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Variadic argument lists for ODEs #1641
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2d696c8
omit recover_memory_global which is not needed
wds15 8a1d99e
Merge branch 'proto-parallel-v3' of https://github.com/stan-dev/math …
wds15 6d8ad8a
aggregate more efficiently the partial sums
wds15 1a54bde
simplify how values are copied
wds15 f689c93
const correctness
wds15 0da9de0
make code more generic (some meta magic bits are missing)
wds15 73fb5ae
make parallel reduce sum work with posted example... need more meta-p…
wds15 e7a83c6
rename to reduce_sum
wds15 2a370e7
add up to 4 arguments for reduce function
wds15 bd13907
make arguments optional
wds15 e1deb4f
more doc and const declares
wds15 358525c
doc
wds15 13641ea
Merge remote-tracking branch 'origin/develop' into proto-parallel-v3
wds15 5f76ca2
generalize possible input data structures
wds15 d9e5276
refactor such that any data strcuture (contained in an array) can be …
wds15 5e01bf0
fix looping order error
wds15 f2ed8a9
still struggling with performance regression
wds15 a3b4ad4
Merge remote-tracking branch 'origin/develop' into proto-parallel-v3
wds15 f3b37ae
start going back to better abstracted code
wds15 940fc82
move to shared_ptr, simplify counstructor call
wds15 8b66f94
move to partials being stored as flat vector
wds15 e56cdf2
get rid of obsolete code
wds15 2cece58
add preliminary support for structured slicing arguments which are no…
wds15 71c0196
add special case of local_operands_and_partials for non-var in a work…
wds15 e2b20d7
start cleanup bits of the reduce_sum code. Mostly to get an idea of w…
SteveBronder c0c118a
start cleanup bits of the reduce_sum code. Mostly to get an idea of w…
SteveBronder ff0f582
start cleanup bits of the reduce_sum code. Mostly to get an idea of w…
SteveBronder 96e8c8e
start cleanup bits of the reduce_sum code. Mostly to get an idea of w…
SteveBronder 3d62fa8
loose stuff needed removed
SteveBronder cbcf42f
Added variadic implementation of rev parallel_sum
bbbales2 8f90d8c
Adds enable_ifs to reduce_sum_impl
SteveBronder 617d6e2
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot fbfa9ba
Fixup little templating things
SteveBronder 008255e
merge to develop
SteveBronder 00e5743
Make accumulate adjoints accept more types
SteveBronder 623ed9e
Catch arithmetics in count_var_impl
SteveBronder 16db0f2
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot 9305fb0
move operator_paren checker out one scope
SteveBronder bb9a1b2
Merge branch 'cleanup/proto-parallel-v3' of github.com:stan-dev/math …
SteveBronder 430ba3f
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot 0248bcb
add left_fold helper func
SteveBronder b2c1dec
Merge branch 'cleanup/proto-parallel-v3' of github.com:stan-dev/math …
SteveBronder cf8b530
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot a27047f
Get slicing tests to pass
SteveBronder 2dd8881
Merge branch 'cleanup/proto-parallel-v3' of github.com:stan-dev/math …
SteveBronder 5e3e078
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot 92fe766
some fixes, but not yet there
weberse2 2d1d57e
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot 906c262
Merging in changes from pull
bbbales2 747c73a
Allow vars in sliced argument, fixed (at least temporarily) a couple …
bbbales2 3da42ff
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot 70001ac
make things work with proper cleanup
wds15 be1ff0c
Changed how the sliced gradients work again
bbbales2 7a6b558
[Jenkins] auto-formatting by clang-format version 5.0.2-svn328729-1~e…
stan-buildbot d440aab
Merge branch 'cleanup/proto-parallel-v3' of https://github.com/stan-d…
wds15 89bad42
ensure proper cleaning of vars on all child threads
wds15 c1ac292
Adds metaprogramming to accept std vectors and eigen vectors
SteveBronder 4ea5f1c
Remove dead code
SteveBronder 6075dcc
[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/…
stan-buildbot af7791e
