Qserv team has to provide ssh scripts to do this.
| 5 |
414 |
DM-2343
|
03/16/2015 13:33:59
|
Move afw_extensions_rgb functionality into afw proper
|
See RFC-32
| 1 |
415 |
DM-2347
|
03/16/2015 17:35:27
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(In)equality semantics of Coords are confusing
|
Viz: {code} In [1]: from lsst.afw.coord import Coord In [2]: c1 = Coord("11:11:11", "22:22:22") In [3]: c1 == c1, c1 != c1 Out[3]: (True, False) In [4]: c2 = Coord("33:33:33", "44:44:44") In [5]: c1 == c2, c1 != c2 Out[5]: (False, True) In [6]: c3 = Coord("11:11:11", "22:22:22") In [7]: c1 == c3, c1 != c3 Out[7]: (True, True) {code} {{c1}} is simultaneously equal to *and* not equal to {{c3}}!
| 1 |
416 |
DM-2349
|
03/17/2015 08:34:11
|
Add unit tests to SchemaToMeta
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Add unit tests, also improve variable names as suggested by K-T in comments in DM-2139
| 1 |
417 |
DM-2356
|
03/18/2015 10:15:46
|
Identify the hardware resources needed at NCSA for short term development
|
Supply the hardware resources needed at NCSA for short term development. It is captured in DM-2327
| 1 |
418 |
DM-2363
|
03/19/2015 08:56:12
|
RGB code introduces dependency on matplotlib
|
While the new RGB code looks like it's just calling NumPy, NumPy is actually delegating to matplotlib under the hood when it writes RGB(A) arrays. It also turns out that code is broken in matplotlib prior to 1.3.1 (though that shouldn't be a problem for anyone but those who - like me - are trying to use slightly older system Python packages). I think think this means we should add an optional dependency on matplotlib to the afw table file, and condition the running of the test code on matplotlib's presence (and, ideally, having the right version). I'm happy to do this myself (since I'm probably the only one affected by it right now).
| 1 |
419 |
DM-2364
|
03/19/2015 10:23:32
|
Revisit the choice of using flask
|
We should quickly revisit if flask is the right choice for us. Related: reportedly, our simple flask-based webserver is using more CPU in an idle state than expected. It might be useful to profile things, and look into that.
| 1 |
420 |
DM-2367
|
03/19/2015 11:10:50
|
run lsstswBuild.sh in a clean sandbox
|
The "driver" script, lsstswBuild.sh, used by the buildbot slave on lsst-dev to initiate a "CI run" has a number of environment assumptions (binaries in the $PATH, paths to various components, hostnames, etc.). This prevents it from [easily] being invoked on any other host. As lsstswBuild.sh builds a number of packages that are not in the lsst_distrib product, the os level dependencies for these other products need to be determined. In addition, the current version of lsstswBuild.sh and related scripts on lsst-dev are not version controlled.
| 8 |
421 |
DM-2380
|
03/23/2015 10:27:45
|
Retrieve HSC engineering data
|
HSC data becomes public 18 months after it was taken, so data taken during commissioning are now available. We would like to use this data for testing the LSST pipeline. It needs to be downloaded from Japan.
| 2 |
422 |
DM-2382
|
03/23/2015 12:34:53
|
Make sure the command-line parser warns loudly enough if no data found
|
A user recently got confused when calling parseAndRun didn't call the task's run method. It turns out there was no data matching the specified data ID. Make sure this generates a loud and clear warning.
| 1 |
423 |
DM-2383
|
03/23/2015 16:19:09
|
migrate package deps from sandbox-stackbuild to a proper puppet module
|
There is a growing list of known package dependencies in the sandbox-stackbuild repo and a need to use this information for independent environments (such as CI). This list of packages should be lifted out into an independent puppet module that can be reused.
| 2 |
424 |
DM-2387
|
03/24/2015 11:46:00
|
Build testQDisp.cc on ubuntu
|
testQDisp.cc needs flags -lpthread -lboost_regex to build on ubuntu.
| 1 |
425 |
DM-2390
|
03/24/2015 16:08:54
|
Errors need to be checked in UserQueryFactory from QuerySession objects
|
UserQueryFactory doesn't check its QuerySession object for errors after setQuery. Thus it continues setting things up after the QuerySession knows the state is invalid.
| 1 |
426 |
DM-2411
|
03/25/2015 16:29:09
|
Allow qserv-admin.py to delete a node
|
Registered workers in CSS with qserv-admin.py are currently not able to be removed (no DELETE NODE type command). Also, changing node status from ACTIVE to INACTIVE needs to be fixed.
