# New install of lsst\_stack, numpy not found

**URL:** <https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124>\
**Category:** Support\
**Created:** [April 26, 2020, 11:16pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124 "2020-04-26T23:16:51Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [April 26, 2020, 11:16pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/1 "2020-04-26T23:16:51Z")

</div>

Fresh install of lsst\_stack.

Running sdss demo and I get this error:

(lsst-scipipe-4d7b902) MacBook-Pro-79:lsst\_dm\_stack\_demo-19.0.0 blum$ ./bin/demo.sh

Traceback (most recent call last):

File “/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pipe\_tasks/19.0.0+2/bin/processCcd.py”, line 23, in \<module\>

from lsst.pipe.tasks.processCcd import ProcessCcdTask

File “/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pipe\_tasks/19.0.0+2/python/lsst/pipe/tasks/processCcd.py”, line 22, in \<module\>

from lsst.ip.isr import IsrTask

File “/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/ip\_isr/19.0.0/python/lsst/ip/isr/ **init**.py”, line 27, in \<module\>

from .isrFunctions import \*

File “/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/ip\_isr/19.0.0/python/lsst/ip/isr/isrFunctions.py”, line 23, in \<module\>

import numpy

ModuleNotFoundError: No module named ‘numpy’

Then

(lsst-scipipe-4d7b902) MacBook-Pro-79:lsst\_dm\_stack\_demo-19.0.0 blum$ conda install numpy

Collecting package metadata (current\_repodata.json): done

Solving environment: done

# All requested packages already installed.

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<div class="post-metadata">

**Author:** ![ktl](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/ktl/32/1373_2.png) [@ktl](https://www.rubin.community/u/ktl)\
**Post date:** [April 27, 2020, 3:38am UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/2 "2020-04-27T03:38:45Z")

</div>

Did you have the LSST conda environment activated when you ran `shebangtron`? What’s the first line of `/Users/blum/lsst_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pipe_tasks/19.0.0+2/bin/processCcd.py` ?

---

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**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [April 27, 2020, 2:44pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/3 "2020-04-27T14:44:00Z")

</div>

> [@ktl](#):
>
> /Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pipe\_tasks/19.0.0+2/bin/processCcd.py

#!/Users/blum/lsst\_stack/python/miniconda3-4.7.10/bin/python

---

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**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [April 27, 2020, 2:44pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/4 "2020-04-27T14:44:46Z")

</div>

#!/Users/blum/lsst\_stack/python/miniconda3-4.7.10/bin/python

I believe I did have LSST miniconda active, yes.

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**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [April 27, 2020, 2:47pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/5 "2020-04-27T14:47:54Z")

</div>

I did this before shebangtron: source loadLSST.bash # for bash

---

<div class="post-metadata">

**Author:** ![ktl](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/ktl/32/1373_2.png) [@ktl](https://www.rubin.community/u/ktl)\
**Post date:** [April 27, 2020, 2:59pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/6 "2020-04-27T14:59:30Z")

</div>

That’s the LSST-installed miniconda, but not the one from the scipipe\_conda\_env environment, which should be something like `/Users/blum/lsst_stack/python/miniconda3-4.7.10/envs/lsst-scipipe-4d7b902/bin/python`

But if you followed these directions:

```bash
source loadLSST.bash
eups distrib install -t v19_0_0 lsst_distrib
curl -sSL https://raw.githubusercontent.com/lsst/shebangtron/master/shebangtron | python

```

I’m not sure how things could have gone wrong.

What is the output of this?

```bash
source loadLSST.bash
command -v python

```

---

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**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [April 27, 2020, 3:07pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/7 "2020-04-27T15:07:57Z")

</div>

> [@ktl](#):
>
> source loadLSST.bash command -v python

/Users/blum/lsst\_stack/python/miniconda3-4.7.10/bin/python

---

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**Author:** ![ktl](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/ktl/32/1373_2.png) [@ktl](https://www.rubin.community/u/ktl)\
**Post date:** [April 27, 2020, 3:11pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/8 "2020-04-27T15:11:41Z")

</div>

That’s interesting. How about the output of `echo $PATH; echo $LSST_CONDA_ENV_NAME`?