idiot slaps keyboard
SteveBronder 103333c
merge to remote
SteveBronder ab1e653
[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/…
stan-buildbot 29f1f71
Merge branch 'develop' into cleanup/proto-parallel-v3
bbbales2 37b516f
[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/…
stan-buildbot b76cd8c
Added tests for reduce_sum
bbbales2 6b93f93
[Jenkins] auto-formatting by clang-format version 5.0.2-svn328729-1~e…
stan-buildbot e804157
Fix cpplint errors
SteveBronder 66acef6
[Jenkins] auto-formatting by clang-format version 5.0.2-svn328729-1~e…
stan-buildbot 906d7b0
Fix headers
SteveBronder 71d8c71
Merge branch 'cleanup/proto-parallel-v3' of github.com:stan-dev/math …
SteveBronder d05d452
Added msgs argument to reduce_sum
bbbales2 658755d
Merge commit '10cc6ba675743f09832c6749fbb1a92d74888bd2' into HEAD
yashikno 4e18f1e
[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/…
stan-buildbot d834a4f
Allow arrays of all the Stan types to reduce_sum
bbbales2 145ae95
[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/…
stan-buildbot 9957909
Allocate deep copied varis on no-chain stack
bbbales2 3ecf79e
[Jenkins] auto-formatting by clang-format version 5.0.2-svn328729-1~e…
stan-buildbot 3c56f6d
Initial commit of variadic ode functions with existing tests working
bbbales2 cf48965
[Jenkins] auto-formatting by clang-format version 5.0.2-svn328729-1~e…
stan-buildbot 94989a0
Fixed off by one error on start/end indices passed by reduce_sum to u…
bbbales2 c9ac276
Merge commit 'dd9774dbc03935433b25a00be21763b43a242191' into HEAD
yashikno 70546f4
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot 4cfcfe8
Revert "Fixed off by one error on start/end indices passed by reduce_…
bbbales2 d46c022
Added extra template conditions for accumulate_adjoints_, count_vars_…
bbbales2 ccc82e7
Merge branch 'cleanup/proto-parallel-v3' of https://github.com/stan-d…
bbbales2 87a86ea
Absorbed cvodes_ode_data.hpp stuff into cvodes_integrator.hpp
bbbales2 6c88e6a
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 144bb9c
Changed how arg_adjoints_ is allocated in reduce_sum and added out of…
bbbales2 4adf05d
Merge commit '8fbce61858ae95745567d8c5f7e054e3d3b20834' into HEAD
yashikno 80ae1bf
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot 7a1a27b
Made deep copy in reduce_sum a little more efficient
bbbales2 9e15292
Merge branch 'cleanup/proto-parallel-v3' of https://github.com/stan-d…
bbbales2 b6b215b
Merge commit 'b29eff6b027fb2a1bcc5af53d868ce8024235272' into HEAD
yashikno 66ba573
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot a5a50e2
Merge remote-tracking branch 'origin/develop' into cleanup/proto-para…
SteveBronder 55171a4
Adds pf (yes I know but seriously this time it's good I think) to the…
SteveBronder bc3b7c6
add inline to functions
SteveBronder 89d0781
Added signature that for exposing variadic arguments to higher level
bbbales2 e8b0294
Made some changes so ode rhs functions with variadic arguments work w…
bbbales2 a017619
Add docs for templates in reduce_sum
SteveBronder 2561972
Merge remote-tracking branch 'origin/develop' into cleanup/parallel-v5
SteveBronder 3e36ba8
[Jenkins] auto-formatting by clang-format version 5.0.2-svn328729-1~e…
stan-buildbot 38aa2af
Merge remote-tracking branch 'origin/develop' into cleanup/proto-para…
SteveBronder b99d299
Merge branch 'cleanup/proto-parallel-v3' into cleanup/parallel-v5
SteveBronder cc37f22
Add includes for test-headers and add threading environment variable …
SteveBronder b64fe87
remove -fopenmp from CXXFLAGS
SteveBronder 7d27f90
remove old prim/scal.hpp include from apply_test
SteveBronder c53d29d
Fix broadcast_array to remove vec_partial_
SteveBronder fb9f25a
[Jenkins] auto-formatting by clang-format version 5.0.0-3~16.04.1 (ta…
stan-buildbot 86bf06a
a few inlines added
rok-cesnovar ee1e0d7
Merge pull request #1768 from stan-dev/cleanup/parallel-v5
bbbales2 7aa19ce
Changed reduce_sum so sliced argument can be an array of any Stan type