| 1 |
427 |
DM-2417
|
03/26/2015 17:23:45
|
Data loader script crashes trying to create chunk table
|
Vaikunth discovered a bug in data loader when trying to load a data into Object table: {noformat} [CRITICAL] root: Exception occured: Table 'Object_7480' already exists Traceback (most recent call last): File "/usr/local/home/vaikunth/src/qserv/bin/qserv-data-loader.py", line 318, in <module> sys.exit(loader.run()) File "/usr/local/home/vaikunth/src/qserv/bin/qserv-data-loader.py", line 254, in run self.loader.load(self.args.database, self.args.table, self.args.schema, self.args.data) File "/usr/local/home/vaikunth/src/qserv/lib/python/lsst/qserv/admin/dataLoader.py", line 171, in load return self._run(database, table, schema, data) File "/usr/local/home/vaikunth/src/qserv/lib/python/lsst/qserv/admin/dataLoader.py", line 209, in _run self._loadData(database, table, files) File "/usr/local/home/vaikunth/src/qserv/lib/python/lsst/qserv/admin/dataLoader.py", line 586, in _loadData self._loadChunkedData(database, table) File "/usr/local/home/vaikunth/src/qserv/lib/python/lsst/qserv/admin/dataLoader.py", line 653, in _loadChunkedData self._makeChunkAndOverlapTable(conn, database, table, chunkId) File "/usr/local/home/vaikunth/src/qserv/lib/python/lsst/qserv/admin/dataLoader.py", line 727, in _makeChunkAndOverlapTable cursor.execute(q) File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 176, in execute if not self._defer_warnings: self._warning_check() File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 92, in _warning_check warn(w[-1], self.Warning, 3) Warning: Table 'Object_7480' already exists {noformat} It looks like I did not do enough testing after my recent improvement in creating chunk tables. It tries to create the chunk table with "CREATE TABLE IF NOT EXISTS ..." but that actually generates "warning exception" on mysql side when table is already there. Need to catch this exception and ignore it.
| 1 |
428 |
DM-2423
|
03/27/2015 11:32:02
|
Weighting in photometric calibration is incorrect
|
Dominique points out that the zero point calibration uses errors not inverse errors to calculate the zero point. git annotate reveals: bq. 24c9149f python/lsst/meas/photocal/PhotoCal.py (Robert Lupton the Good 2010-12-13 05:03:12 +0000 353) return np.average(dmag, weights=dmagErr), np.std(dmag, ddof=1), len(dmag) Please fix this. At the same time, we should add a config parameter to soften the errors.
| 1 |
429 |
DM-2426
|
03/27/2015 13:34:31
|
Implement SpanSet+ellipse operations
|
Implement the following SpanSet operations: - Construct from an ellipse - note geom::ellipses::PixelRegion; this should do most of the work. - Compute centroid - see old Footprint implementation - Compute shape (quadrupole moments) - see old Footprint implementation One complication here is that this will introduce a circular dependency between afw::geom and afw::geom::ellipses. That's easy to address at the C++ level, but it's tricky in Python (which package imports the other?) I'll be emailing dm-devel shortly to start a discussion on how to address this problem.
| 2 |
430 |
DM-2427
|
03/27/2015 13:36:53
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Implement SpanSet applyFunctor methods
|
Implement methods that apply arbitrary functors to pixels within a SpanSet, as described on RFC-37. The only tricky part of this implementation will be the "traits" classes that allow different target objects to interpreted differently. I'd be happy to consult on this; I have a rough idea in my head, but it needs to be fleshed out.
| 3 |
431 |
DM-2429
|
03/28/2015 12:29:12
|
Add aperture corrections to meas_extensions_photometryKron
|
When transitioning {{meas_extensions_photometryKron}} to the new measurement framework, aperture correction was omitted pending the completion of DM-85. It needs to be re-enabled when that epic is complete.
| 1 |
432 |
DM-2430
|
03/29/2015 07:48:52
|
Make qserv server-side log messages more standard
|
Qserv server-side Python logging appears to mostly use a common format: "{{%(asctime)s %(name)s %(levelname)s: %(message)s}}". It also mostly uses a common date format: "{{%m/%d/%Y %I:%M:%S}}". But I see instances of: * "{{%(asctime)s %(levelname)s %(message)s}}" * "{{%(asctime)s - %(name)s - %(levelname)s - %(message)s}}" * "{{%(asctime)s \{%(pathname)s:%(lineno)d\} %(levelname)s %(message)s}}" * and now, after DM-2176, "{{%(asctime)s \[PID:%(process)d\] \[%(levelname)s\] (%(funcName)s() at %(filename)s:%(lineno)d) %(name)s: %(message)s}}" Unless these are used in very different contexts, it will aid automated log processing for them to be more standardized. In addition, the date format is unacceptable as it does not use RFC 3339 (ISO8601) format and does not include a timezone indicator (which means the default {{datefmt}} is insufficient). This must be fixed. See also DM-1203.
