WIP. add py-pyyaml@5.3.1, py-morph-tool@0.2.10 by asanin-epfl · Pull Request #930 · BlueBrain/spack

asanin-epfl · 2020-10-06T15:45:44Z

No description provided.

asanin-epfl · 2020-10-06T15:56:18Z

For [email protected] I had to download its tar.gz, and get sha256 from it manually. Is that correct? This package is not on pypi.
For plotly I switched to pypi releases otherwise I had to follow the path of py-pyyaml as above.

matz-e · 2020-10-07T10:03:00Z

* For `[email protected]` I had to download its tar.gz, and get sha256 from it manually. Is that correct? This package is not on pypi.

You should be able to do spack checksum py-pyyaml, too.

asanin-epfl · 2020-10-08T08:53:05Z

thank you @matz-e . I've checked with spack checksum and it gave the same sha256. I keep receiving this error at CI:

caxzuyno4x/lib/python3.7/site-packages/IPython/core/events.py", line 16, in <module>
    from backcall import callback_prototype
ModuleNotFoundError: No module named 'backcall'

However this module is present. May be you saw this before because I'm puzzled how to fix it.

asanin-epfl · 2020-10-08T12:02:22Z

retest this please Jenkins

asanin-epfl · 2020-10-08T13:24:07Z

And what is the problem now? I don't see anything in the logs by searching with 'error' of 'fail' keyword. Just a general failure mark in the end of logs without any explanation.

matz-e · 2020-10-09T08:17:28Z

And what is the problem now? I don't see anything in the logs by searching with 'error' of 'fail' keyword. Just a general failure mark in the end of logs without any explanation.

In general, it's way easier to use BleuOcean. So… after clicking on "Details", following up with BleuOcean, I see that the subsequent hpc.module-testing failed. Note the build number, look in BleuOcean for that plan and build number. In your case, I see that the failure is:

ImportError: /gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/deploy/applications/2020-02-01/linux-rhel7-x86_64/intel-19.0.4/py-scipy-1.3.1-3lmmoqxl7d/lib/python3.7/site-packages/scipy/linalg/_fblas.cpython-37m-x86_64-linux-gnu.so: undefined symbol: __intel_sse2_strcat

script returned exit code 1

Which looks like a thing that occurs with %intel… @pramodk or @jorblancoa might have seen and solved this before, I've seen it, too. Need to dig around a little.

asanin-epfl · 2020-10-09T08:58:05Z

Thank you for explanation! Next time I will try to deal with such errors on my own.

asanin-epfl · 2020-10-15T08:26:25Z

@matz-e or @pramodk could please advice on this problem? I have no idea what to do.

matz-e · 2020-10-23T15:43:53Z

var/spack/repos/builtin/packages/py-plotly/package.py

-    version('2.2.0', sha256='dad2a49fe355dddb6ae159e96c10ac22413a33cbac513b4dbf3791e63ec33c1f')
+    version('4.1.0', sha256='9333f28feacaa0751df04cccfb266463bf5029dcb106d3f81d7af5942fd3d998')
+    version('3.0.0', sha256='baab7f8d54f37df89f31d6e6e5d2d4b491bccb79e5d490e25d5762bb762a277c')
+    version('2.2.0', sha256='ca668911ffb4d11fed6d7fbb12236f8ecc6a7209db192326bcb64bdb41451a58')


Seems like there are more dependencies here:

pkg_resources.DistributionNotFound: The 'retrying>=1.3.3' distribution was not found and is required by plotly

Thank you! it helped. I also rebased the PR on the latest develop. Manually checked that everything works via source /gpfs/bbp.cscs.ch/apps/hpc/jenkins/pulls/930/config/modules.sh.

…orph-tool

asanin-epfl · 2020-10-28T12:36:23Z

Yay, thank you!

