Issue installing lsst_apps and _distrib, OSX

fraserw · November 21, 2019, 5:55am

I am hoping to run through the pipeline tutorial, but am unable to install the pipeline, following the installation steps.

I have provided a complete terminal session copy to show what happens when I attempt to install using miniconda as recommended, but the essential part is, that is seems eups as installed is broken. I get the following traceback during the source loadLSST.bash.

Traceback (most recent call last):
File “/Users/fraserw/lsst_stack/eups/2.1.5/bin/eups_setup”, line 42, in
import eups.setupcmd
ModuleNotFoundError: No module named ‘eups.setupcmd’
-bash: export: setup: not a function
-bash: export: unsetup: not a function

Any ideas on how to fix this?

Details:
OSX 10.14
Anaconda installed
cmake from homebrew
Note - PYTHONPATH is set to ‘’ before installation is attempted

Terminal output:
lsst_stack : fraserw $ export PYTHON_PATH=’’
lsst_stack : fraserw $ !bash
bash newinstall.sh -ct

LSST Software Stack Builder

############################## 42.2%!!! This script differs from the official version on the distribution server.
If this is not intentional, get the current version from here:
https://raw.githubusercontent.com/lsst/lsst/master/scripts/newinstall.sh
######################################################################## 100.0%
(23) Failed writing body
Detected git version 2.21.0 (Apple Git-122). OK.

LSST stack requires Python >= 3.6; you seem to have Python 2.7.10 on your path
(/usr/bin/python).

In addition to Python >= 3.6, some LSST packages depend on recent versions of
numpy, matplotlib, and scipy. If you do not have all of these, the
installation may fail. Using the Miniconda Python distribution will ensure
all these are set up.

Would you like us to install the Miniconda Python distribution (if unsure, say
yes)?yes
::: Deploying Miniconda3-4.5.12-MacOSX-x86_64.sh
######################################################################## 100.0%
PREFIX=/Users/fraserw/lsst_stack/python/miniconda3-4.5.12
installing: python-3.7.1-haf84260_7 …
Python 3.7.1
installing: ca-certificates-2018.03.07-0 …
installing: conda-env-2.6.0-1 …
installing: libcxxabi-4.0.1-hcfea43d_1 …
installing: xz-5.2.4-h1de35cc_4 …
installing: yaml-0.1.7-hc338f04_2 …
installing: zlib-1.2.11-h1de35cc_3 …
installing: libcxx-4.0.1-hcfea43d_1 …
installing: openssl-1.1.1a-h1de35cc_0 …
installing: tk-8.6.8-ha441bb4_0 …
installing: libffi-3.2.1-h475c297_4 …
installing: ncurses-6.1-h0a44026_1 …
installing: libedit-3.1.20170329-hb402a30_2 …
installing: readline-7.0-h1de35cc_5 …
installing: sqlite-3.26.0-ha441bb4_0 …
installing: asn1crypto-0.24.0-py37_0 …
installing: certifi-2018.11.29-py37_0 …
installing: chardet-3.0.4-py37_1 …
installing: idna-2.8-py37_0 …
installing: pycosat-0.6.3-py37h1de35cc_0 …
installing: pycparser-2.19-py37_0 …
installing: pysocks-1.6.8-py37_0 …
installing: python.app-2-py37_9 …
installing: ruamel_yaml-0.15.46-py37h1de35cc_0 …
installing: six-1.12.0-py37_0 …
installing: cffi-1.11.5-py37h6174b99_1 …
installing: setuptools-40.6.3-py37_0 …
installing: cryptography-2.4.2-py37ha12b0ac_0 …
installing: wheel-0.32.3-py37_0 …
installing: pip-18.1-py37_0 …
installing: pyopenssl-18.0.0-py37_0 …
installing: urllib3-1.24.1-py37_0 …
installing: requests-2.21.0-py37_0 …
installing: conda-4.5.12-py37_0 …
installation finished.
WARNING:
You currently have a PYTHONPATH environment variable set. This may cause
unexpected behavior when running the Python interpreter in Miniconda3.
For best results, please verify that your PYTHONPATH only points to
directories of packages that are compatible with the Python interpreter
in Miniconda3: /Users/fraserw/lsst_stack/python/miniconda3-4.5.12
######################################################################## 100.0%
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.5.12
latest version: 4.8.0rc0

Please update conda by running

$ conda update -n base -c defaults conda

To activate this environment, use

$ conda activate lsst-scipipe-1172c30

To deactivate an active environment, use

$ conda deactivate

name: lsst-scipipe-1172c30
channels:

http://ssb.stsci.edu/astroconda
http://conda.lsst.codes/sims
http://conda.lsst.codes/stack/0.13.0
https://conda.anaconda.org/NLeSC
defaults
http://repo.continuum.io/pkgs/free
dependencies:
asn1crypto=0.24.0=py37_0
astropy=3.1.2=py37h1de35cc_0
atomicwrites=1.3.0=py_0
attrs=19.1.0=py_0
blas=1.0=mkl
blosc=1.15.0=hd9629dc_0
bottleneck=1.2.1=py37h1d22016_1
bzip2=1.0.6=h1de35cc_5
ca-certificates=2019.1.23=0
certifi=2019.3.9=py37_0
cffi=1.12.2=py37hb5b8e2f_1
chardet=3.0.4=py37_1
cryptography=2.6.1=py37ha12b0ac_0
cycler=0.10.0=py37_0
cython=0.29.6=py37h0a44026_0
freetype=2.9.1=hb4e5f40_0
future=0.17.1=py37_0
h5py=2.9.0=py37h3134771_0
hdf5=1.10.4=hfa1e0ec_0
idna=2.8=py37_0
intel-openmp=2019.1=144
kiwisolver=1.0.1=py37h0a44026_0
libcxx=4.0.1=hcfea43d_1
libcxxabi=4.0.1=hcfea43d_1
libedit=3.1.20181209=hb402a30_0
libffi=3.2.1=h475c297_4
libgfortran=3.0.1=h93005f0_2
libpng=1.6.36=ha441bb4_0
lzo=2.10=h362108e_2
matplotlib=3.0.3=py37h54f8f79_0
mkl=2019.1=144
mkl_fft=1.0.10=py37h5e564d8_0
mkl_random=1.0.2=py37h27c97d8_0
more-itertools=6.0.0=py37_0
ncurses=6.1=h0a44026_1
numexpr=2.6.9=py37h7413580_0
numpy=1.16.2=py37hacdab7b_0
numpy-base=1.16.2=py37h6575580_0
openssl=1.1.1b=h1de35cc_1
pandas=0.24.2=py37h0a44026_0
pip=19.0.3=py37_0
pluggy=0.9.0=py37_0
psutil=5.6.1=py37h1de35cc_0
py=1.8.0=py37_0
pycparser=2.19=py37_0
pyopenssl=19.0.0=py37_0
pyparsing=2.3.1=py37_0
pysocks=1.6.8=py37_0
pytables=3.5.1=py37h5bccee9_0
pytest=4.3.1=py37_0
pytest-arraydiff=0.3=py37h39e3cac_0
pytest-astropy=0.5.0=py37_0
pytest-doctestplus=0.3.0=py37_0
pytest-openfiles=0.3.2=py37_0
pytest-remotedata=0.3.1=py37_0
python=3.7.2=haf84260_0
python-dateutil=2.8.0=py37_0
pytz=2018.9=py37_0
pyyaml=5.1=py37h1de35cc_0
readline=7.0=h1de35cc_5
requests=2.21.0=py37_0
scikit-learn=0.20.3=py37h27c97d8_0
scipy=1.2.1=py37h1410ff5_0
setuptools=40.8.0=py37_0
six=1.12.0=py37_0
snappy=1.1.7=he62c110_3
sqlalchemy=1.3.1=py37h1de35cc_0
sqlite=3.27.2=ha441bb4_0
tk=8.6.8=ha441bb4_0
tornado=6.0.1=py37h1de35cc_0
urllib3=1.24.1=py37_0
wheel=0.33.1=py37_0
wrapt=1.11.1=py37h1de35cc_0
xz=5.2.4=h1de35cc_4
yaml=0.1.7=hc338f04_2
zlib=1.2.11=h1de35cc_3
pip:
- deprecated==1.2.5
- tables==3.5.1
- trippy==1.1.1
  prefix: /Users/fraserw/lsst_stack/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30

Configured EUPS_PKGROOT:
Using python at /Users/fraserw/lsst_stack/python/miniconda3-4.5.12/envs/lsst-scipipe-1172c30/bin/python to install EUPS
Installing EUPS (2.1.5)… done.
Creating startup scripts (bash) … done.
Creating startup scripts (ksh) … done.
Creating startup scripts (csh) … done.
Creating startup scripts (zsh) … done.

Bootstrap complete. To continue installing (and to use) the LSST stack type
one of:

source “/Users/fraserw/lsst_stack/loadLSST.bash” # for bash
source “/Users/fraserw/lsst_stack/loadLSST.csh” # for csh
source “/Users/fraserw/lsst_stack/loadLSST.ksh” # for ksh
source “/Users/fraserw/lsst_stack/loadLSST.zsh” # for zsh

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://pipelines.lsst.io

and feel free to ask any questions via the LSST Community forum:

https://community.lsst.org/c/support

                                   Thanks!
                                            -- The LSST Software Teams
                                                   http://dm.lsst.org/

lsst_stack : fraserw $ eups distrib install lsst_app
-bash: eups: command not found
lsst_stack : fraserw $ source
_build/ eupsbuild.log loadLSST.csh loadLSST.zsh python/
eups/ loadLSST.bash loadLSST.ksh newinstall.sh stack/
lsst_stack : fraserw $ source loadLSST.bash
Traceback (most recent call last):
File “/Users/fraserw/lsst_stack/eups/2.1.5/bin/eups_setup”, line 28, in
import eups.setupcmd
ModuleNotFoundError: No module named ‘eups.setupcmd’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/Users/fraserw/lsst_stack/eups/2.1.5/bin/eups_setup”, line 42, in
import eups.setupcmd
ModuleNotFoundError: No module named ‘eups.setupcmd’
-bash: export: setup: not a function
-bash: export: unsetup: not a function

KSK · November 21, 2019, 4:35pm

It seems like your shell may be confused. Try opening a fresh terminal and do:
source “/Users/fraserw/lsst_stack/loadLSST.bash”, assuming you are using bash.

I guess I would be a little surprised if that works, but we use a lot of environment variables, so having a fresh env may help.

swinbank · November 21, 2019, 6:28pm

See also Problem when loading loadLSST.bash — the problem there seems to be related to $PYTHONPATH.