| 1 |
433 |
DM-2435
|
03/29/2015 21:00:34
|
Reading an Exposure from disk aborts if the Psf is of an unknown type
|
Attempting to read an Exposure (in this case via the butler) fails if the PSF class isn't available. An exception would be reasonable, but an assertion failure is not. Running the attached script on tiger-sumire with bq. setup python anaconda; setup -T v10_1_rc2 lsst_apps; setup -j distEst -t HSC; setup -j -r ~/LSST/obs/subaru {code} WARNING: Could not read PSF; setting to null: PersistableFactory with name 'PsfexPsf' not found, and import of module 'lsst.meas.extensions.psfex' failed (possibly because Python calls were not available from C++). {0}; loading object with id=4, name='PsfexPsf' {1}; loading object with id=28, name='CoaddPsf' {2} python: src/table/io/InputArchive.cc:109: boost::shared_ptr<lsst::afw::table::io::Persistable> lsst::afw::table::io::InputArchive::Impl::get(int, const lsst::afw::table::io::InputArchive&): Assertion `r.first->second' failed. Aborted {code}
| 1 |
434 |
DM-2436
|
03/30/2015 07:48:57
|
Cherry-pick "fix makeRGB so it can replace saturated pixels and produce an image" from HSC
|
HSC-1196 includes fixes and test cases for {{afw}}. After review on HSC, they should be checked/merged to LSST.
| 0.5 |
435 |
DM-2441
|
03/30/2015 11:53:09
|
iRODS test: Register data in place
|
In our first tests of iRODS, we have used "iput" to load data into iRODS cache spaces (the iRODS Vault). For large collections already in a well known location on a server, one may want to leave the data in place but still manage it with iRODS. To do this one can use "ireg" to register the data with IRODS without the upload process.
| 2 |
436 |
DM-2442
|
03/30/2015 11:55:51
|
iRODS usage, devel survey
|
Read up on current IRODS usage and development track.
| 3 |
437 |
DM-2451
|
03/31/2015 15:35:09
|
Fix interface between QservOss and new cmsd version
|
QservOSS gives an error when attempting to run queries on the worker from the czar. Error log snippet: {code} QservOss (Qserv Oss for server cmsd) "worker" 150331 16:06:17 9904 Meter: Unable to calculate file system space; operation not supported 150331 16:06:17 9904 Meter: Write access and staging prohibited. ------ [email protected] phase 2 server initialization completed. ------ cmsd [email protected]:36050 initialization completed. {code}
| 1 |
438 |
DM-2455
|
03/31/2015 19:12:48
|
uncaught exceptions in GaussianFlux
|
{{SdssShapeAlgorithm::computeFixedMomentsFlux}}, which is used to implement {{GaussianFlux}}, now throws an exception when the moments it is given are singular. That shouldn't have affected the behavior of {{GaussianFlux}}, as it contains an earlier check that should have detected all such bad input shapes. But that doesn't seem to be the case: we now see that exception being thrown and propagating up until it is caught and logged by the measurement framework, resulting in noisy logs. We need to investigate what's going wrong with these objects, and fix them, which may be in {{SdssShape}} or in the {{SafeShapeExtractor}} {{GaussianFlux}} uses to sanitize its inputs.
| 1 |
439 |
DM-2456
|
03/31/2015 23:36:12
|
Participate in April design process
|
Most work here was with designing firefly tools API related details.
| 8 |
440 |
DM-2466
|
04/01/2015 10:46:29
|
lsstsw ./bin/deploy needs LSSTSW set to install products in the right place
|
I cloned lsstsw into ~/Desktop/templsstsw and cd'd into it and typed ./bin/deploy and was shocked to find it installed everything into ~/lsstsw, leaving an unsable mess: some files were in templsstsw and some in ~/lsstsw. The short-term workaround is to manually set LSSTSW before running ./bin/deploy, but this should not be necessary; bin/deploy should either set LSSTSW or not rely on it. I don't recall this problem with earlier versions of lsstsw; I think this is a regression. For now I updated the instructions at https://confluence.lsstcorp.org/display/LDMDG/The+LSST+Software+Build+Tool but I look forward to being able to revert that change.