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<div class="post-metadata">

**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [April 27, 2020, 3:12pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/9 "2020-04-27T15:12:38Z")

</div>

(base) MacBook-Pro-79:lsst\_stack blum$ echo $PATH

/Users/blum/lsst\_stack/python/miniconda3-4.7.10/bin:/Users/blum/lsst\_stack/python/miniconda3-4.7.10/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/obs\_sdss/19.0.0+2/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/dax\_ppdb/19.0.0/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/verify/19.0.0+2/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/ip\_isr/19.0.0/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pipe\_tasks/19.0.0+2/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/meas\_astrom/19.0.0/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/meas\_base/19.0.0/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pykg\_config/1.3.0+6/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/daf\_butler/19.0.0/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/astro\_metadata\_translator/0.1.0-5-g1039c3c+8/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/starlink\_ast/lsst-dev-gd6cc4e835a/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/gsl/2.6/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/cfitsio/3360.lsst6/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/fftw/3.3.4.lsst2/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pex\_config/19.0.0/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/afw/19.0.0/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pex\_policy/19.0.0/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/apr\_util/1.5.4.lsst1/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/apr/1.5.2/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pyyaml/5.1+2/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/python\_psutil/5.4.3+4/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/boost/1.69.lsst1/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/doxygen/1.8.13.lsst3/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pep8\_naming/0.8.2+3/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pyflakes/2.1.0+2/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/flake8/3.7.5+3/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/scons/3.0.0.lsst1+5/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/sconsUtils/19.0.0/bin:/Users/blum/lsst\_stack/eups/2.1.5/bin:/Users/blum/lsst\_stack/python/miniconda3-4.7.10/bin:/Users/blum/lsst\_stack/python/miniconda3-4.7.10/bin:/opt/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/git/bin:/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/meas\_algorithms/19.0.0/bin

---

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**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [April 27, 2020, 3:13pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/10 "2020-04-27T15:13:20Z")

</div>

> [@ktl](#):
>
> echo $LSST\_CONDA\_ENV\_NAME

and  
lsst-scipipe-4d7b902

---

<div class="post-metadata">

**Author:** ![ktl](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/ktl/32/1373_2.png) [@ktl](https://www.rubin.community/u/ktl)\
**Post date:** [April 27, 2020, 3:19pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/11 "2020-04-27T15:19:45Z")

</div>

> [@rblum5](#):
>
> (base)

Ah, something has gotten confused here, and the pair of minicondas at the beginning of the path is another indication of this. You’ll need to start in a fresh shell. The first entries in your `PATH` after `source loadLSST.bash` should be `/Users/blum/lsst_stack/eups/2.1.5/bin:/Users/blum/lsst_stack/python/miniconda3-4.7.10/envs/lsst-scipipe-4d7b902/bin:/Users/blum/lsst_stack/python/miniconda3-4.7.10/bin`

I guess it might be good to look at the contents of your `loadLSST.bash` as well.

I’m also wondering if `/opt/anaconda3/condabin` could be part of the problem, although it shouldn’t be.

---

<div class="post-metadata">

**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [April 27, 2020, 3:26pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/12 "2020-04-27T15:26:44Z")

</div>

> [@ktl](#):
>
> source loadLSST.bash

In a fresh shell, after source loadLSST.bash the second and third paths are reversed from what you write above.

---

<div class="post-metadata">

**Author:** ![ktl](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/ktl/32/1373_2.png) [@ktl](https://www.rubin.community/u/ktl)\
**Post date:** [April 27, 2020, 3:36pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/13 "2020-04-27T15:36:48Z")

</div>

Ah! I think I may have found the problem (which would be in `newinstall.sh`). I’ll try to reproduce and then file a bug.