bbbales2 cb57e75
Merge commit 'fe3a41c3e854fe604841b237fa0475f26d29fe98' into HEAD
yashikno 09d3f52
[Jenkins] auto-formatting by clang-format version 5.0.2-svn328729-1~e…
stan-buildbot 3522bbe
Merge remote-tracking branch 'origin/cleanup/proto-parallel-v3' into …
bbbales2 80449e0
[Jenkins] auto-formatting by clang-format version 6.0.0 (tags/google/…
stan-buildbot 12f6ad9
Changed order of arguments for all the ODE stuff so the variadic argu…
bbbales2 a2e9c92
Merge remote-tracking branch 'origin/develop' into feature/parameter-…
bbbales2 64a017e
Variadic versions of ode solvers named ode_bdf and ode_rk45
bbbales2 b8168e1
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 2a3d24a
Merge remote-tracking branch 'origin/develop' into feature/parameter-…
bbbales2 085c3bc
[Jenkins] auto-formatting by clang-format version 6.0.0
stan-buildbot 8642b08
Reverting accidental changes to reduce_sum on this branch (Issue #1833)
bbbales2 f1d7b6c
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 a3a3121
Cleaning up merge (Issue #1833)
bbbales2 7a8e3d5
Cleaning up merge (reverting Jenkinsfile to develop) (Issue #1833)
bbbales2 e012d1f
2 missing inlines
rok-cesnovar 03756de
Switched ODE states to be expressed as Eigen Vectors (variadic odes, …
bbbales2 2cc1f3d
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 257afa0
Fixed bug with how ode sensitivities with respect to t0 work (design-…
bbbales2 a3530bb
Merge remote-tracking branch 'origin/develop' into feature/parameter-…
bbbales2 e3e2b9e
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 8bf8b87
Updated ODE function docs
bbbales2 9553f64
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 cb602ad
Updated ode_store_sensitivities references (design-doc #19)
bbbales2 36a15e2
Merge commit 'c02589c1513c57593661ec7b21f17923b55cd9f3' into HEAD
yashikno 9831634
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 44529fd
Adjoint ode_bdf passing ode_bdf tests. integrate_ode_bdf not working …
bbbales2 e9cca92
Merge commit '6025c339b0fad05ac568a678d38cc6e74cddf57b' into HEAD
yashikno 92314d0
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot c719ec5
integrate_ode_bdf tests mostly working now (Issue #1887)
bbbales2 7b3f7b7
Merge remote-tracking branch 'origin/develop' into feature/parameter-…
bbbales2 94fdd3e
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 1b2b066
template parameter fixes, reversed order of functions
rok-cesnovar 962ba83
Revert back to forward mode sensitivity for cvodes (to make separate …
bbbales2 e6d7dcf
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 46d7230
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 7f5e7db
Made some minor changes with coupled_ode_system to make new code matc…
bbbales2 61cfd25
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 d962970
Merge commit 'd5849314500d88fe04719ec27b45adf5ed3d1ee2' into HEAD
yashikno 7007256
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot ad58f9d
Allow integer initial times and output times (design-doc #19)
bbbales2 8c1a10d
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 8bd267f
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 8f28f3e
Add new adams interface (design-doc #19)
bbbales2 4ca2912
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 8dfa0d1
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot b4e89d3
Added tests for new adams ode interface (design-doc #19)
bbbales2 a1f928b
Times to ODE solvers only need to be sorted, not strictly increasing …
bbbales2 f16df92
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 ae99813
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot ea303ff
Added new prim tests for bdf solver. Added new interfaces that include
bbbales2 ae43edf
Merge commit '27afd26a854d7be23e6e20b0eaff4dbbbe700b13' into HEAD
yashikno c982322
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 6ae558c
Hopefully completed adding tests to new ode functions.
