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Split nrn_setup.cpp in phase1 / phase2#283

Merged

pramodk merged 81 commits into

masterfrom

phase1

Aug 9, 2020

Commits on Aug 9, 2020

Rewrite phase1

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Move in files

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Revert "Move in files"

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Remove global static user variables

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Phase2 compile but still FIXME

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Less fixme

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Put Phase1 outside nrn_setup

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Move phase2

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Add more variable for using omp mutex

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Use read_vector in phase1

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add a state inside Phase2

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Split Phase2::populate

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Use MUT outside Phase1

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Fix use of type inside of i

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Several fixes

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Fix Phase2::read_file

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Fix use of dparam_size and param_size

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Fix use on nt.ncell before setting

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Load iArray / dArray only if there is elements

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Fix last things?

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Take care of tqueue items

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Fix push_back of vecplay

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Don't use nt before populate

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Even if data is copied and not allocated, nodeindices stay allocated on neuron size

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More fixes

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Fix more errors

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Fix stupid error

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Last fix

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Fix very last stupid error

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add fill_ba_lists

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Debug neuron installation with spack

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rename stage install_neuron

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Apply suggestions from code review

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Apply suggestions from code review

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Apply suggestions from code review

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Update coreneuron/io/nrn_setup.cpp

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Rename nrn_soa to mem_layout_util

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Last fix from Omar

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Rename do_not_open to in_memory_transfer

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Apply suggestions from code review

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Rename some variables

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Remove things related to endianess

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Make user_params as much const as possible now

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Use name of phase instead of numbers

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Remove setted and direct in phase2

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Fix for previous patch

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Layout as an enum, and a bit of more documentation.

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from zz to new_maxgid

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From pastim_index to patstim_index

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mech_layout => mech_data_layout_transform

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from camel to snake

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save_events to restore_events

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Batch of changes

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Merge permutation, but be careful, jenkins will tell us if it's possible or not

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More split inside Phase2::populate

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batch 2

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batch 3

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More std::string in FileHandler

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Remove handle_extracon from Phase2::populate

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From ne to n_data_padded

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Make test executable from any place

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First attempt to fix the problem of Mutex in a nice way

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To avoid copies, we use the old way to handle _data.

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Read ml->data directly into _data to avoid copy

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Fix error during computation of offset for _data in phase2

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Fix computing of maxgid

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Need to append the offset after reading

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Disable GPU test because PGI is broken for now

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Don't copy yvec and tvec

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Avoid copy of v_parent_index

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Give ownership of y_, t_ to VecPlayContinuous

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Enable GPU tests
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Fix copy of IVocVect for gpu

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Random tries for acc

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Fix compilation issues for IvocVect with OpenACC (validation test next)
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Fix typo between yvec and tvec

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Fix missing initialization mechanism type in TML
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Check mechanism compatibility before reading data
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abort is now moved to phase2.cpp
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Copy nodeindices if it's not null
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update comments
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