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<div class="post-metadata">

**Author:** ![ktl](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/ktl/32/1373_2.png) [@ktl](https://www.rubin.community/u/ktl)\
**Post date:** [April 27, 2020, 3:44pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/14 "2020-04-27T15:44:15Z")

</div>

Nope, that wasn’t it, things look fine in my brand new (but not macOS) installation. I will need the output of `cat loadLSST.bash`

---

<div class="post-metadata">

**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [April 27, 2020, 4:32pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/15 "2020-04-27T16:32:47Z")

</div>

cat loadLSST.bash

# This script is intended to be used with bash to load the minimal LSST

# environment

# Usage: source loadLSST.bash

export PATH="/Users/blum/lsst\_stack/python/miniconda3-4.7.10/bin:${PATH}"

export LSST\_CONDA\_ENV\_NAME=${LSST\_CONDA\_ENV\_NAME:-lsst-scipipe-4d7b902}

# shellcheck disable=SC1091

source activate “$LSST\_CONDA\_ENV\_NAME”

LSST\_HOME="$( cd “$( dirname “${BASH\_SOURCE[0]}” )” && pwd )"

# Bootstrap EUPS

EUPS\_DIR="${LSST\_HOME}/eups/2.1.5"

source “${EUPS\_DIR}/bin/setups.sh”

export -f setup

export -f unsetup

export EUPS\_PKGROOT=${EUPS\_PKGROOT:-[https://eups.lsst.codes/stack/osx/10.9/clang-1000.10.44.4/miniconda3-4.7.10-4d7b902|https://eups.lsst.codes/stack/src](https://eups.lsst.codes/stack/osx/10.9/clang-1000.10.44.4/miniconda3-4.7.10-4d7b902%7Chttps://eups.lsst.codes/stack/src)}

---

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**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [May 3, 2020, 9:56pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/16 "2020-05-03T21:56:40Z")

</div>

I did a sudo \rm -r lsst\_stack and reinstalled. The reversal of the two paths noted above was corrected, but the result of running the demo script was still the same. Seems numpy must be in the wrong place.

---

<div class="post-metadata">

**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [May 16, 2020, 9:02pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/17 "2020-05-16T21:02:18Z")

</div>

(lsst-scipipe-4d7b902) MacBook-Pro-79:lsst\_dm\_stack\_demo-19.0.0 blum$ conda list |grep numpy  
numpy 1.16.2 py37hacdab7b\_0  
numpy-base 1.16.2 py37h6575580\_0

---

<div class="post-metadata">

**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [May 16, 2020, 9:02pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/18 "2020-05-16T21:02:50Z")

</div>

(lsst-scipipe-4d7b902) MacBook-Pro-79:lsst\_dm\_stack\_demo-19.0.0 blum$ ./bin/demo.sh  
Traceback (most recent call last):  
File “/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pipe\_tasks/19.0.0+2/bin/processCcd.py”, line 23, in   
from lsst.pipe.tasks.processCcd import ProcessCcdTask  
File “/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/pipe\_tasks/19.0.0+2/python/lsst/pipe/tasks/processCcd.py”, line 22, in   
from lsst.ip.isr import IsrTask  
File “/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/ip\_isr/19.0.0/python/lsst/ip/isr/ **init**.py”, line 27, in   
from .isrFunctions import \*  
File “/Users/blum/lsst\_stack/stack/miniconda3-4.7.10-4d7b902/DarwinX86/ip\_isr/19.0.0/python/lsst/ip/isr/isrFunctions.py”, line 23, in   
import numpy  
ModuleNotFoundError: No module named ‘numpy’

---

<div class="post-metadata">

**Author:** ![MelissaGraham](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/melissagraham/32/2549_2.png) [@MelissaGraham](https://www.rubin.community/u/MelissaGraham)\
**Post date:** [June 11, 2020, 8:56pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/19 "2020-06-11T20:56:40Z")

</div>

Hi @rblum5, just checking in to see if you found a way to resolve the issue of numpy not being found, or if you’re still in need of assistance on this topic?

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<div class="post-metadata">

**Author:** ![rblum5](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/rblum5/32/949_2.png) [@rblum5](https://www.rubin.community/u/rblum5)\
**Post date:** [June 11, 2020, 11:56pm UTC](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124/20 "2020-06-11T23:56:42Z")

</div>

Thanks for asking @MelissaGraham!

I have not had time to get back to this and its still an open issue. Important but not urgent.

[Next page](https://www.rubin.community/t/new-install-of-lsst-stack-numpy-not-found/4124.md?page=2)