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ChangeLog
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------------------------------------------------------------------------
r466 | gonnet | 2013-05-11 12:13:04 +0100 (Sat, 11 May 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
use multiple of warp size.
------------------------------------------------------------------------
r465 | achalk124 | 2013-05-10 16:09:26 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
Fixed CUDA to run with correct number of threads
------------------------------------------------------------------------
r464 | gonnet | 2013-05-10 14:09:58 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/src/potential_eval.h
fix typo.
------------------------------------------------------------------------
r463 | achalk124 | 2013-05-10 14:06:57 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/src/engine.c
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
Working copy of CUDA code, metis no longer required
------------------------------------------------------------------------
r462 | gonnet | 2013-05-10 14:01:12 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/src/potential_eval.h
fix minor bug.
------------------------------------------------------------------------
r461 | gonnet | 2013-05-10 11:22:31 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/examples/jac/jac.c
fix a number of things, especially energy reporting.
------------------------------------------------------------------------
r460 | gonnet | 2013-05-10 11:14:28 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
trying to undo the damage from previous botched commit.
------------------------------------------------------------------------
r459 | gonnet | 2013-05-10 11:04:30 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/src/fptype.h
M /trunk/src/potential_eval.h
fix double avx stuff, not tested yet.
------------------------------------------------------------------------
r458 | gonnet | 2013-05-10 09:16:19 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/engine.h
M /trunk/src/engine_io.c
M /trunk/src/fptype.h
M /trunk/src/runner.c
M /trunk/src/runner.h
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
M /trunk/src/runner_dopair.c
add type-agnostic fabs.
------------------------------------------------------------------------
r457 | gonnet | 2013-05-10 09:14:35 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/src/potential.h
add switched LJ interactions.
------------------------------------------------------------------------
r456 | gonnet | 2013-05-10 09:13:10 +0100 (Fri, 10 May 2013) | 1 line
Changed paths:
M /trunk/src/rigid.c
judicious use of doubles when computing the residuals.
------------------------------------------------------------------------
r455 | gonnet | 2013-05-09 18:45:25 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/engine_bonded.c
M /trunk/src/exclusion.c
M /trunk/src/exclusion.h
clean up bonded interactions, remove dead code.
------------------------------------------------------------------------
r454 | gonnet | 2013-05-09 18:38:42 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/angle.c
M /trunk/src/angle.h
M /trunk/src/bond.c
M /trunk/src/bond.h
M /trunk/src/dihedral.c
M /trunk/src/dihedral.h
M /trunk/src/engine_bonded.c
M /trunk/src/exclusion.c
M /trunk/src/exclusion.h
clean up bonded interactions, remove dead code.
------------------------------------------------------------------------
r453 | gonnet | 2013-05-09 16:10:23 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/examples/apoa1/apoa1.c
M /trunk/examples/stmv/stmv.c
increase potentials precision for better energy conservation.
------------------------------------------------------------------------
r452 | gonnet | 2013-05-09 16:06:33 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/engine_io.c
hard-wire torsion tolerance for odd deltas.
------------------------------------------------------------------------
r451 | gonnet | 2013-05-09 15:47:06 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/potential.c
more fixes for complicated potentials.
------------------------------------------------------------------------
r450 | gonnet | 2013-05-09 15:05:01 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/potential.c
forgot to remove a sanity test no longer valid.
------------------------------------------------------------------------
r449 | gonnet | 2013-05-09 15:02:12 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/potential.c
allow tricky dihedrals to avoid derivative.
------------------------------------------------------------------------
r448 | gonnet | 2013-05-09 14:50:17 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/angle.c
M /trunk/src/bond.c
M /trunk/src/dihedral.c
M /trunk/src/exclusion.c
M /trunk/src/fptype.h
M /trunk/src/runner_dopair.c
fix alignment for avx vectorization.
------------------------------------------------------------------------
r447 | achalk124 | 2013-05-09 14:41:09 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/engine.c
Fixed not defining metis.h in engine.c
------------------------------------------------------------------------
r446 | gonnet | 2013-05-09 14:35:12 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/examples/Makefile.am
M /trunk/examples/bulk/bulk.c
M /trunk/examples/flexible/flexible.c
M /trunk/examples/neon/Makefile.am
M /trunk/examples/neon/neon.c
M /trunk/examples/stmv/stmv.c
fixes for new release.
