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2nd sprint
Carsten Fortmann-Grote edited this page Oct 2, 2020
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- A lot got done
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- understand role of libpyvinyl now
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- much work was done in parallel
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- releases took much longer than anticipated
- -> should communicate expectations far ahead of the sprint
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- many things got done
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- many bugs fixed in simex although at slower pace
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- thanks to dan for docker images
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- nothing particular -> work better together, involve ELI people better
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- finished almost all tasks
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- very dedicated, good team spirit
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- better team collaboration than last sprint
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- did not involve ELI people
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- did not advance the simex tutorial
- -> define tasks better fitted to personal profiles
not much to contribute since out of office most of the time
- now working on MPI compatibility of openpmd (which was on the board)
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- good experience to be on the sprint
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- guidance went well
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- inspiring, good team spirit
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- mcstas docker image improvements expensive, so leave it for now.
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- have not yet had any feedback on simex image (latest)
- new releases for wiser and
- demo of oasys workflow in oasys served in VUO
- new features in oasys:
- find best focus
- true focus scan (scan z)
- collaborators can get accounts
- openpmd validator and widget almost done
- simex release for D5.2
- branch cleanup
- tests: fixed 9 failures, 33 errors to 4 errors and 5 skips (can tag as allowed failure)
- demo for MS5.2
- crystallography notebook
- paths should be in place if conda env is selected in kernels
- rotation: uniform vs. random
- harmonized simulation interface
- open simulation results in hdf viewer from wp4 ?
- numerous analysis options directly in simex, but due to hdf format (cxi format) also wp6 analysis tools usable
- use cases: users come from EuXFEL, estimate number of patterns to get good reconstruction. can get user testimonials
- documentation updated, not online yet.
- will go for versioned documentations
- travis not working for now -> register as scientific organization with github, fw details to andy
- crystallography notebook
- docker images
- simex: not all cmakelists have find cmake
- demo of mcstas script for mcstas and mcxtrace on ess jhub
- libpyvinyl now available on pypi, tested on travis-CI and documentation on rtd.
- almost done with basic API documentation for libpyvinyl
- straightened out missing reqs in mcstas docker image
- will test the new image today
- discovered pygments needs to be in 2.6.1
- simex release: v0.5.0-alpha is tagged
- documentation needs to be on gh-pages, for now have to build manually and push to gh-pages branch
- demo notebook from 18M review updated
- new demo for spi
- still problems with MKL
- will get some working version today
- will not finish validator widget
- IO widgets are finished
- integrated into vuo version of oasys
- will fill in details into MS5.2 report
- improve oasys documentation
- reviewed raytracing extension
- more discussion needed, shervin, mads, andrea, aljosa will schedule a meeting
- libpyvinyl now available on pypi
- will add documentation for libpyvinyl
- will review MS5.2 report draft
- simex prerelease 0.5
- dan helped build a new docker image
- make one base layer image and on top of that customized images for specific (hpc) systems
- will try to add documentatian to libpyvinyl
- will prepare demo notebook
- should include jupyter for testing images
- will assist Juncheng to get docker and demo notebooks up and running
- cntd documentation
- tried to pull docker image
- updated instructions for local installations
- works well with conda but not without (mpi4py)
- changes in readme should go into simex release
- meeting with aljosa
- fixes to pyvinyl
- will rename pyvinyl to libpyvinyl
- will review x-raytracing openpmd extension
- make pypi package
- fixed sdf issue in TNSACalculator
- merged all fixes to develop
- will fix sdf cmake file in forked sdf repo
- updated mcstasscript to support mcxtrace
- needs more documentation
- ILL-ESS user meeting: andy will give talk today, link will be
- will update milestone report
- consider pyvinyl as possible interface to mcstas
- will finish two widgets today
- will start on validator widget that displays beam properties
- Heard that RIs ran out of funds.
- ESRF works on hdf5 viewer, same as h5nuvola.
- PR to ocelot to fix observed test failure in simex tests
- successfully tested xmdyn and xcsit calculators
- observed some problems in reading geom files in
- merge simex forks into simex dev
- will try to fix TNSA Calculator (sdf)
- renaming mcstas script
- testing mcxtrace
- setup pyvynil for pypi and add as dependency
- name suggestion for pypi package?
- should take shervin into account
- started on openpmd widget but needs to talk to manuel: py3.8 has problems with shadow3
- modified existing widgets but not tested
- informal "virtual coffee meeting" at 3pm in the same zoom
- patch genesis/ocelot
- work on pyvinyl this week and if time permits on the source |+ prop notebook
- cleanup and demo notebooks
- continue work on MS5.2: added sections on pyvinyl
- will try to make a pyvinyl dependend version of mcstasscript
- needs some discussion with luca rebuffi
- some tweaks needed to automatically update docker images from pypi
- will start on oasys as a service
- openpmd io update
- integration of services currently only possible in VUO
- meet carsten at 8pm in our zoom room
- fixing tests for non-public backengines
- works on several remaining simex issues to be fixed
- draft for ms5.2 report
- juncheng will move the draft to overleaf
- pushed simex docker image: https://hub.docker.com/r/cloudbusting/simex-cloudbusting
- mcstas/mcstasscript: https://hub.docker.com/repository/docker/cloudbusting/mcstasscript-cloudbusting
- oasys: to be done today
- jupyter hub: can't get the persistent storage on desy openstack
- finished the two features
- docker images for oasys are available
- new image with new features available next week
- prepare demos, if possible on the jupyter hub instance with new docker images.
- fixed tests, will continue with missing backengines
- fixed mpi issues
- distributed remaining issues between carsten and juncheng (in issue #43)
- reduced mcstas docker image size by ~1GB
- has a openshift instance at desy now on egi test cloud
- made demo for jupyter hub, video. data not published yet
- wants to read up on jupyter hub deployment
- will draft M5.2 report
- installed simex
- some changes to build system in PR:
- downgrade cmake to 3.11
- gapd not installed by default
- will look into making a docker image, dan can help
- crystfel updated
- will implement one more feature in gauss photon source
- cleaned up all branches
- will fix tests (locally bec. travis above size limit)
- clean up in readme and install notes
- will finish two major wiser features today (focus find, focus sweep)
- will have release ready by friday
- pack wiser with oasys and rafec into docker container -> can then deploy all services through docker!!!
- looking into docker recent developments: howto combining docker images
- can make template of combined docker images
- removed branches from simex
- recommends to use develop branch for test installations (e.g. shervin)
- fights with installing simex, will try again with develop branch
- waits for mcstas script to be released
- cleaned up branches
- will not merge gapd branch, still in development
- plans to test example scripts
- will assist Shervin
- prepares mcstas script release
- serialization (string representation) needed more work
- Carsten recommends using a standardized data format (eg json) for storing the serialized version.
- release is on pip
- will demo on ess jupyter hub
- We start with the tasks on D5.2
- Shervin can start working on the metarepo
- Dan will help getting it to work on a cloud instance.