* Update bbp-packages.yaml Adding my currentscape module to bbp-packages. * Update modules.yaml Adding my currentscape package to the whitelist. * Create package.py Added my currentscape package. * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update package.py Modified the version. Is it better now? * update bglibpy to 4.4.6 (#937) * Update package.py Changing tag to match the one from source on gerrit. * Bglibpy 4.4.10 (#938) * update bglibpy to 4.4.6 * updated to bglpy 4.4.10 v 4.4.10 does not have the pandas, pyrsistent or the bluepy-configfile dependencies * Updates Libsonata package to include readers improvements (#940) * update glm to 0.9.9.3 (#943) * Bump neurodamus for most recent patches (#942) Bump neurodamus-py 2.0.0 to 2.0.2: - Fixing replay to work with multiple populations - Ensure data dir when skipping model build - Fix skipping synapse creation when weight is 0 (BBPBGLIB-673) - Fix deadlock when an exception is thrown from NEURON (BBPBGLIB-678) - Logging colors only for tty Bump neurodamus-core 3.0.0 to 3.0.1: - Avoid getting nilSecRef from objects (HPCTM-1381) * Update py-sonata-network-reduction dependencies: [email protected], [email protected] (#930) * Update bbp-packages.yaml Updated currentscape version. * Update package.py Updated version & tag. * Brion and Brayns are dependent on GLM (#944) * Steps updates (#941) * gmsh: add version 4.6.0 * omega-h: new version 9.32.5.dev3 * steps: new test requirements * libsonata-report: Improves initialization performance (#945) * adapt brion test to a new python module name (#946) * Adding nvidia-hpc-sdk based on upstream PR (#935) * New compiler: nvhpc (NVIDIA HPC SDK) (spack#19294) * Add nvhpc compiler definition: "spack compiler add" will now look for instances of the NVIDIA HPC SDK compiler executables (nvc, nvc++, nvfortran) in supplied paths * Add the nvhpc package which installs the nvhpc compiler * Add testing for nvhpc detection and C++-standard/pic flags Based on spack#19294 * Add CUDA@11 required for latest NVIDIA-HPC-SDK * Fix legacy apis : setup_environment to setup_run_environment * NEURON and CoreNEURON should use legacy units for BBP/HBP deployment (#947) * Update bbp-packages.yaml Adding my currentscape module to bbp-packages. * Update modules.yaml Adding my currentscape package to the whitelist. * Create package.py Added my currentscape package. * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update package.py Modified the version. Is it better now? * Update package.py Changing tag to match the one from source on gerrit. * Update bbp-packages.yaml Updated currentscape version. * Update package.py Updated version & tag. Co-authored-by: Matthias Wolf <[email protected]> Co-authored-by: anilbey <[email protected]> Co-authored-by: Sergio <[email protected]> Co-authored-by: ppodhajski <[email protected]> Co-authored-by: Fernando Pereira <[email protected]> Co-authored-by: asanin-epfl <[email protected]> Co-authored-by: Nadir Román Guerrero <[email protected]> Co-authored-by: Tristan Carel <[email protected]> Co-authored-by: Pramod Kumbhar <[email protected]> Co-authored-by: Jaquier Aurélien Tristan <[email protected]>

matz-e suggested changes Oct 23, 2020

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asanin-epfl added 13 commits October 27, 2020 11:35

add [email protected], [email protected]

0775c76

update py-plotly to pypi url

5d2dc7a

update py-sonata-network-reduction with the latest py-pyyaml and py-m…

492e6ec

…orph-tool

lint

21bf213

ease pandas dependency cosntraint for py-sonata-network-reduction

11a81db

ease pandas dependency constraint for aibs-circuit-converter

7ea7ac0

ease pandas dependency constraint for sonata-network-reduction

8f891ee

missing dependencies to py-morph-tool

fd0dd34

ease py-plotly constraint for py-neurom

c1d7a2d

add py-pyrsistent package

9b8e07d

add py-pyrsistent to bglibpy dependencies

fbf0c5b

add py-retrying to py-plotly dependencies

6d8fc09

move py-pyrsistent to py-bluepy dependecies

d93e724

asanin-epfl requested a review from matz-e October 28, 2020 11:58

matz-e approved these changes Oct 28, 2020

View reviewed changes

asanin-epfl merged commit db42a32 into BlueBrain:develop Oct 28, 2020

asanin-epfl deleted the [email protected] branch December 7, 2020 17:49

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WIP. add [email protected], [email protected]#930

WIP. add [email protected], [email protected]#930
asanin-epfl merged 13 commits intoBlueBrain:developfrom
asanin-epfl:[email protected]

asanin-epfl commented Oct 6, 2020

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