Using the shared_stack.py utility for weeklies installation

Support
#1

Hello,

I try to exploit the utility shared_stack.py to maintain regular weekly based evolution of the stack in the Unix machines at CCIN2P3

I did manage to make it work some weeks ago but now it fails:

[lsstprod@ccwige0003 shared-stack]$ ./shared_stack.py 
$* is no longer supported at /usr/bin/latex2html line 10588.
texexpand V2008 (Revision 1.12)

 *** initialising colors ***

Warning: No implementation found for package: hyperref
Warning: No implementation found for package: fullpageThis is dvips(k) 5.96.1 Copyright 2007 Radical Eye Software (www.radicaleye.com)
' TeX output 2016.07.11:1025' -> /tmp/l2h100210/image
(-> /tmp/l2h100210/image001) </usr/share/texmf/dvips/base/tex.pro>
</usr/share/texmf/dvips/config/alt-rule.pro>
</usr/share/texmf/dvips/base/texps.pro>
</usr/share/texmf/dvips/base/special.pro>
</usr/share/texmf/dvips/base/color.pro>
</usr/share/texmf/fonts/type1/bluesky/latex-fonts/line10.pfb>
</usr/share/texmf/fonts/type1/bluesky/cm/cmr10.pfb>[1] 
(-> /tmp/l2h100210/image002) </usr/share/texmf/dvips/base/tex.pro>
</usr/share/texmf/dvips/config/alt-rule.pro>
</usr/share/texmf/dvips/base/texps.pro>
</usr/share/texmf/dvips/base/special.pro>
</usr/share/texmf/dvips/base/color.pro>
</usr/share/texmf/fonts/type1/bluesky/latex-fonts/line10.pfb>
</usr/share/texmf/fonts/type1/bluesky/cm/cmr10.pfb>[2] 
(-> /tmp/l2h100210/image003) </usr/share/texmf/dvips/base/tex.pro>
</usr/share/texmf/dvips/config/alt-rule.pro>
</usr/share/texmf/dvips/base/texps.pro>
</usr/share/texmf/dvips/base/special.pro>
</usr/share/texmf/dvips/base/color.pro>
</usr/share/texmf/fonts/type1/bluesky/latex-fonts/line10.pfb>
</usr/share/texmf/fonts/type1/bluesky/cm/cmr10.pfb>[3] 
(-> /tmp/l2h100210/image004) </usr/share/texmf/dvips/base/tex.pro>
</usr/share/texmf/dvips/config/alt-rule.pro>
</usr/share/texmf/dvips/base/texps.pro>
</usr/share/texmf/dvips/base/special.pro>
</usr/share/texmf/dvips/base/color.pro>
</usr/share/texmf/fonts/type1/bluesky/cm/cmsy10.pfb>[4] 
Creating user data directory: /tmp/tmpPt3vpY
eups list: No products found
  [  1/1  ]  miniconda2 3.19.0.lsst4 ... done.

Error: no packages found to remove from environment: /sps/lsst/Library/weeklies/Linux64/miniconda2/3.19.0.lsst4
Failed process output:
Fetching package metadata .......
Solving package specifications: ..........

Traceback (most recent call last):
  File "./shared_stack.py", line 590, in <module>
    main()
  File "./shared_stack.py", line 554, in main
    sm = StackManager.create_stack(ROOT, userdata=userdata)
  File "./shared_stack.py", line 498, in create_stack
    sm.conda("remove", package)
  File "./shared_stack.py", line 391, in conda
    universal_newlines=True)
  File "./shared_stack.py", line 542, in _check_output
    raise subprocess.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['conda', 'remove', '--yes', 'mkl-service']' returned non-zero exit status 1

The tool is unchanged from the master branch.
I setup the running context by specifying Anaconda + proper vesion of the CC compiler

Can someone help me ?

Regards
Christian

#2

I see the same error. I’ll try to chase it down.

#3

DM-6926.

#4

I believe this is now fixed (or, at least, worked-around—the problem seems to be a change in Anaconda behaviour which I don’t understand) in the current master version of shared_stack.py Please let me know if that works for you.

#5

Much better!!
Thanks for the fix
I’ll let you know if something else happens

Christian

#6

Hi

Unfortunately there is now another failure (in getting the log package) :

[lsstprod@cca004 shared-stack]$ ./shared_stack.py 
Creating user data directory: /scratch/tmp_fusRR
Considering lsst_distrib
  Installing lsst_distrib tagged w_2016_28

             Using /sps/lsst/Library/weeklies/Linux64/miniconda2/3.19.0.lsst4/bin/python (Python 2.7.11 :: Anaconda custom (64-bit)).

