[lsst-dm-stack-users] LSST DM Stack demo
Tim Jenness
tjenness at cornell.edu
Wed Jun 11 20:26:36 PDT 2014
On Jun 11, 2014, at 20:23 , Dick Shaw <shaw at noao.edu<mailto:shaw at noao.edu>> wrote:
Hi Tim,
The demo has and does work for v8.0 with the build procedure and platforms on which we've tested. Can you say more about what steps you followed to install the stack? For instance, did you allow the Anaconda installation, or did you choose to use existing installations of the various packages? This info will help us diagnose the problem.
I followed that wiki page and I asked it to do the anaconda part of the build.
thrylos:lsst timj$ bash newinstall.sh
LSST Software Stack Builder
=======================================================================
Detected git version 1.8.5.2 (Apple Git-48). OK.
In addition to Python 2.7, some LSST packages depend on recent versions of numpy,
matplotlib, and scipy. If you don't have all of these, the installation may fail.
Using the Anaconda Python distribution will ensure all these are set up.
Anaconda Python installed by this installer will be managed by LSST's EUPS
package manager, and will not replace or modify your system python.
Would you like us to install Anaconda Python distribution (if unsure, say yes)? yes
Installing EUPS (v1.3.0)... done.
Installing Anaconda Python Distribution ...
Creating user data directory: /Users/timj/.eups
[ 1/1 ] anaconda 1.8.0 done.
Installing the basic environment ...
[ 1/5 ] doxygen 1.8.2+2 done.
[ 2/5 ] python 0.0.1 ...
Using externally provided Python 2.7.5 :: Anaconda 1.8.0 (x86_64).
[ 2/5 ] python 0.0.1 done.
[ 3/5 ] scons 2.1.0+7 done.
[ 4/5 ] sconsUtils 8.0.0.0 done.
[ 5/5 ] lsst 8.0.0.2 done.
Creating startup scripts (sh) ... done.
Creating startup scripts (csh) ... done.
Creating startup scripts (ksh) ... done.
Bootstrap complete. To continue installing (and to use) the LSST stack
type one of:
source "/Users/timj/work/lsst/loadLSST.sh" # for bash
source "/Users/timj/work/lsst/loadLSST.csh" # for csh
source "/Users/timj/work/lsst/loadLSST.ksh" # for ksh
Individual LSST packages may now be installed with the usual `eups
distrib install' command. For example, to install the science pipeline
elements of the LSST stack, use:
eups distrib install lsst_apps
Next, read the documentation at:
https://confluence.lsstcorp.org/display/LSWUG/LSST+Software+User+Guide
and feel free to ask any questions via our mailing list at:
http://listserv.lsstcorp.org/mailman/listinfo/lsst-dm-stack-users
Thanks!
-- The LSST Software Teams
thrylos:lsst timj$ source loadLSST.sh
thrylos:lsst timj$ eups distrib install lsst_apps
[ 1/54 ] apr 1.3.3+3 done.
[ 2/54 ] cfitsio 3310+2 done.
[ 3/54 ] doxygen 1.8.2+2 (already installed) done.
[ 4/54 ] eigen 3.1.1+2 done.
[ 5/54 ] fftw 3.3.2+2 done.
[ 6/54 ] gsl 1.15+2 done.
[ 7/54 ] minuit2 5.22.00+2 done.
[ 8/54 ] mysqlclient 5.1.65+3 done.
[ 9/54 ] python 0.0.1 (already installed) done.
[ 10/54 ] sqlite 3.7.14+2 done.
[ 11/54 ] swig 2.0.12 done.
[ 12/54 ] xpa 2.1.14+2 done.
[ 13/54 ] astrometry_net 0.30+3 done.
[ 14/54 ] boost 1.55.0.1 done.
[ 15/54 ] mysqlpython 1.2.3+7 done.
[ 16/54 ] numpy 0.0.1 ...
Using externally provided numpy v1.7.1.
[ 16/54 ] numpy 0.0.1 done.
[ 17/54 ] scisql 0.3+3 done.
[ 18/54 ] scons 2.1.0+7 (already installed) done.
[ 19/54 ] wcslib 4.14+3 done.
[ 20/54 ] matplotlib 0.0.1 ...
Using externally provided matplotlib v1.3.1.
[ 20/54 ] matplotlib 0.0.1 done.
[ 21/54 ] pyfits 3.1.2+2 done.
[ 22/54 ] sconsUtils 8.0.0.0 (already installed) done.
[ 23/54 ] astrometry_net_data 8.0.0.0 done.
[ 24/54 ] base 8.0.0.0+1 done.
[ 25/54 ] lsst_thirdparty 8.0.0.0+1 done.