------------------------------------------------------------------------
r445 | gonnet | 2013-05-09 14:34:39 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/examples/jac/jac.c
fix for better energy conservation.
------------------------------------------------------------------------
r444 | gonnet | 2013-05-09 14:32:49 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/engine.h
M /trunk/src/runner_cuda.cu
minor fixes for release.
------------------------------------------------------------------------
r443 | gonnet | 2013-05-09 14:29:12 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/configure.in
neon was already there.
------------------------------------------------------------------------
r442 | gonnet | 2013-05-09 14:28:37 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/configure.in
removed btree, added neon.
------------------------------------------------------------------------
r441 | gonnet | 2013-05-09 09:54:00 +0100 (Thu, 09 May 2013) | 1 line
Changed paths:
M /trunk/src/potential.c
fix derivatives at interval end points.
------------------------------------------------------------------------
r440 | gonnet | 2013-05-08 22:08:48 +0100 (Wed, 08 May 2013) | 1 line
Changed paths:
M /trunk/src/exclusion.c
fix sign problem in excluded potential.
------------------------------------------------------------------------
r439 | gonnet | 2013-05-07 17:32:51 +0100 (Tue, 07 May 2013) | 2 lines
Changed paths:
D /trunk/examples/btree
remove out-dated example.
------------------------------------------------------------------------
r438 | gonnet | 2013-05-07 17:19:54 +0100 (Tue, 07 May 2013) | 1 line
Changed paths:
M /trunk/src/dihedral.c
remove old debug code.
------------------------------------------------------------------------
r437 | gonnet | 2013-05-07 17:19:05 +0100 (Tue, 07 May 2013) | 1 line
Changed paths:
M /trunk/src/fptype.h
temporarily cripple fptype_r2 for double precision, needs fixing.
------------------------------------------------------------------------
r436 | gonnet | 2013-05-07 17:17:08 +0100 (Tue, 07 May 2013) | 1 line
Changed paths:
M /trunk/src/engine.c
M /trunk/src/engine_bonded.c
M /trunk/src/space.c
M /trunk/src/space.h
be more specific with regards to energy reporting.
------------------------------------------------------------------------
r435 | gonnet | 2013-05-07 17:16:01 +0100 (Tue, 07 May 2013) | 1 line
Changed paths:
M /trunk/src/engine.h
M /trunk/src/engine_rigid.c
use pshake by default.
------------------------------------------------------------------------
r434 | gonnet | 2013-05-07 17:15:03 +0100 (Tue, 07 May 2013) | 1 line
Changed paths:
M /trunk/src/rigid.c
M /trunk/src/rigid.h
add pshake constraint solver.
------------------------------------------------------------------------
r433 | gonnet | 2013-05-07 17:14:20 +0100 (Tue, 07 May 2013) | 1 line
Changed paths:
M /trunk/src/angle.c
simplify angle derivative calculation.
------------------------------------------------------------------------
r432 | achalk124 | 2013-05-06 14:47:54 +0100 (Mon, 06 May 2013) | 1 line
Changed paths:
M /trunk/configure.in
M /trunk/ltmain.sh
M /trunk/src/Makefile.am
M /trunk/src/cell.h
M /trunk/src/engine.c
M /trunk/src/engine.h
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
Updated main branch to use latest GPU code
------------------------------------------------------------------------
r426 | gonnet | 2013-04-11 15:52:36 +0100 (Thu, 11 Apr 2013) | 1 line
Changed paths:
M /trunk/examples/apoa1/apoa1.c
use multiple devices.
------------------------------------------------------------------------
r424 | gonnet | 2013-04-08 17:06:48 +0100 (Mon, 08 Apr 2013) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
M /trunk/src/runner_cuda_main.h
use more than one warp, one-sided interaction.
------------------------------------------------------------------------
r423 | gonnet | 2013-04-04 11:42:40 +0100 (Thu, 04 Apr 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
better load-balancing between GPUs.
------------------------------------------------------------------------
r422 | gonnet | 2013-04-04 11:24:07 +0100 (Thu, 04 Apr 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
small fix to make async multi-GPU work.