| 1 |
441 |
DM-2467
|
04/01/2015 13:45:00
|
Implement stitching multiple patches across tract boundaries in a coadd v2
|
* Find region that returns multiple tractPatchLists for testing. * Request region via central point (RA, Dec) with width and height definable in arcseconds and pixels. * May be extend web interface to other data sets, and/or good seeing SkyMaps.
| 8 |
442 |
DM-2475
|
04/02/2015 11:14:05
|
Build 2015_04 Qserv release
|
See https://confluence.lsstcorp.org/display/DM/Qserv+Release+Procedure for recipe.
| 1 |
443 |
DM-2477
|
04/02/2015 16:34:27
|
Design API and RFC design
|
Use the HSC implementation of the base class as a point of reference for designing an integrated Approximate and Interpolate class. The design take into account Chebyshev, spline, and Gaussian process mechanisms. Want to take into consideration client code. I.e. it shouldn't make current consumers more complicated (background and aperture correction to name two). RFC the designed API.
| 8 |
444 |
DM-2491
|
04/06/2015 12:49:49
|
Initial survey of Datacat for LSST
|
Jacek, Brian Van Klaveren have sent along some initial overview/description of their work on Datacat; https://confluence.slac.stanford.edu/display/~bvan/LSST+Datacat+Overview We start examining this in the context of our studies of managing data collections at NCSA.
| 1 |
445 |
DM-2492
|
04/06/2015 16:09:13
|
shapelet unit tests attempts to access display on failure
|
When tests/profiles.py tests fail, they attempt to create live plots without checking for any variables that indicate that the display should be used. These plots should be disabled, as they obscure the real error when the display is not available.
| 1 |
446 |
DM-2497
|
04/07/2015 18:06:53
|
Fix g++ 4.9 return value implicit conversion incompato
|
g++ 4.9 enforces the "explicit" keyword on type conversion operators in return value context. This mean bool checkers along the lines of bool isValidFoo() { return _smartPtrFoo; } require an explicit cast to compile under g++ 4.9 with -std=c++0x. There were a handful of these in our code; found and fixed.
| 1 |
447 |
DM-2506
|
04/09/2015 00:02:13
|
Document structure of our custom ddl ascii schema
|
Need to better document what is supported / accepted by schemaToMeta.py. We are currently relying on cat/sql/baselineSchema.sql as the guide.
| 2 |
448 |
DM-2508
|
04/09/2015 01:01:49
|
Information exchange between processes - implementation
|
Implement system for information exchange between cmsd and xrootd, per instructions in DM-2507
| 8 |
449 |
DM-2511
|
04/09/2015 09:35:09
|
The distance field of match lists should be set
|
The meas_astrom AstrometryTask returns a match list that has distance = 0 for all elements. Neither the matcher nor the WCS fitter are setting this field, and both ought to.
| 2 |
450 |
DM-2518
|
04/10/2015 02:25:44
|
Add a CFHT-based post-build integration test to the sandbox build
|
From [~boutigny] I have installed some simple stack validation tools working on CFHT data in {{/lsst8/boutigny/valid_cfht}} Here is the content of the README file : ------------------------------------------------------------------------------------------------------------------------ This directory contains a set of utilities to validate a stack release with CFHT data At the moment, only validation plots for the astrometry are produced Directories : ------------- rawDownload : contain raw CFHT images (flat, dark, bias, fringe,... corrected) reference_plots : contain reference plots corresponding to the best results obtain so far. Files : ------- setup.cfht : stack environment setup valid_cfht.sh : run processCcd taks on the cfht images valid_cfht.sh init : create the input/ouput directories, ingest raw images and run processCcd valid_cfht.sh : without the "init" argument, runs processCcd assuming that the directory structure exists and that the raw images have been ingested. valid_cfht.py : run some analysis on the output data produced by valid_cfht.sh processConfig.py : configuration parameters for processCcd run.list : list of vistits / ccd to be processed by processCcd Requirements : -------------- obs_cfht : tickets/DM-1593 astrometry_net_data : SDSS_DR9 reference catalog corresponding for CFHT Deep Field #3 ------------------------------------------------------------------------------------------------------------------------ Basically it produces a set of plots stored in a png image that can be compared to a reference plot corresponding to the best results obtained so far with stack_v10_0 I hope that this is useful. Just be careful that I wrote these scripts with my own "fat hand full of fingers" and that it is just basic code from a non expert. If it is useful, I can certainly add more plots to validate the psf determination, photometry, etc. Comments, suggestions and criticisms are very welcome.
| 1 |
451 |
DM-2521
|
04/10/2015 12:06:52
|
Update repo.yaml for first set of Sims Stash repo moves
|
The repos.yaml file needs to be updated with correct repository locations once SIM-1074 is completed.