[ 26/54 ] ndarray 8.0.0.0+1 done.
[ 27/54 ] pex_exceptions 8.0.0.0+1 done.
[ 28/54 ] utils 8.0.0.0+1 done.
[ 29/54 ] daf_base 8.0.0.0+1 done.
[ 30/54 ] geom 8.0.0.0+1 done.
[ 31/54 ] pex_logging 8.0.0.0+1 done.
[ 32/54 ] pex_policy 8.0.0.0+1 done.
[ 33/54 ] daf_persistence 8.0.0.0+1 done.
[ 34/54 ] pex_config 8.0.0.0+1 done.
[ 35/54 ] afw 8.0.0.3 done.
[ 36/54 ] lsst_libs 8.0.0.1+1 done.
[ 37/54 ] obs_test 8.0.0.0+1 done.
[ 38/54 ] pipe_base 8.0.0.0+3 done.
[ 39/54 ] shapelet 8.0.0.0+3 done.
[ 40/54 ] skymap 8.0.0.0+3 done.
[ 41/54 ] skypix 8.0.0.0+3 done.
[ 42/54 ] coadd_utils 8.0.0.0+3 done.
[ 43/54 ] daf_butlerUtils 8.0.0.0+3 done.
[ 44/54 ] meas_algorithms 8.0.0.0+3 done.
[ 45/54 ] coadd_chisquared 8.0.0.0+3 done.
[ 46/54 ] ip_isr 8.0.0.0+3 done.
[ 47/54 ] meas_astrom 8.0.0.0+3 done.
[ 48/54 ] meas_deblender 8.0.0.0+3 done.
[ 49/54 ] meas_extensions_multiShapelet 8.0.0.0+3 done.
[ 50/54 ] ip_diffim 8.0.0.0+3 done.
[ 51/54 ] pipe_tasks 8.0.0.1+3 done.
[ 52/54 ] obs_lsstSim 8.0.0.0+5 done.
[ 53/54 ] obs_sdss 8.0.0.0+5 done.
[ 54/54 ] lsst_apps 8.0.0.1+5 done.
Compiler:
$ clang --version
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.2.0
Thread model: posix
$ gfortran --version
GNU Fortran (GCC) 4.8.1
Copyright (C) 2013 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
Thanks,
Dick
On Thu, 12 Jun 2014 03:06:59 +0000
Tim Jenness <tjenness at cornell.edu<mailto:tjenness at cornell.edu>> wrote:
I've been following the instructions on installing the LSST DM stack and had no trouble installing v8.0.0.0 on OS X Mavericks following
https://confluence.lsstcorp.org/display/LSWUG/Building+the+v8.0+LSST+Stack+from+Source
The problem I have is that the demo is not available for this version. Browsing around gives me the v7.2.0.0 demo and that fails badly:
thrylos:lsst_dm_stack_demo-7.2.0.0 timj$ setup obs_sdss
thrylos:lsst_dm_stack_demo-7.2.0.0 timj$ ./bin/demo.sh
Setting up: astrometry_net_data Flavor: DarwinX86 Version: LOCAL:/Users/timj/work/lsst_dm_stack_demo-7.2.0.0/astrometry_net_data
: Loading config overrride file '/Users/timj/work/lsst/DarwinX86/obs_sdss/8.0.0.0+5/config/processCcd.py'
: Config override file does not exist: '/Users/timj/work/lsst/DarwinX86/obs_sdss/8.0.0.0+5/config/sdss/processCcd.py'
: input=/Users/timj/work/lsst_dm_stack_demo-7.2.0.0/input
: calib=None
: output=/Users/timj/work/lsst_dm_stack_demo-7.2.0.0/output
CameraMapper: Loading registry registry from /Users/timj/work/lsst_dm_stack_demo-7.2.0.0/output/_parent/registry.sqlite3
ERROR: Mismatch in the CFITSIO_SONAME value in the fitsio.h include file
that was used to build the CFITSIO library, and the value in the include file
that was used when compiling the application program:
Version used to build the CFITSIO library = 2
Version included by the application program = 1606384168
Fix this by recompiling and then relinking this application program
with the CFITSIO library.
./bin/demo.sh: line 14: 90827 Segmentation fault: 11 processCcdSdss.py input --id run=4192 filter=u^g^r^i^z camcol=4 field=300 --id run=6377 filter=u^g^r^i^z camcol=4 field=399 --output output
Is the 7.2 demo meant to work with v8.0 or is it hopeless? Is there a plan for a v8.0 demo?
That segv still worries me though. DYLD_LIBRARY_PATH does seem to be filled with LSST stuff so it doesn't seem like it's being confused by other libcfitsio libraries I have.
--
Tim Jenness
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