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cleaned up GPU consensus calling #661

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cleaned up GPU consensus calling #661

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Commits on Jun 7, 2018

  1. acuda stubs

    @vellamike
    vellamike committed Jun 7, 2018
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  2. Sending event means to device

    @vellamike
    vellamike committed Jun 7, 2018
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Commits on Jun 11, 2018

  1. estimating emission probabilities

    @vellamike
    vellamike committed Jun 11, 2018
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  2. estimating emission probabilities

    @vellamike
    vellamike committed Jun 11, 2018
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  3. kermel Executing to completion but incomplete -WIP

    @vellamike
    vellamike committed Jun 11, 2018
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Commits on Jun 12, 2018

  1. Sending correct sequences to GPU

    @vellamike
    vellamike committed Jun 12, 2018
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  2. Correct grid size

    @vellamike
    vellamike committed Jun 12, 2018
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Commits on Jun 15, 2018

  1. Match state almost working

    @vellamike
    vellamike committed Jun 15, 2018
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  2. All states now being updated, but no terminal kmer or scaling

    @vellamike
    vellamike committed Jun 15, 2018
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Commits on Jun 25, 2018

  1. diagnosing issue

    @vellamike
    vellamike committed Jun 25, 2018
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Commits on Jun 27, 2018

  1. Dynamic Programming Table the same for GPU and CPU except end

    @vellamike
    vellamike committed Jun 27, 2018
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Commits on Jul 2, 2018

  1. first two base scores correct, bug for other ones

    @vellamike
    vellamike committed Jul 2, 2018
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Commits on Jul 3, 2018

  1. GPU and CPU versions now giving same results

    @vellamike
    vellamike committed Jul 3, 2018
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  2. Removed print statements

    @vellamike
    vellamike committed Jul 3, 2018
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Commits on Jul 4, 2018

  1. Fixed bug with overly-large host allocations

    @vellamike
    vellamike committed Jul 4, 2018
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  2. removed some print statements

    @vellamike
    vellamike committed Jul 4, 2018
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  3. removed some print statements

    @vellamike
    vellamike committed Jul 4, 2018
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  4. Sharing a lot more memory

    @vellamike
    vellamike committed Jul 4, 2018
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Commits on Jul 5, 2018

  1. Kernel now fast but some numerical errors remain

    @vellamike
    vellamike committed Jul 5, 2018
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Commits on Jul 6, 2018

  1. Fixed bug which was causing incorrect forward strand results

    @vellamike
    vellamike committed Jul 6, 2018
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  2. tidyup

    @vellamike
    vellamike committed Jul 6, 2018
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  3. some performance improvments

    @vellamike
    vellamike committed Jul 6, 2018
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Commits on Jul 9, 2018

  1. Fix error and tidy up

    @vellamike
    vellamike committed Jul 9, 2018
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Commits on Jul 10, 2018

  1. Merge branch 'master' into benchmark

    @vellamike
    vellamike committed Jul 10, 2018
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  2. tidy up

    @vellamike
    vellamike committed Jul 10, 2018
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  3. small performance improvments

    @vellamike
    vellamike committed Jul 10, 2018
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  4. tidyup

    @vellamike
    vellamike committed Jul 10, 2018
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  5. Update README.md

    @vellamike
    vellamike authored Jul 10, 2018
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  6. Update README.md

    @vellamike
    vellamike authored Jul 10, 2018
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  7. Update README.md

    @vellamike
    vellamike authored Jul 10, 2018
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  8. tidup

    @vellamike
    vellamike committed Jul 10, 2018
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  9. Merge branch 'benchmark' of https://github.com/nanoporetech/nanopolish … 

    …into benchmark
    @vellamike
    vellamike committed Jul 10, 2018
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  10. typo fix

    @vellamike
    vellamike committed Jul 10, 2018
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Commits on Jul 11, 2018

  1. Storing kmer ranks in one buffer

    @vellamike
    vellamike committed Jul 11, 2018
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  2. fixed a makefile error

    @vellamike
    vellamike committed Jul 11, 2018
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Commits on Jul 12, 2018

  1. Some simple CUDA API error reporting

    @vellamike
    vellamike committed Jul 12, 2018
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  2. One buffer for pore model

    @vellamike
    vellamike committed Jul 12, 2018
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  3. One buffer for pore model

    @vellamike
    vellamike committed Jul 12, 2018
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  4. Keeping pore model in registers

    @vellamike
    vellamike committed Jul 12, 2018
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  5. Removed print statement

    @vellamike
    vellamike committed Jul 12, 2018
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Commits on Jul 13, 2018

  1. Async kernel invocations for improved occupancy

    @vellamike
    vellamike committed Jul 13, 2018
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Commits on Jul 16, 2018

  1. Adding restrict flag to nvcc

    @vellamike
    vellamike committed Jul 16, 2018
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  2. transferring means data and pre/post-flanks

    @vellamike
    vellamike committed Jul 16, 2018
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Commits on Jul 19, 2018

  1. WIP - modifications to kernel for performance improvments

    @vellamike
    vellamike committed Jul 19, 2018
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Commits on Jul 20, 2018

  1. Both Kernels giving similar but not identical results

    @vellamike
    vellamike committed Jul 20, 2018
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  2. Split work into smaller threadBlocks