| 1 |
452 |
DM-2533
|
04/13/2015 12:43:05
|
Remove version attribute from Schema
|
Remove the Schema attribute and its getters and setters. This change won't be something we can merge to master on its own, as it doesn't provide backwards-compatible FITS reading that will added in future tasks.
| 1 |
453 |
DM-2535
|
04/13/2015 12:47:14
|
Backwards compatibility for reading compound fields from FITS
|
Read old-style afw::table compound fields in as scalar fields, using the new FunctorKey conventions.
| 2 |
454 |
DM-2536
|
04/13/2015 12:48:33
|
Backwards compatibility for reading slots and measurements from FITS
|
Rename fields to match the new slot and measurement naming conventions.
| 2 |
455 |
DM-2538
|
04/13/2015 13:32:38
|
RESTful python client
|
Develop basic abstractions for restful apis in a python client
| 3 |
456 |
DM-2543
|
04/14/2015 10:58:35
|
Python APIs for Firefly
|
We need Python APIs to interface with Firefly visualization components. This is the first set of many functions.
| 8 |
457 |
DM-2545
|
04/15/2015 06:48:44
|
LaTeX support in Doxygen broken
|
LaTeX markup in Doxygen documentation ought to be rendered properly for display in HTML. It isn't: it's just dumped to the page as raw text. See, for example, [the documentation for {{AffineTransform}}|https://lsst-web.ncsa.illinois.edu/doxygen/xlink_master_2015_04_15_07.01.28/classlsst_1_1afw_1_1geom_1_1_affine_transform.html#details].
| 1 |
458 |
DM-2546
|
04/15/2015 11:02:52
|
Host.cc doesn't find gethostname and HOST_NAME_MAX under el7
|
el7 gives an error that it can't find HOST_NAME_MAX.
| 1 |
459 |
DM-2547
|
04/15/2015 13:29:21
|
Fix again interface between QservOss and new cmsd version
|
QservOSS gives an error when attempting to run queries on the worker from the czar. Error log snippet: {code} QservOss (Qserv Oss for server cmsd) "worker" 150331 16:06:17 9904 Meter: Unable to calculate file system space; operation not supported 150331 16:06:17 9904 Meter: Write access and staging prohibited. ------ [email protected] phase 2 server initialization completed. ------ cmsd [email protected]:36050 initialization completed. {code}
| 8 |
460 |
DM-2549
|
04/15/2015 18:48:27
|
The string repr of Coord should show the coordsys and angles in degrees
|
The default string representation of Coord (e.g. std::cout << coord in C++ and str(coord) in Python) is to show class name and a pair of angles in radians. It would be much more useful if the default display showed the angles in degrees, as that is what people are used to. Also, it would be very helpful if the display included the name of the coordinate system. This is especially needed for the base class, as it is quite common to get shared_ptr to Coord and have no idea what coordinate system it is. At present there is a lot of code that unpacks the angles and explicitly displays them as degrees to get around this problem. But it seems silly to have to do that.
| 2 |
461 |
DM-2551
|
04/15/2015 19:08:56
|
ANetAstrometryTask's debug doesn't fully work
|
{{ANetAstrometryTask}}'s debug code calls (deprecated) method {{Task.display}}, which raises an AttributeError on this coce: {code} try: sources[0][0] except IndexError: # empty list pass except (TypeError, NotImplementedError): # not a list of sets of sources {code}
| 1 |
462 |
DM-2552
|
04/16/2015 03:24:06
|
xrootd can't be started via ssh
|
{code:bash} qserv@clrinfopc04:~/src/qserv$ ssh localhost -vvv "~qserv/qserv-run/2015_02/etc/init.d/xrootd start" ... debug3: Ignored env _ debug1: Sending command: ~qserv/qserv-run/2015_02/etc/init.d/xrootd start debug2: channel 0: request exec confirm 1 debug2: callback done debug2: channel 0: open confirm rwindow 0 rmax 32768 debug2: channel 0: rcvd adjust 2097152 debug2: channel_input_status_confirm: type 99 id 0 debug2: exec request accepted on channel 0 Starting xrootd.. debug1: client_input_channel_req: channel 0 rtype exit-status reply 0 debug1: client_input_channel_req: channel 0 rtype [email protected] reply 0 debug2: channel 0: rcvd eow debug2: channel 0: close_read debug2: channel 0: input open -> closed {code} Here ssh command freeze, it is possible to lauch xrootd with this (example) script: {code:bash} set -e set -x . /qserv/run/etc/sysconfig/qserv export QSW_XRDQUERYPATH="/q" export QSW_DBSOCK="${MYSQLD_SOCK}" export QSW_MYSQLDUMP=`which mysqldump` QSW_SCRATCHPATH="${QSERV_RUN_DIR}/tmp" QSW_SCRATCHDB="qservScratch" export QSW_RESULTPATH="${XROOTD_RUN_DIR}/result" export LSST_LOG_CONFIG="${QSERV_RUN_DIR}/etc/log4xrootd.properties" eval '/qserv/stack/Linux64/xrootd/xssi-1.0.0/bin/xrootd -c /qserv/run/etc/lsp.cf -l /qserv/run/var/log/xrootd.log -n worker -I v4 &' echo "SCRIPT STARTED" {code} and the same problem occurs. So the problem seems to be with xrootd, and not the startup scripts.