------------------------------------------------------------------------
r415 | gonnet | 2013-03-08 11:09:20 +0000 (Fri, 08 Mar 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
fix so that at least single-GPU mode works.
------------------------------------------------------------------------
r414 | gonnet | 2013-03-07 23:54:35 +0000 (Thu, 07 Mar 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
some fixes to multi-gpu operation, still sub-optimal as streams on multiple GPUs seem broken.
------------------------------------------------------------------------
r413 | gonnet | 2013-03-07 21:06:53 +0000 (Thu, 07 Mar 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
tentative commit for multiple stream/gpu problem.
------------------------------------------------------------------------
r412 | gonnet | 2013-03-07 20:48:21 +0000 (Thu, 07 Mar 2013) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/runner_cuda.cu
possible fix for timing bug.
------------------------------------------------------------------------
r409 | gonnet | 2013-03-04 14:42:34 +0000 (Mon, 04 Mar 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
bug fix, part and force data allocation.
------------------------------------------------------------------------
r408 | gonnet | 2013-03-03 22:25:45 +0000 (Sun, 03 Mar 2013) | 1 line
Changed paths:
M /trunk/examples/jac/Makefile.am
M /trunk/examples/jac/jac.c
M /trunk/examples/stmv/stmv.c
minor fixes for multiple GPU use.
------------------------------------------------------------------------
r407 | gonnet | 2013-03-03 22:25:06 +0000 (Sun, 03 Mar 2013) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/runner_cuda.cu
several bug fixes for multiple GPUs, still something wrong with streams though.
------------------------------------------------------------------------
r406 | gonnet | 2013-03-03 19:00:31 +0000 (Sun, 03 Mar 2013) | 1 line
Changed paths:
M /trunk/src/engine.h
M /trunk/src/engine_cuda.cu
M /trunk/src/runner_cuda.cu
M /trunk/src/space.h
commit of tentative new multi-gpu code, still untested.
------------------------------------------------------------------------
r405 | gonnet | 2013-02-28 22:11:28 +0000 (Thu, 28 Feb 2013) | 1 line
Changed paths:
M /trunk/src/engine.c
M /trunk/src/engine.h
fix bug affecting initial shuffling of particles on engine_start.
------------------------------------------------------------------------
r404 | gonnet | 2013-02-28 18:24:04 +0000 (Thu, 28 Feb 2013) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/mdcore.h
M /trunk/src/queue.c
M /trunk/src/queue.h
M /trunk/src/runner.c
M /trunk/src/runner.h
added timers and queue_maxhit to avoid looking too long for good tasks on long queues.
------------------------------------------------------------------------
r402 | gonnet | 2013-02-25 16:49:25 +0000 (Mon, 25 Feb 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
M /trunk/src/space.c
M /trunk/src/space.h
M /trunk/src/task.h
several fixes to get half-cells working again.
------------------------------------------------------------------------
r401 | gonnet | 2013-02-25 12:18:19 +0000 (Mon, 25 Feb 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
minor fixes to make sure all the flags work.
------------------------------------------------------------------------
r400 | gonnet | 2013-02-25 00:14:27 +0000 (Mon, 25 Feb 2013) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
several bug fixes, more code clean-up, task dependencies on GPU now work.
------------------------------------------------------------------------
r399 | gonnet | 2013-02-24 16:33:36 +0000 (Sun, 24 Feb 2013) | 1 line
Changed paths:
M /trunk/src/engine.c
M /trunk/src/engine.h
M /trunk/src/engine_cuda.cu
M /trunk/src/runner.c
M /trunk/src/runner.h
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
M /trunk/src/runner_cuda_main.h
M /trunk/src/runner_dopair.c
M /trunk/src/runner_dosort.c
M /trunk/src/space.c
M /trunk/src/space.h
M /trunk/src/task.h
major overhaul of the GPU code to handle new tasks with dependencies, separate sorting. not tested yet.
------------------------------------------------------------------------
r397 | gonnet | 2013-02-15 11:17:44 +0000 (Fri, 15 Feb 2013) | 1 line
Changed paths:
M /trunk/src/engine_cuda.cu
removed fifo.h which is no longer needed.
