64fdb1f528
Kokkos/pair_exp6_rx_kokkos optimized for SIMD on the inner j-loop.
2017-03-17 15:52:40 -04:00
eb1a4d11dd
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, as of patch 17March17
2017-03-17 15:18:24 -04:00
1c749d5cf5
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos
2017-03-17 12:09:25 -06:00
4a90bca7a3
patch 17Mar17
2017-03-17 11:29:23 -06:00
9f35b764f8
Merge pull request #424 from timattox/dpd_restart_fix
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Remove unneeded restart_peratom flags in USER-DPD package
2017-03-17 11:19:04 -06:00
7ca5dce2f5
Merge pull request #423 from timattox/master_bugfix_irregular
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bugfix for irregular::create_atom and create_data
2017-03-17 11:18:52 -06:00
fcc3b3bd36
Merge pull request #421 from akohlmey/memory-output
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improve memory usage reporting in info and output class
2017-03-17 11:18:08 -06:00
a936b7b2ab
Merge pull request #419 from rbberger/python_fixes
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Library interface fixes, Python example fixes and better Python 3 compatibility
2017-03-17 11:16:58 -06:00
d31c591b60
Remove unneeded restart_peratom flags
2017-03-17 09:40:39 -06:00
ae5ebf6001
add support for MPI_Request_free() to MPI STUBS library
2017-03-17 11:40:09 -04:00
7fb741d53d
Revert "In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block()"
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This reverts commit 8e75616c14
2017-03-17 11:35:59 -04:00
a719f41426
Merge remote-tracking branch 'thunder/USER-DPD_kokkos_gb_test' into USER-DPD_GBhacks_cps
2017-03-17 10:26:44 -04:00
ba069fb755
Merge remote-tracking branch 'thunder/USER-DPD_GBhacks' into USER-DPD_GBhacks_cps
2017-03-17 10:11:00 -04:00
4a7bc115cb
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, bring in MPI deadlock fix
2017-03-17 03:24:03 -04:00
5ea096d08c
Merge branch 'master_bugfix_irregular' into USER-DPD_kokkos
2017-03-17 03:19:29 -04:00
8e75616c14
In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block()
2017-03-17 03:02:42 -04:00
411c069ba6
BUGFIX: Prevent possible deadlock in Irregular::create_atom and create_data
2017-03-17 03:02:19 -04:00
ac82d041cc
ignore package pair style
2017-03-16 23:12:49 -04:00
ec192a95cb
Cleaned up the non-kokkos part of KOKKOS/pair_exp6_rx_kokkos.cpp
2017-03-16 22:28:19 -04:00
f5b7361ef6
Non-kokkos candidate of PairExp6rxKokkos::getMixingWeights to improve vectorization on the KNL.
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- Moved the particle loop inside a replica of getMixingWeights, getMixingWeightsVect,
and refactored to improve vectorization.
- Added OMP SIMD and OMP threading directly inside that function but will replace with
kokkos parallel_for and parallel_reduce methods later.
2017-03-16 21:31:30 -04:00
070ce33a13
improve memory usage reporting in info and output class
2017-03-16 18:35:04 -04:00
f604f86cfc
add fix filter/corotate to some administrative files
2017-03-16 15:08:17 -04:00
1995f434f3
fix some more code formatting issues, add newline at EOF
2017-03-16 14:24:28 -04:00
acdb932c4e
Fixing index issue in pair_exp6_rx_kokkos
2017-03-16 09:28:27 -06:00
2f5e711acd
Merge remote-tracking branch 'upstream/master' into filter_corotate
2017-03-16 10:00:12 +01:00
bdb7669e27
Fixed coding style.
2017-03-16 09:44:07 +01:00
a210867025
Fixes lammps_create_atoms library function and its Python interface variant
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The interface of that function has changed and includes two additional
parameters, which haven't been added to the Python interface either.
This showed up by trying to run the simple.py example.
2017-03-15 22:13:06 -04:00
ce9b3f4fcb
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks
2017-03-15 18:17:39 -05:00
7ebed717de
Adding gb_test
2017-03-15 16:05:51 -06:00
bdee2fa234
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos
2017-03-15 15:59:55 -06:00
3a2da51a82
Merge pull request #413 from ohenrich/user-cgdna
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User cgdna
2017-03-15 13:12:43 -06:00
f4a08ba4fc
pass Views by reference for pair_table_rx_kokkos
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this greatly speeds up pair_table_rx_kokkos,
and should put it on par with pair_table_rx
in the Serial case
2017-03-15 09:25:16 -06:00
ec1778b586
add pair_zhou
2017-03-15 11:10:04 -04:00
c3ce3747e0
Added fix filter/corotate.
2017-03-15 11:34:01 +01:00
5925460a27
Improve the performance of read_data of gzip'ed files using taskset.
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Normally, the gzip process would be pinned to the same core as the
MPI rank 0 process, which makes the pipe stay in one core's cache,
but forces the two process to fight for that core, slowing things down.
2017-03-14 14:27:23 -05:00
580f6b567b
Add neigh/qeq option to Kokkos
2017-03-14 10:44:31 -06:00
7a75cd111c
Minor updates in documentation and setup tool, merge before upgrade to oxDNA2
2017-03-14 11:39:09 +00:00
d2cbfef13b
Add CUDA support to atom_vec_hybrid_kokkos
2017-03-13 09:01:35 -06:00
6311d33a5d
UPLOAD source files
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source files and install.sh added
2017-03-13 22:49:04 +09:00
e136a9db02
Create README
2017-03-13 22:48:12 +09:00
4b4bc7dc3b
USER-DPD: specialize PairTableRXKokkos's compute_all_items() on NEWTON_PAIR
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No noticable performance change, but it does eliminate a deep conditional.
2017-03-13 03:03:27 -04:00
d5eceebf32
USER-DPD Kokkos: add support for full neighbor lists.
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Note: "newton on" still required if using non-kokkos pair styles or fixes.
Non-kokkos pairs/fixes don't expect their half lists with newton off,
which happens if newton is turned off globally by kokkos via commandline.
Note2: Regardless, fix_shardlow* will still use half lists and newton on.
2017-03-13 01:56:00 -04:00
b1b377cb59
USER-DPD: fix_shardlow's neighbor request needs "newton on" override.
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Even if other stuff is doing newton off, SSA must have it turned on.
2017-03-12 17:48:51 -04:00
e908b8dbea
USER-DPD Kokkos: correct some error messages
2017-03-12 16:20:09 -04:00
d6f6c6faf1
USER-DPD: Make newton-off warning in pair_dpd_fdt* be more selective.
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If using fix_shardlow, the pair_dpd_fdt* styles are okay with newton off,
because the stocastic forces are thus only done in fix_shardlow.
2017-03-12 16:05:28 -04:00
17c8e695a4
Merge branch 'master' into USER-DPD_kokkos as of patch 10 Mar 2017
2017-03-10 21:37:52 -05:00
f871ecdc67
change to RCB cuts in load-balancing commands, also a new option for fix halt
2017-03-10 15:55:07 -07:00
470353e320
Merge pull request #408 from giacomofiorin/colvars-update-2017-03-10
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Colvars update 2017-03-10
2017-03-10 14:51:16 -07:00
ffe02d20ca
Merge pull request #406 from stanmoore1/kokkos_bugfix
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Fix Kokkos issues
2017-03-10 14:51:04 -07:00
c7eadfdefd
Merge branch 'master' into USER-DPD_kokkos
2017-03-10 16:29:09 -05:00