    @vellamike
    vellamike committed Jul 20, 2018
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Commits on Jul 21, 2018

  1. New Kernel working in multi-base mode. Code needs big refactor and te… 

    …sting
    @vellamike
    vellamike committed Jul 21, 2018
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Commits on Jul 23, 2018

  1. Increased buffer sizes

    @vellamike
    vellamike committed Jul 23, 2018
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  2. Fixed issue with bases at end not being corrected

    @vellamike
    vellamike committed Jul 23, 2018
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  3. 16 workers - better on V100 for now

    @vellamike
    vellamike committed Jul 23, 2018
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Commits on Jul 24, 2018

  1. Refactor of nanopolish_call_variants.cpp

    @vellamike
    vellamike committed Jul 24, 2018
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  2. Fewer and bigger streams

    @vellamike
    vellamike committed Jul 24, 2018
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Commits on Jul 25, 2018

  1. fixing a memory leak

    @vellamike
    vellamike committed Jul 25, 2018
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  2. 40x coverage

    @vellamike
    vellamike committed Jul 25, 2018
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Commits on Jul 26, 2018

  1. added max coverage

    @vellamike
    vellamike committed Jul 26, 2018
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  2. Finding good max coverage to use

    @vellamike
    vellamike committed Jul 26, 2018
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  3. Performance tuning for V100

    @vellamike
    vellamike committed Jul 26, 2018
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Commits on Jul 27, 2018

  1. set sleep to 100us

    @vellamike
    vellamike committed Jul 27, 2018
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Commits on Aug 2, 2018

  1. Merged upstream master

    @vellamike
    vellamike committed Aug 2, 2018
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Commits on Aug 15, 2018

  1. Adding files for VCF handling which for some reason are absent

    @vellamike
    vellamike committed Aug 15, 2018
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Commits on Sep 20, 2018

  1. resolved merge conflict

    @vellamike
    vellamike committed Sep 20, 2018
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  2. tidying makefile

    @vellamike
    vellamike committed Sep 20, 2018
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  3. tidying

    @vellamike
    vellamike committed Sep 20, 2018
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  4. GPU acceleration of nanopolish consensus

    @vellamike
    vellamike committed Sep 20, 2018
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  5. removed spurious comment

    @vellamike
    vellamike committed Sep 20, 2018
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  6. setting indentation to 4 to match rest of nanopolish

    @vellamike
    vellamike committed Sep 20, 2018
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  7. removed some outdated comments

    @vellamike
    vellamike committed Sep 20, 2018
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  8. removed old debug code

    @vellamike
    vellamike committed Sep 20, 2018
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  9. removed deprecated code

    @vellamike
    vellamike committed Sep 20, 2018
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  10. removed old debug code

    @vellamike
    vellamike committed Sep 20, 2018
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  11. revert typo

    @vellamike
    vellamike committed Sep 20, 2018
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  12. Made indentation consistent

    @vellamike
    vellamike committed Sep 20, 2018
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  13. fixed indentation

    @vellamike
    vellamike committed Sep 20, 2018
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  14. Merge branch 'master' into candidate-scoring-gpu

    @vellamike
    vellamike authored Sep 20, 2018
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Commits on Sep 25, 2019

  1. changes to the makefile to get it compiled

    @hasindu2008
    hasindu2008 committed Sep 25, 2019
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Commits on Sep 27, 2019

  1. cleaned up the make file and added cuda support as an option with min… 

    …imal changes to the original source
    @hasindu2008
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  2. Merge remote-tracking branch 'upstream/master' into gpu-varcall

    @hasindu2008
    hasindu2008 committed Sep 27, 2019
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  3. cleaned up to be consistent with the original code

    @hasindu2008
    hasindu2008 committed Sep 27, 2019
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Commits on Sep 28, 2019

  1. restructured to minimise changes to the original source code

    @hasindu2008
    hasindu2008 committed Sep 28, 2019
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  2. make the --gpu more clear

    @hasindu2008
    hasindu2008 committed Sep 28, 2019
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  3. Merge remote-tracking branch 'upstream/master' into gpu-varcall-update

    @hasindu2008
    hasindu2008 committed Sep 28, 2019
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  4. set to cuda static runtime library

    @hasindu2008
    hasindu2008 committed Sep 28, 2019
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  5. removed .gitignore in test/

    @hasindu2008
    hasindu2008 committed Sep 28, 2019
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Commits on Oct 3, 2019

  1. add cida object file to make file clean option

    @hasindu2008
    hasindu2008 committed Oct 3, 2019
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Commits on Mar 12, 2020

  1. Merge remote-tracking branch 'upstream/master' into gpu-varcall-update

    @hasindu2008
    hasindu2008 committed Mar 12, 2020
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Commits on Mar 13, 2020

  1. implementation of the methylation aware polishing option for the GPU

    @hasindu2008
    hasindu2008 committed Mar 13, 2020
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Commits on Mar 22, 2020

  1. Merge remote-tracking branch 'upstream/master' into gpu-varcall-update

    @hasindu2008
    hasindu2008 committed Mar 22, 2020
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Commits on May 1, 2020

  1. Fixed edge case causing segfault when no reads are present in a scoreSet

    @vellamike
    vellamike committed May 1, 2020
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