------------------------------------------------------------------------
r396 | gonnet | 2013-02-15 10:25:14 +0000 (Fri, 15 Feb 2013) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/fptype.h
M /trunk/src/potential_eval.h
M /trunk/src/runner_dopair.c
M /trunk/src/spme.c
minor fixes to work with avx.
------------------------------------------------------------------------
r395 | gonnet | 2013-02-10 19:43:20 +0000 (Sun, 10 Feb 2013) | 1 line
Changed paths:
A /trunk/src/runner_dosort.c
forgot one.
------------------------------------------------------------------------
r394 | gonnet | 2013-02-10 19:35:10 +0000 (Sun, 10 Feb 2013) | 1 line
Changed paths:
M /trunk/configure.in
M /trunk/examples/apoa1/Makefile.am
M /trunk/examples/apoa1/apoa1.c
M /trunk/examples/argon/Makefile.am
M /trunk/examples/argon/argon.c
M /trunk/examples/bulk/Makefile.am
M /trunk/examples/bulk/bulk.c
M /trunk/examples/flexible/Makefile.am
M /trunk/examples/flexible/flexible.c
M /trunk/examples/hybrid/Makefile.am
M /trunk/examples/hybrid/hybrid.c
M /trunk/examples/jac/Makefile.am
M /trunk/examples/jac/jac.c
M /trunk/examples/stmv/Makefile.am
M /trunk/examples/stmv/stmv.c
M /trunk/ltmain.sh
M /trunk/src/Makefile.am
M /trunk/src/angle.c
M /trunk/src/bond.c
M /trunk/src/cell.c
M /trunk/src/cell.h
M /trunk/src/dihedral.c
M /trunk/src/engine.c
M /trunk/src/engine.h
M /trunk/src/engine_bonded.c
M /trunk/src/engine_exchange.c
M /trunk/src/engine_io.c
M /trunk/src/engine_rigid.c
M /trunk/src/exclusion.c
D /trunk/src/fifo.c
D /trunk/src/fifo.h
M /trunk/src/mdcore.h
M /trunk/src/queue.c
M /trunk/src/queue.h
M /trunk/src/rigid.c
M /trunk/src/runner.c
M /trunk/src/runner.h
M /trunk/src/runner_dopair.c
D /trunk/src/runner_pwverlet.c
D /trunk/src/runner_verlet.c
M /trunk/src/space.c
M /trunk/src/space.h
A /trunk/src/spme.c
A /trunk/src/spme.h
A /trunk/src/task.c
A /trunk/src/task.h
major clean-up, removed a lot of dead code, added basic spme (untested), split sorting from force, added task dependencies.
------------------------------------------------------------------------
r391 | gonnet | 2013-01-18 15:52:38 +0000 (Fri, 18 Jan 2013) | 1 line
Changed paths:
M /trunk/examples/stmv/stmv.c
M /trunk/src/engine_io.c
input/output changes.
------------------------------------------------------------------------
r387 | gonnet | 2012-12-17 08:57:51 +0000 (Mon, 17 Dec 2012) | 1 line
Changed paths:
M /trunk/src/angle.c
M /trunk/src/bond.c
M /trunk/src/dihedral.c
M /trunk/src/engine_io.c
M /trunk/src/exclusion.c
fix bug in dummy bonded interactions.
------------------------------------------------------------------------
r386 | gonnet | 2012-12-16 23:07:08 +0000 (Sun, 16 Dec 2012) | 1 line
Changed paths:
A /trunk/examples/stmv
A /trunk/examples/stmv/Makefile.am
A /trunk/examples/stmv/par_all27_prot_na.inp
A /trunk/examples/stmv/stmv.c
A /trunk/examples/stmv/stmv.pdb
A /trunk/examples/stmv/stmv.psf
added satellite tobacco mosaic virus.
------------------------------------------------------------------------
r385 | gonnet | 2012-12-16 23:04:08 +0000 (Sun, 16 Dec 2012) | 1 line
Changed paths:
M /trunk/configure.in
M /trunk/doc/Doxyfile
M /trunk/examples/Makefile.am
M /trunk/examples/apoa1/apoa1.c
M /trunk/examples/jac/jac.c
M /trunk/examples/neon/neon.c
M /trunk/src/engine.h
M /trunk/src/engine_io.c
M /trunk/src/lock.h
M /trunk/src/potential.c
M /trunk/src/reader.c
M /trunk/src/reader.h
M /trunk/web/documentation.html
M /trunk/web/download.html
M /trunk/web/features.html
M /trunk/web/index.html
M /trunk/web/publications.html
M /trunk/web/tutorial.html
fix some things in potentials and make engine_io use numbered files instead of FILE *.