             Using externally provided astropy v1.2.1.

             Using externally provided numpy v1.11.1.

             Using externally provided matplotlib v1.5.1.

             Using externally provided scipy v0.17.1.


***** error: from /sps/lsst/Library/weeklies/EupsBuildDir/Linux64/log-12.0+2/build.log:
----------------------------------------------------------------------
Traceback (most recent call last):
  File "tests/logTest.py", line 66, in tearDown
    shutil.rmtree(self.tempDir)
  File "/sps/lsst/Library/weeklies/Linux64/miniconda2/3.19.0.lsst4/lib/python2.7/shutil.py", line 256, in rmtree
    onerror(os.rmdir, path, sys.exc_info())
  File "/sps/lsst/Library/weeklies/Linux64/miniconda2/3.19.0.lsst4/lib/python2.7/shutil.py", line 254, in rmtree
    os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/scratch/tmptZiOOc'

----------------------------------------------------------------------
Ran 9 tests in 0.143s

FAILED (errors=1)
The following tests failed:
/sps/lsst/Library/weeklies/EupsBuildDir/Linux64/log-12.0+2/log-12.0+2/tests/.tests/logTest.py.failed
1 tests failed
scons: *** [checkTestStatus] Error 1
scons: building terminated because of errors.
+ exit -4
eups distrib: Failed to build log-12.0+2.eupspkg: Command:
        source /sps/lsst/Library/weeklies/eups/bin/setups.sh; export EUPS_PATH=/sps/lsst/Library/weeklies; (/sps/lsst/Library/weeklies/EupsBuildDir/Linux64/log-12.0+2/build.sh) >> /sps/lsst/Library/weeklies/EupsBuildDir/Linux64/log-12.0+2/build.log 2>&1 4>/sps/lsst/Library/weeklies/EupsBuildDir/Linux64/log-12.0+2/build.msg 
exited with code 252
Failed process output:
  [  1/91 ]  apr 1.5.2 ... done.
  [  2/91 ]  cfitsio 3360.lsst4 ... done.
  [  3/91 ]  doxygen 1.8.5.lsst1 ... done.
  [  4/91 ]  eigen 3.2.5.lsst2 ... done.
  [  5/91 ]  fftw 3.3.4.lsst2 ... done.
  [  6/91 ]  gsl 1.16.lsst3 ... done.
  [  7/91 ]  mariadb 10.1.11.lsst2 ... done.
  [  8/91 ]  mariadbclient 10.1.11.lsst3 ... done.
  [  9/91 ]  minuit2 5.34.14 ... done.
  [ 10/91 ]  mpich 3.2 ... done.
  [ 11/91 ]  python 0.0.4 ... done.
  [ 12/91 ]  python_d2to1 0.2.12.lsst1 ... done.
  [ 13/91 ]  swig 3.0.2.lsst1 ... done.
  [ 14/91 ]  xpa 2.1.15.lsst3 ... done.
  [ 15/91 ]  activemqcpp 3.9.0.lsst2+3 ... done.
  [ 16/91 ]  apr_util 1.5.4 ... done.
  [ 17/91 ]  astropy 0.0.1.lsst2 ... done.
  [ 18/91 ]  boost 1.60+1 ... done.
  [ 19/91 ]  mpi 0.0.1+1 ... done.
  [ 20/91 ]  mysqlpython 1.2.3.lsst2+2 ... done.
  [ 21/91 ]  numpy 0.0.2+1 ... done.
  [ 22/91 ]  python_psutil 4.1.0+1 ... done.
  [ 23/91 ]  pyyaml 3.11.lsst1+1 ... done.
  [ 24/91 ]  scons 2.5.0.lsst1 ... done.
  [ 25/91 ]  sqlalchemy 1.0.8.lsst3+1 ... done.
  [ 26/91 ]  stsci_distutils 0.3.7.lsst1 ... done.
  [ 27/91 ]  wcslib 5.13.lsst1 ... done.
  [ 28/91 ]  astrometry_net 0.50.lsst3+1 ... done.
  [ 29/91 ]  esutil 0.5.3+1 ... done.
  [ 30/91 ]  log4cxx 0.10.0.lsst6+1 ... done.
  [ 31/91 ]  matplotlib 0.0.2-1-g49c793a ... done.
  [ 32/91 ]  mpi4py 1.3.1.lsst2+1 ... done.
  [ 33/91 ]  pyfits 3.4.0+4 ... done.
  [ 34/91 ]  scipy 0.0.1.lsst1+1 ... done.
  [ 35/91 ]  scisql 0.3.5+14 ... done.
  [ 36/91 ]  sconsUtils 12.0-1-g08b90fd ... done.
  [ 37/91 ]  tmv 0.73+2 ... done.
  [ 38/91 ]  astrometry_net_data 10.0+78 ... done.
  [ 39/91 ]  base 12.0-4-g0d328d3 ... done.
  [ 40/91 ]  galsim 1.3.2.lsst2+2 ... done.
  [ 41/91 ]  geom 10.0+62 ... done.
  [ 42/91 ]  lmfit 0.9.3+2 ... done.
  [ 43/91 ]  lsst 12.0.rc1-2-g4137827+3 ... done.
  [ 44/91 ]  psfex 12.0+1 ... done.
  [ 45/91 ]  log 12.0+2 ... 
Traceback (most recent call last):
  File "./shared_stack.py", line 594, in <module>
    main()
  File "./shared_stack.py", line 572, in main
    sm.distrib_install(product, tag=tag)
  File "./shared_stack.py", line 416, in distrib_install
    print(self._run_cmd("distrib", *args))
  File "./shared_stack.py", line 368, in _run_cmd
    universal_newlines=True)
  File "./shared_stack.py", line 546, in _check_output
    raise subprocess.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['eups', '--nolocks', 'distrib', 'install', '--no-server-tags', 'lsst_distrib', '-t', 'w_2016_28']' returned non-zero exit status 9