bbbales2 4ad49f4
Merge commit '576c358ce7427bffeee1c5055f2750058c652b1c' into HEAD
yashikno 0eb1382
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 961780f
Performance optimizations for coupled_ode_system (design-doc #19)
bbbales2 3b5f18d
Merge remote-tracking branch 'origin/develop' into feature/parameter-…
bbbales2 dfdd989
Merge commit 'de6e454a7db5854c413dbb943a5a4f056d9085ec' into HEAD
yashikno 5668b09
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 11605da
fix linting/docs errors
rok-cesnovar a1db0b4
Merge commit '93898d06805f7e54e801ddfcd5d7457d79ed46b3' into HEAD
yashikno 28affd2
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot c42eec7
fix missing headers
rok-cesnovar 27d4f49
Added eval statement to handle `value_of` expressions (design-doc #19)
bbbales2 69e5f86
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 1038387
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot bae0be9
Added tests for cvodes error prints, grad with no argument, and clean…
bbbales2 573dc1a
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 0eff931
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 9a10def
More optimizations to make the new ode interfaces fast (design-doc #19)
bbbales2 1fc074c
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 9c82020
Merge remote-tracking branch 'origin/develop' into feature/parameter-…
bbbales2 18f5c2d
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 1ef29d9
Updated function name in error messages to better reflect which funct…
bbbales2 e65fb97
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 9a84b50
Merge commit '5c6a4dd7a814a60bd3ea766ab8701ea2234724b3' into HEAD
yashikno 4851d6b
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 9592cba
Added more time points to ode prim tests (design-doc #19)
bbbales2 d4f8fe1
Updated docs, cleaned up template naming, avoided unncessary nested a…
bbbales2 cbdace5
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 9f923e8
Added support for general arguments to variadic ODEs (design-doc #19)
bbbales2 40ba7a8
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 3b3a9f3
Merge remote-tracking branch 'origin/develop' into feature/parameter-…
bbbales2 7e411bc
Updated value_of implementation to work with holder again. Added test…
bbbales2 52c85a4
Added eigen version of harm_osc_ode_fun and reverse mode tests for co…
bbbales2 158ec02
Merge remote-tracking branch 'origin' into feature/parameter-pack-odes
bbbales2 8ab9809
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot b76e7a5
Made zero_adjoints its own standalone function (design-doc #19)
bbbales2 ea0f8b8
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 ce1377a
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 64805e3
Added tests for old ode interface adapter code (design-docs #19)
bbbales2 467b53a
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 393b2c9
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 66bf060
Clean up doxygen and test names (design-doc #19)
bbbales2 0ce1fe5
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 2b53b2d
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot f745294
Updated headers in zero_adjoints.hpp (design-doc #19)
bbbales2 c045a69
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 444ae2a
Updated types in coupled_ode_system tests (design-doc #19)
bbbales2 b8bc8e4
Added missing error print (design-doc #19)
bbbales2 9f62feb
Merge commit 'b95dd5a46e8bdfdf984d11413dc86bc98306a3d8' into HEAD
yashikno 56196a3
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 15eb4ec
Fixed check_finite to work with expressions (design-doc #19)
bbbales2 efd5763
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 5773195
Updated check_finite to work with eigen arrays (design-doc #19)
bbbales2 6d365ce
Cleanup responding to review comments (design-doc #19)
bbbales2 0c18338
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 7538e97
Updated some includes (design-doc #19)
bbbales2 1a732b0
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 c2499be
Responding to comments. Added too much work tests to _tol versions of…
bbbales2 5f216f4
Merge commit 'd48a48744910f99cd94abf0a5789ad6a8031c758' into HEAD
yashikno 29cde14
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 35267b1
Added ode_store_sensitivities tests (design-doc #19)
bbbales2 c6a687d
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 4646593
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 19e029c
Responding to reviews (design-doc #19)
bbbales2 51e8f24
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 7a42c5a
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 3e7abbf
Updated variable naming/docs (design-doc #19)
bbbales2 879510e
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 54de59b
Added some comments around strange code.
bbbales2 509f7b2
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 10acf66
Fixed wrong pointer name (design-doc #19)
bbbales2 ab7c503
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 0ce6e18
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot a5ee85d
Added eval function to call `.eval()` on expressions buried in parame…
bbbales2 49bfc45
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2~16.0…
stan-buildbot 2e83467
Fixed doxygen problem though I'm not sure how (design-doc #19)
bbbales2 9c7f88d
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 3b4c217
Updated eval implementation and tests (design-docs #19)
bbbales2 a589de9
Removed unnecessary headers (design-doc #19)
bbbales2 a37be47
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 43fb63b
Switched integrate_ode_bdf, integrate_ode_adams, and integrate_ode_rk…
bbbales2 0d2e975
[Jenkins] auto-formatting by clang-format version 6.0.0-1ubuntu2 (tag…
stan-buildbot 1908f1c
Fixed error message printing with too much work and extended tests to…
bbbales2 a3f438b
Merge branch 'feature/parameter-pack-odes' of https://github.com/stan…
bbbales2 e51700b
Merge remote-tracking branch 'origin/develop' into feature/parameter-…
bbbales2 bec1c2a
comment-out dont run async tests
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Adjoint ode_bdf passing ode_bdf tests. integrate_ode_bdf not working …
…yet. (design-doc #19)
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I recall that boost odeint required strictly sorted time vectors. The code looks as if that is not anymore needed. From what I see there is also a test for this. However, the test should be extended a bit...will comment there.
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I think I added these tests, lemme know if not.