------------------------------------------------------------------------
r384 | gonnet | 2012-12-07 19:26:16 +0000 (Fri, 07 Dec 2012) | 1 line
Changed paths:
M /trunk/src/angle.c
M /trunk/src/engine.h
M /trunk/src/fptype.h
M /trunk/src/potential.c
M /trunk/src/runner_cuda.cu
M /trunk/src/space.c
minor bug fixes.
------------------------------------------------------------------------
r377 | gonnet | 2012-11-22 17:43:35 +0000 (Thu, 22 Nov 2012) | 1 line
Changed paths:
M /trunk/examples/Makefile.am
M /trunk/examples/apoa1/apoa1.c
M /trunk/examples/argon/Makefile.am
M /trunk/examples/argon/argon.c
M /trunk/examples/bulk/bulk.c
M /trunk/examples/flexible/flexible.c
M /trunk/examples/hybrid/Makefile.am
M /trunk/examples/hybrid/hybrid.c
M /trunk/examples/jac/jac.c
M /trunk/examples/neon/Makefile.am
M /trunk/examples/neon/neon.c
use dimension-specific minimum cell edge lengths.
------------------------------------------------------------------------
r376 | gonnet | 2012-11-22 17:42:09 +0000 (Thu, 22 Nov 2012) | 1 line
Changed paths:
M /trunk/src/engine.c
M /trunk/src/engine.h
M /trunk/src/space.c
M /trunk/src/space.h
pass dimension-specific minimum cell edge lengths.
------------------------------------------------------------------------
r373 | gonnet | 2012-11-20 21:07:01 +0000 (Tue, 20 Nov 2012) | 1 line
Changed paths:
M /trunk/examples/apoa1/apoa1.c
dump all atom types.
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r372 | gonnet | 2012-11-20 21:00:47 +0000 (Tue, 20 Nov 2012) | 1 line
Changed paths:
M /trunk/src/engine.c
be a bit more careful when freeing allocated memory.
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r371 | gonnet | 2012-11-20 20:59:45 +0000 (Tue, 20 Nov 2012) | 1 line
Changed paths:
M /trunk/src/engine_io.c
correctly terminate PDB files.
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r370 | gonnet | 2012-11-19 14:49:55 +0000 (Mon, 19 Nov 2012) | 1 line
Changed paths:
M /trunk/src/engine.c
do not de-allocate runners if they were never allocated.
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r369 | gonnet | 2012-11-19 14:34:26 +0000 (Mon, 19 Nov 2012) | 1 line
Changed paths:
M /trunk/examples/bulk/Makefile.am
M /trunk/examples/bulk/bulk.c
adapt Makefile.am and make output match that of jac.
------------------------------------------------------------------------
r368 | gonnet | 2012-11-19 14:18:28 +0000 (Mon, 19 Nov 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda_main.h
fixed timer name bug.
------------------------------------------------------------------------
r367 | gonnet | 2012-11-19 11:45:22 +0000 (Mon, 19 Nov 2012) | 1 line
Changed paths:
M /trunk/examples/apoa1/apoa1.c
make timers compatible with jac.
------------------------------------------------------------------------
r366 | gonnet | 2012-11-19 11:41:24 +0000 (Mon, 19 Nov 2012) | 1 line
Changed paths:
M /trunk/examples/apoa1/apoa1.c
forgot one.
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r365 | gonnet | 2012-11-19 11:37:36 +0000 (Mon, 19 Nov 2012) | 2 lines
Changed paths:
M /trunk/examples/apoa1/Makefile.am
M /trunk/examples/apoa1/apoa1.c
modernize the Makefile.am and put options for MPI in defines.
------------------------------------------------------------------------
r364 | gonnet | 2012-11-15 18:01:05 +0000 (Thu, 15 Nov 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda_main.h
fix rather embarassing bug when using FORCES_LOCAL.