| 5 |
463 |
DM-2554
|
04/16/2015 13:23:11
|
Remove most compound fields from afw::table
|
Remove all Point, Moment, Coord, and Covariance compound fields. Array fields should be retained for now; it's not clear if we want to remove it or not, or how to handle variable-length arrays if we do.
| 2 |
464 |
DM-2555
|
04/17/2015 12:23:15
|
Create and advertise Firefly mailing list
|
Create an IPAC mailing list for all users of Firefly. Advertise it to the interested communities (including the LSST Camera group) and through the Github site. The mailing list [email protected] has been created and all the interested partied have been subscribed to the list.
| 1 |
465 |
DM-2579
|
04/20/2015 14:59:15
|
Calling AliasMap::get("") can return incorrect results
|
It looks like empty string arguments can cause AliasMap to produce some incorrect results, probably due to the partial-match logic being overzealous.
| 1 |
466 |
DM-2580
|
04/21/2015 04:21:31
|
Implement user-friendly template customization
|
Qserv configuration tool has to be improved to allow developers/sysadmin to easily use their custom configuration files (with custom log level, ...) for each Qserv services. An optional custom/ config file directory will be added, and configuration files templates which will be here will override the ones in the install directory. This should be thinked alongside configuration management inside Docker container.
| 5 |
467 |
DM-2581
|
04/21/2015 06:32:49
|
log4cxx build failure on OS X
|
[~frossie] writes: {quote} I have a log4cxx failure on a Macp while building lsst_distrib. Attaching file in case someone has any bright ideas for me in the morning {quote}
| 1 |
468 |
DM-2582
|
04/21/2015 10:08:33
|
Research MaxScale as a mysql-proxy replacement
|
We have been told by Monty that MaxScale is the replacement of the mysql-proxy. Based on DM-2057 the sentiment is that it won't work for our needs. We should very briefly document what our needs are, how we use the proxy now, and if we think MaxScale is not good-enough, say it why, and discuss with Monty and his team.
| 5 |
469 |
DM-2593
|
04/22/2015 13:16:47
|
Client API for new worker management service
|
We have new worker management service which has HTTP interface, now we need to provide simple way to access it from Python basically wrapping all HTTP details into simple Python API.
| 8 |
470 |
DM-2594
|
04/22/2015 14:26:14
|
Change repos.yaml for next set of Simulations Stash repos
|
The next set of Simulations Stash repository migrations is laid out in SIM-1121.
| 1 |
471 |
DM-2595
|
04/23/2015 03:36:21
|
Symlink data directory at configuration
|
We decided to introduce symlinks in order to protect data. This is in particular useful when we need to reinstall qserv, but we have valuable, large data set that we want to preserve. This story introduces symlinks to data: when Qserv is reinstalled, only the symlink is destroyed, and the data stay untouched.
| 5 |
472 |
DM-2599
|
04/23/2015 21:42:12
|
afw.Image.ExposureF('file.fits.fz[i]') returns the image in 'file.fits.fz[1]'
|
It seems that afwImage.ExposureF ignores the extension number when this is passed on as part of the filename and uses the image in extension number 1. This is not the case with afwImage.MaskedImageF which correctly uses the input extension number passed in the same way. The problem has been checked on OSX Yosemite 10.10.3 with the is illustrated in the following code https://gist.github.com/anonymous/d10c4a79d94c1393a493 which also requires the following image in the working directory: http://www.astro.washington.edu/users/krughoff/data/c4d_130830_040651_ooi_g_d1.fits.fz
| 3 |
473 |
DM-2606
|
04/24/2015 13:39:59
|
HSC backport: recent Footprint fixes
|
This is a backport issue to capture subsequent HSC-side work on features already backported to afw. It includes (so far) the following HSC issues: - [HSC-1135|https://hsc-jira.astro.princeton.edu/jira/browse/HSC-1135] - [HSC-1129|https://hsc-jira.astro.princeton.edu/jira/browse/HSC-1129] - [HSC-1215|https://hsc-jira.astro.princeton.edu/jira/browse/HSC-1215]
| 2 |
474 |
DM-2623
|
04/27/2015 16:32:06
|
Design Basic Watcher
|
Design watcher, including its interactions with other components (mysql, css, etc). In the near term, the watcher will handle deleting tables and databases.