Christian

#7

…

Other failure in meas_extensions_shapeHSM-12.0+11

***** error: from /sps/lsst/Library/weeklies/EupsBuildDir/Linux64/meas_extensions_shapeHSM-12.0+11/build.log:
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
ERROR: ImportError: /usr/local/grid/emi-3/WN/SL6_64/3.10.0-1.2/usr/lib64/libgomp.so.1: version `GOMP_4.0' not found (required by /sps/lsst/Library/weeklies/Linux64/tmv/0.73+2/lib/libtmv.so.0) [lsstimport]
Traceback (most recent call last):
  File "tests/testHsm.py", line 43, in <module>
    import lsst.meas.extensions.shapeHSM
  File "/sps/lsst/Library/weeklies/EupsBuildDir/Linux64/meas_extensions_shapeHSM-12.0+11/meas_extensions_shapeHSM-12.0+11/python/lsst/meas/extensions/shapeHSM/__init__.py", line 25, in <module>
    from .hsmLib import *
  File "/sps/lsst/Library/weeklies/EupsBuildDir/Linux64/meas_extensions_shapeHSM-12.0+11/meas_extensions_shapeHSM-12.0+11/python/lsst/meas/extensions/shapeHSM/hsmLib.py", line 34, in <module>
    _hsmLib = swig_import_helper()
  File "/sps/lsst/Library/weeklies/EupsBuildDir/Linux64/meas_extensions_shapeHSM-12.0+11/meas_extensions_shapeHSM-12.0+11/python/lsst/meas/extensions/shapeHSM/hsmLib.py", line 30, in swig_import_helper
    _mod = imp.load_module('_hsmLib', fp, pathname, description)
  File "/sps/lsst/Library/weeklies/Linux64/base/12.0-4-g0d328d3/python/lsstimport.py", line 102, in imp_load_module
    module = orig_imp_load_module(name, *args)
ImportError: /usr/local/grid/emi-3/WN/SL6_64/3.10.0-1.2/usr/lib64/libgomp.so.1: version `GOMP_4.0' not found (required by /sps/lsst/Library/weeklies/Linux64/tmv/0.73+2/lib/libtmv.so.0)
The following tests failed:
/sps/lsst/Library/weeklies/EupsBuildDir/Linux64/meas_extensions_shapeHSM-12.0+11/meas_extensions_shapeHSM-12.0+11/tests/.tests/testHsm.py.failed
1 tests failed

Christian

#8

shapeHSM problem moved here: Problem in trying to install meas_extensions_shapeHSM-12.0+11

Am I correct in assuming you solved the log problem, since the shapeHSM issue occurs after that in the build?