------------------------------------------------------------------------
r363 | gonnet | 2012-11-12 16:13:01 +0000 (Mon, 12 Nov 2012) | 1 line
Changed paths:
M /trunk/examples/jac/jac.c
added facilities for cleaning up, i.e. finalizing the engine.
------------------------------------------------------------------------
r362 | gonnet | 2012-11-12 16:12:43 +0000 (Mon, 12 Nov 2012) | 1 line
Changed paths:
M /trunk/src/engine.c
M /trunk/src/engine.h
M /trunk/src/potential.c
M /trunk/src/potential.h
M /trunk/src/space.h
added facilities for cleaning up, i.e. finalizing the engine.
------------------------------------------------------------------------
r361 | gonnet | 2012-10-18 22:00:10 +0100 (Thu, 18 Oct 2012) | 1 line
Changed paths:
M /trunk/src/runner.c
more robust blocking on potential dining philosopher's problem.
------------------------------------------------------------------------
r360 | gonnet | 2012-10-18 12:27:59 +0100 (Thu, 18 Oct 2012) | 1 line
Changed paths:
M /trunk/examples/bulk/Makefile.am
M /trunk/examples/bulk/bulk.c
make this example compatible with the latest improvements to the library.
------------------------------------------------------------------------
r359 | gonnet | 2012-10-15 16:24:04 +0100 (Mon, 15 Oct 2012) | 1 line
Changed paths:
M /trunk/src/runner.c
make idle threads wait on a signal.
------------------------------------------------------------------------
r358 | gonnet | 2012-10-15 13:03:38 +0100 (Mon, 15 Oct 2012) | 1 line
Changed paths:
M /trunk/src/runner.c
M /trunk/src/runner.h
add microsecond sleep and incremental backoff when leaving task queue empty-handed.
------------------------------------------------------------------------
r357 | gonnet | 2012-10-15 12:35:01 +0100 (Mon, 15 Oct 2012) | 1 line
Changed paths:
M /trunk/src/queue.c
M /trunk/src/runner.c
make order of task locking depend on runner id.
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r356 | gonnet | 2012-10-12 11:30:01 +0100 (Fri, 12 Oct 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
M /trunk/src/runner_cuda_main.h
use multipole queues and work-stealing.
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r355 | gonnet | 2012-10-11 12:53:57 +0100 (Thu, 11 Oct 2012) | 1 line
Changed paths:
M /trunk/src/runner.c
bail if more queues than tasks.
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r354 | gonnet | 2012-10-09 11:05:31 +0100 (Tue, 09 Oct 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
M /trunk/src/runner_cuda_main.h
use multiple queues and work stealing on GPU.
------------------------------------------------------------------------
r353 | gonnet | 2012-10-08 12:57:13 +0100 (Mon, 08 Oct 2012) | 1 line
Changed paths:
M /trunk/src/engine.c
M /trunk/src/queue.c
M /trunk/src/runner.c
make tuples use queues too.
------------------------------------------------------------------------
r352 | gonnet | 2012-10-08 12:11:22 +0100 (Mon, 08 Oct 2012) | 1 line
Changed paths:
M /trunk/src/queue.c
M /trunk/src/queue.h
M /trunk/src/runner.c
look for task with best data re-use in queue.
------------------------------------------------------------------------
r351 | gonnet | 2012-10-04 20:33:57 +0100 (Thu, 04 Oct 2012) | 1 line
Changed paths:
M /trunk/examples/jac/jac.c
aggregate counters when using mpi.
------------------------------------------------------------------------
r350 | gonnet | 2012-10-04 18:01:47 +0100 (Thu, 04 Oct 2012) | 1 line
Changed paths:
M /trunk/examples/jac/jac.c
hide debugging code.
------------------------------------------------------------------------
r349 | gonnet | 2012-10-04 17:59:43 +0100 (Thu, 04 Oct 2012) | 1 line
Changed paths:
A /trunk/src/queue.c
A /trunk/src/queue.h
added sources for queue.
------------------------------------------------------------------------
r348 | gonnet | 2012-10-04 17:58:36 +0100 (Thu, 04 Oct 2012) | 1 line
Changed paths:
M /trunk/examples/jac/jac.c
switch to multiple queues and work-stealing.