| 2 |
475 |
DM-2624
|
04/27/2015 16:33:12
|
Implement DROP table in watcher
|
Implement DROP table using the watcher designed in DM-2623.
| 1 |
476 |
DM-2625
|
04/27/2015 16:34:43
|
Create service for managing watcher
|
We need to be able to start/stop the watcher implemented through DM-2624. This story involves extending our scripts for starting various qserv services to manage watcher.
| 1 |
477 |
DM-2627
|
04/28/2015 09:59:10
|
Add support for configuring multi-node integration tests
|
The multi-node integration test software produced through DM-2175 has hardcoded node names. This story will allow user to configure it. Current plan is to pre-set integration test for several different configurations, e.g., single-node, 2-node, 8-node (and maybe eg 24-node), and user would supply node names through a configuration file.
| 5 |
478 |
DM-2629
|
04/28/2015 10:38:52
|
Fix build for gcc 4.7.2 and gcc 4.8.2
|
#include <condition_variable> is missing in threadSafe.h
| 1 |
479 |
DM-2630
|
04/28/2015 10:50:49
|
Document configuration tool main use cases
|
- Document main use case for qserv-configure.py: install Qserv master/worker node with externalized data directory - Hide complex configuration options? {code} Configuration steps: General configuration steps -d, --directory-tree Create directory tree in QSERV_RUN_DIR, eventually create symbolic link from QSERV_RUN_DIR/var/lib to QSERV_DATA_DIR. -e, --etc Create Qserv configuration files in QSERV_RUN_DIR using values issued from meta-config file QSERV_RUN_DIR/qserv-meta.conf -c, --client Create client configuration file (used by integration tests for example) Components configuration: Configuration of external components -X, --xrootd Create xrootd query and result directories -C, --css-watcher Configure CSS-watcher (i.e. MySQL credentials) Database components configuration: Configuration of external components impacting data, launched if and only if QSERV_DATA_DIR is empty -M, --mysql Remove MySQL previous data, install db and set password -Q, --qserv-czar Initialize Qserv master database -W, --qserv-worker Initialize Qserv worker database -S, --scisql Install and configure SciSQL {code}
| 3 |
480 |
DM-2634
|
04/28/2015 11:37:14
|
add new image stretch algorithm to Firefly visualization
|
There is a need to include two new stretch algorithms, which are asinh and power law gamma. The algorithm is as follow: * asinh ## input zp: zero point of data mp: maximum point of data dr: dynamic range scaling factor of data. It ranges from 1-100,000 bp: black point for image display wp: white point for image display ## calculate rescaled data value rd = dr *(xPix - zp)/mp ## calculate normalized stretch data value nsd = asinh(rd)/asinh(mp-zp) ## calculate display pixel value dPix = 255 * (nsd-bp)/wp Note: The bp, wp values specify how far outside of the scale data one wants the image to display. By default, setting bp=0 and wp=dr. * power law gamma ## input \br zp: zero point of data mp: maximum point of data gamma: gamma value for exponent ## calculate rescaled data value rd = xPix - zp ## calculate normalized stretch data value nsd = rd^(1/gamma) / (mp0zp)^(1/gamma) ## calculate display pixel data value dPix = 255 * nsd
| 8 |
481 |
DM-2635
|
04/28/2015 13:35:00
|
Provide a function to return the path to a package, given its name
|
As per RFC-44 we want a simple function in utils that returns the path to a package given a package name. This has the same API as eups.getProductDir, but hides our dependence on eups, as per the RFC.
| 2 |
482 |
DM-2636
|
04/28/2015 13:37:13
|
Update code to use the function provided in DM-2635
|
As per RFC-44: update existing code that finds packages using eups.getProductDir or by using environment variables to use the function added in DM-2635
| 3 |
483 |
DM-2671
|
05/01/2015 10:13:55
|
Build 2015_05 Qserv Release
|
See https://confluence.lsstcorp.org/display/DM/Qserv+Release+Procedure for recipe.
| 1 |
484 |
DM-2672
|
05/01/2015 10:15:07
|
Build 2015_06 Qserv Release
|
See https://confluence.lsstcorp.org/display/DM/Qserv+Release+Procedure for recipe.