------------------------------------------------------------------------
r347 | gonnet | 2012-10-04 17:58:10 +0100 (Thu, 04 Oct 2012) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/engine.c
M /trunk/src/engine.h
M /trunk/src/mdcore.h
M /trunk/src/runner.c
switch to multiple queues and work-stealing.
------------------------------------------------------------------------
r346 | gonnet | 2012-10-03 17:14:35 +0100 (Wed, 03 Oct 2012) | 1 line
Changed paths:
A /trunk/examples/jac/jac_hybrid.sh
add test script for hybrid simulations.
------------------------------------------------------------------------
r345 | gonnet | 2012-10-03 12:39:18 +0100 (Wed, 03 Oct 2012) | 1 line
Changed paths:
M /trunk/src/lock.h
make unlock use a memory barrier.
------------------------------------------------------------------------
r344 | gonnet | 2012-10-03 12:21:28 +0100 (Wed, 03 Oct 2012) | 1 line
Changed paths:
M /trunk/src/lock.h
make unlock use a memory barrier.
------------------------------------------------------------------------
r343 | gonnet | 2012-10-03 11:13:30 +0100 (Wed, 03 Oct 2012) | 1 line
Changed paths:
M /trunk/examples/jac/jac.c
don't go out with a bang on MPI.
------------------------------------------------------------------------
r342 | gonnet | 2012-10-03 10:33:34 +0100 (Wed, 03 Oct 2012) | 1 line
Changed paths:
M /trunk/examples/jac/Makefile.am
make compiling cuda targets conditional.
------------------------------------------------------------------------
r341 | gonnet | 2012-10-03 10:15:21 +0100 (Wed, 03 Oct 2012) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/angle.c
M /trunk/src/bond.c
M /trunk/src/dihedral.c
M /trunk/src/engine.c
M /trunk/src/engine.h
M /trunk/src/engine_bonded.c
M /trunk/src/engine_exchange.c
M /trunk/src/engine_io.c
M /trunk/src/engine_rigid.c
M /trunk/src/exclusion.c
M /trunk/src/fifo.c
M /trunk/src/rigid.c
M /trunk/src/runner.c
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_dopair.c
M /trunk/src/runner_pwverlet.c
M /trunk/src/runner_verlet.c
M /trunk/src/space.c
add flag for MPI.
------------------------------------------------------------------------
r340 | gonnet | 2012-10-03 10:13:53 +0100 (Wed, 03 Oct 2012) | 1 line
Changed paths:
M /trunk/configure.in
add flag for MPI.
------------------------------------------------------------------------
r339 | gonnet | 2012-10-03 10:13:12 +0100 (Wed, 03 Oct 2012) | 1 line
Changed paths:
M /trunk/examples/jac/Makefile.am
M /trunk/examples/jac/jac.c
add flag for MPI.
------------------------------------------------------------------------
r338 | gonnet | 2012-09-22 21:58:55 +0100 (Sat, 22 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
queue now works, excessive use of atomicCAS due to strange memory inconsistencies.
------------------------------------------------------------------------
r337 | gonnet | 2012-09-21 22:26:50 +0100 (Fri, 21 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
safer exit condition.
------------------------------------------------------------------------
r336 | gonnet | 2012-09-21 22:11:39 +0100 (Fri, 21 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
change exit criteria from cuda_queue_gettask().
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r335 | gonnet | 2012-09-21 22:04:22 +0100 (Fri, 21 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda_main.h
typo.
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r334 | gonnet | 2012-09-21 22:03:26 +0100 (Fri, 21 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda_main.h
typo.
------------------------------------------------------------------------
r333 | gonnet | 2012-09-21 22:02:43 +0100 (Fri, 21 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda_main.h
fix queue reset.
------------------------------------------------------------------------
r332 | gonnet | 2012-09-21 22:00:24 +0100 (Fri, 21 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
locking bug with more than one thread.
------------------------------------------------------------------------
r331 | gonnet | 2012-09-21 21:54:57 +0100 (Fri, 21 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
don't put bogus tasks back into the queue.
------------------------------------------------------------------------
r330 | gonnet | 2012-09-21 21:49:20 +0100 (Fri, 21 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda_main.h
locking bug.
------------------------------------------------------------------------
r329 | gonnet | 2012-09-21 21:44:17 +0100 (Fri, 21 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
M /trunk/src/runner_cuda_main.h
use queues when force is not local.
------------------------------------------------------------------------
r328 | gonnet | 2012-09-20 16:31:26 +0100 (Thu, 20 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
add non-local forces to verlet variants too.
------------------------------------------------------------------------
r327 | gonnet | 2012-09-20 14:50:31 +0100 (Thu, 20 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
fixed left- and right-looking interactions.
------------------------------------------------------------------------
r326 | gonnet | 2012-09-12 16:33:46 +0100 (Wed, 12 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
remove unused variable.
------------------------------------------------------------------------
r325 | gonnet | 2012-09-12 16:32:58 +0100 (Wed, 12 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
fixes.
------------------------------------------------------------------------
r324 | gonnet | 2012-09-12 14:26:04 +0100 (Wed, 12 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
M /trunk/src/runner_cuda_main.h
separate pairwise routines for left and right interactions, finer locking scheme.
------------------------------------------------------------------------
r323 | gonnet | 2012-09-11 13:48:48 +0100 (Tue, 11 Sep 2012) | 1 line
Changed paths:
M /trunk/examples/jac/Makefile.am
clean up flags.
------------------------------------------------------------------------
r322 | gonnet | 2012-09-11 13:42:04 +0100 (Tue, 11 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda.h
M /trunk/src/runner_cuda_main.h
add FORCES_LOCAL, requires different locking.
------------------------------------------------------------------------
r321 | gonnet | 2012-09-11 10:28:32 +0100 (Tue, 11 Sep 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda_main.h
add copyright/license header.
------------------------------------------------------------------------
r320 | gonnet | 2012-09-11 10:27:26 +0100 (Tue, 11 Sep 2012) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
add potential energy calculation.
------------------------------------------------------------------------
r319 | gonnet | 2012-09-11 10:26:07 +0100 (Tue, 11 Sep 2012) | 1 line
Changed paths:
M /trunk/configure.in
M /trunk/doc/Doxyfile
M /trunk/examples/apoa1/apoa1.c
M /trunk/examples/argon/argon.c
M /trunk/examples/bulk/Makefile.am
M /trunk/examples/jac/jac.c
M /trunk/ltmain.sh
M /trunk/src/engine.c
M /trunk/src/engine.h
M /trunk/src/runner.c
M /trunk/web/tutorial.html
change engine_flag_verlet_pairwise2 to engine_flag_verlet_pseudo.
------------------------------------------------------------------------
r318 | gonnet | 2012-08-22 11:09:46 +0100 (Wed, 22 Aug 2012) | 1 line
Changed paths:
M /trunk/src/engine_cuda.cu
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
several fixes to work with 5.0, re-use buffers in self-interactions.
------------------------------------------------------------------------
r317 | gonnet | 2012-08-21 10:39:59 +0100 (Tue, 21 Aug 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda_main.h
exit criteria didn't make much sense.
------------------------------------------------------------------------
r316 | gonnet | 2012-08-20 16:10:17 +0100 (Mon, 20 Aug 2012) | 1 line
Changed paths:
M /trunk/src/runner_cuda_main.h
fix loop to avoid sm_13 compiler bugs.
------------------------------------------------------------------------
r315 | gonnet | 2012-08-17 16:40:35 +0100 (Fri, 17 Aug 2012) | 1 line
Changed paths:
M /trunk/examples/jac/Makefile.am
minor fix
------------------------------------------------------------------------
r314 | gonnet | 2012-08-17 16:39:58 +0100 (Fri, 17 Aug 2012) | 1 line
Changed paths:
M /trunk/examples/jac/jac.c
specify cuda device.
------------------------------------------------------------------------
r313 | gonnet | 2012-08-17 11:10:57 +0100 (Fri, 17 Aug 2012) | 1 line
Changed paths:
M /trunk/src/potential.c
resolve nested functions as some compilers will not like this at all.
------------------------------------------------------------------------
r312 | gonnet | 2012-08-15 17:48:21 +0100 (Wed, 15 Aug 2012) | 1 line
Changed paths:
M /trunk/src/Makefile.am
M /trunk/src/runner_cuda.cu
M /trunk/src/runner_cuda_main.h
compute diagonal entries on the fly.