| 1 |
485 |
DM-2679
|
05/01/2015 17:28:45
|
Fix default LOAD DATA options
|
Integration tests in multi-node produced the following error during data loading: {code} 2015-05-01 17:03:03,030 - lsst.qserv.admin.dataLoader - CRITICAL - Failed to load data into non-partitioned table: Data truncated for column 'poly' at row 60 2015-05-01 17:03:03,031 - root - CRITICAL - Exception occured: Data truncated for column 'poly' at row 60 {code} The default options for MySQL LOAD DATA need to be fixed for this.
| 1 |
486 |
DM-2682
|
05/04/2015 09:25:52
|
Add missing empty-chunk-path on Ubuntu 14.04
|
QSERV_DATA_DIR/var/lib/qserv wasn't created on Ubuntu 14.04 and this was breaking loader script. It was working on SL7 for unknown reason. Creation of the directory has been added to qserv-czar config script.
| 1 |
487 |
DM-2683
|
05/04/2015 09:32:50
|
Fix case05 3009_countObjectInRegionWithZFlux freeze
|
This prevents 2014_05 release to pass integration tests.
| 1 |
488 |
DM-2692
|
05/04/2015 12:42:50
|
Rule for automatic replication in iRODS
|
Maintaining extra copies/replicas on separate resources is an important tenet in iRODS, with this practice considered key for prevention of data loss. The automatic replication of files upon ingest can be encoded via a system rule, so that data is preserved as a inherent part of storing in iRODS.
| 2 |
489 |
DM-2694
|
05/04/2015 14:47:46
|
Revisit mysql connections from worker
|
Revisit the code that handles mysql connections in qserv. At the moment Qserv will maintain a connection per chunk-query, up to a hardcoded limit (GroupScheduler: 4, ScanScheduler:32). Also, we have to gracefully handle connection issues (such as dropped connection, or if we hit the max_connections limit).
| 8 |
490 |
DM-2708
|
05/06/2015 11:09:56
|
Understand race condition in Executive::_dispatchQuery
|
Inserting a log (presumably just a delay) in Executive::_dispatchQuery after the new QueryResource but before the Provision call causes queries to fail. The particular test query was "select count(*) from Object" on test case 01.
| 2 |
491 |
DM-2710
|
05/06/2015 14:20:34
|
Mutex use before creation
|
qana/QueryPlugin.cc contains a static boost::mutex, that is used by static class member functions to register plugin implementations. Its constructor is not guaranteed to be called before the static registerXXXPlugin (see e.g. qana/AggregatePlugin.cc) instances use it to register plugin classes.
| 1 |
492 |
DM-2711
|
05/06/2015 14:23:05
|
Migrate boost:thread to std::thread
|
We are mixing boost and std threading libraries. This should be cleaned up - use std:thread consistently everywhere.
| 5 |
493 |
DM-2712
|
05/06/2015 14:25:34
|
Migrate boost::shared_ptr to std::shared_ptr
|
We are mixing boost and std shared_ptrs. This should be cleaned up - use std:shared_ptr consistently everywhere. In a few places we have other types of pointers, (e.g weak_ptr). Migrate these too.
| 2 |
494 |
DM-2716
|
05/07/2015 19:35:38
|
Fix connection leak (2nd iteration)
|
Fix connection leak (and memory leak and thread leak) -- we are leaking 2 per query.
| 2 |
495 |
DM-2718
|
05/08/2015 03:49:07
|
Upgrade EUPS used by lsstsw
|
As discussed, bump it up when you get a chance please.
| 1 |
496 |
DM-2722
|
05/08/2015 13:55:59
|
Revisit design of query poisoner
|
As we discovered through DM-2698, poisoner tends to hold onto query resources even after the query completes. We should revisit whether than can be redesigned and improved, so that when query finishes, all resources related to that query are immediately automatically released. This story involves just the planning part, implementation will be done through separate stories.
| 1 |
497 |
DM-2728
|
05/09/2015 17:26:03
|
Build should fail if node.js is not present
|
Problem: I built Firefly by mistake w/o having node on my path. The build didn't signal any errors, but generated an unusable webapp that wouldn't load. Expected behavior: the build should have failed and warned the user that node.js is missing.
| 2 |
498 |
DM-2729
|
05/09/2015 17:43:54
|
Fix a few more g++ 4.9.2 compatos
|
Some of the recent boost -> std changes don't compile/link under gcc 4.9.2, because of some poor #include hygiene (including <thread> when we should include <condition_variable>, not explicitly including <unistd.h>, etc.) Also, -pthread linker option is required when using std::thread under gcc 4.9.2.
| 1 |
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