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15216 Commits

Author SHA1 Message Date
Richard Berger fef2b8260b Correct CMake FFT settings in docs 
The upper or lowercase matters. It won't work with lower case.
 2018-08-13 11:46:46 -04:00
Axel Kohlmeyer 6e8a68a420 fix a bunch of typos and broken links as detected by ebook-convert 2018-08-12 17:16:24 +02:00
Axel Kohlmeyer 11f04fde5c fix typo 2018-08-12 16:44:31 +02:00
Axel Kohlmeyer e01185c283 correct some errors and misconceptions about zlib and USER-OMP 2018-08-12 16:44:26 +02:00
Steven J. Plimpton 907b061e0b more updates to Build doc page 2018-08-10 15:04:33 -06:00
Richard Berger 135b877161 Make sure -fPIC is passed to ExternalProject VORO if BUILD_SHARED_LIBS=on 2018-08-10 15:01:46 -04:00
Steve Plimpton 28c03e4518
Merge pull request #1046 from rbberger/gpu_fix_deprecated 
Replace deprecated CUDA functions calls in GPU package
 2018-08-10 09:30:02 -06:00
Axel Kohlmeyer b33452040a correct FFT definitions in docs and make -DFFT_KISSFFT explicit in CMake 2018-08-10 17:27:40 +02:00
Axel Kohlmeyer ddd8533d81 make -DLAMMPS_MEMALIGN optional in CMake by checking of 0 alignment. also some rewording. 
this changes the CMake configuration file.
also, the special case of Windows not supporting posix_memalign() is documented.
some more explanations for FFTs and memory alignment are added
 2018-08-10 16:33:20 +02:00
Axel Kohlmeyer bc8939a08b more corrections/rewrites/additions for OpenMP, QM/MM and USER-QUIP 2018-08-10 15:55:32 +02:00
Axel Kohlmeyer f67b198c24 discourage the use of MEAM and REAX, which have been supersede by USER-MEAMC and USER-REAXC 2018-08-10 13:04:31 +02:00
Axel Kohlmeyer 13d1f26a0f provide additional information about building QM/MM with QE 2018-08-10 12:15:49 +02:00
Axel Kohlmeyer 8318b96c11 update OpenMP support info in build basics 2018-08-10 11:54:51 +02:00
Axel Kohlmeyer 0b523cb48e some rewording and updates for the traditional and cmake documentation 2018-08-10 11:38:59 +02:00
Richard Berger 76289cd955 Add LAMMPS shared library instructions for CMake 2018-08-09 17:50:55 -04:00
Richard Berger edb535d36f Fix some of the missing TODOs in cmake docs 2018-08-09 17:21:00 -04:00
Richard Berger 4db08f5351 Some tweaks and corrections 2018-08-09 16:02:54 -04:00
Richard Berger 630a46ad67 Move Manual_version to Intro 
It should not be its own chapter. The intro seems to be the right place for it.
 2018-08-09 14:53:40 -04:00
Axel Kohlmeyer aca9416c7f Merge branch 'master' into doc-reorg-start and resolve merge conflicts with master 
Conflicts:
	doc/src/Speed_kokkos.txt
	doc/src/package.txt
 2018-08-09 20:18:12 +02:00
Axel Kohlmeyer f7164e593e fix a few more broken or non-unique links 2018-08-09 20:09:11 +02:00
Axel Kohlmeyer a5170e93ec fix a bunch more broken, duplicate links and misformatted text 2018-08-09 19:46:25 +02:00
Axel Kohlmeyer 108f2d0ed7 Merge branch 'collected-small-changes' into doc-reorg-start 
Resolved Conflicts:
	doc/src/Packages_details.txt
	doc/src/Python_shlib.txt
	doc/src/fix_manifoldforce.txt
 2018-08-09 18:48:11 +02:00
Steve Plimpton 6663fbeb11
Merge pull request #928 from akohlmey/fix-rcb-balance-issue 
Fix rcb balance issue
 2018-08-09 10:24:38 -06:00
Steven J. Plimpton cfc1b3a823 more changes induced by removing Section_start.txt 2018-08-09 10:20:02 -06:00
Steven J. Plimpton c97e6537c8 changes to replace Section_start.txt 2018-08-09 10:19:10 -06:00
Steve Plimpton 9dde50a4f2
Merge pull request #1042 from akohlmey/kokkos-vs-gpu-direct 
Kokkos vs gpu direct
 2018-08-09 09:25:24 -06:00
Steve Plimpton 08636889ca
Merge pull request #1043 from lammps/compute-cluster-atom 
bug fix for compute cluster/atom when computing values used to update…
 2018-08-09 09:15:09 -06:00
Axel Kohlmeyer bb25e5d98a adjust header levels for Tools section 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer 8e9ea1e4fa formatting tweak for Build the manual page 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer f4ea28cd32 update src/lammps.book file with missing entries 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer 1604f011d2 fix a couple more broken links 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer a065143723 create missing "Build_manual.txt" file from 'doc/README' 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer df20fbbca4 fix a bunch of broken linke or make links unique across files 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer a97ad15d22 update .gitignore 2018-08-09 17:13:06 +02:00
Steven J. Plimpton d5594350c4 change zero-size shrink box to original box 2018-08-09 08:50:11 -06:00
Axel Kohlmeyer 9521814441 rename Kokkos::gpu_direct to Kokkos::gpu_direct_flag 
This is for consistency with other parts of LAMMPS where
such variables have "flag" in their name. Also reduces
confusion with have_gpu_direct() function.

When we can safely detect, that GPU-direct is not available,
change the default setting of Kokkos::gpu_direct_flag from 1 to 0
 2018-08-09 04:52:58 -04:00
Axel Kohlmeyer dd9fed11dc use '-pk kokkos gpu/direct on/off' consistently in comments and docs 2018-08-09 04:16:22 -04:00
Richard Berger 65d11171c4 Replace functions which were deprecated since CUDA 5 2018-08-09 03:36:21 -04:00
Axel Kohlmeyer 01b8134746
Small tweak to GPU direct not available warning 2018-08-09 09:35:11 +02:00
Richard Berger 6d60075d3b GPU Package: Use __shfl_xor_sync starting with CUDA 9 2018-08-09 02:33:35 -04:00
Stan Moore 32658c20d4 Fix typo in gridcomm_kokkos 2018-08-08 17:07:12 -06:00
Stan Moore 1c550d8f39 Change defaults for GPU-direct to use comm host 2018-08-08 16:46:36 -06:00
Stan Moore d8aa6d534b Remove hardcoded GPU-direct in KOKKOS package 2018-08-08 16:09:41 -06:00
Steven J. Plimpton 9202896e75 bug fix for compute cluster/atom when computing values used to update a dynamic group 2018-08-08 09:31:16 -06:00
Steve Plimpton 985318203d
Merge pull request #1038 from stanmoore1/issue-1037 
KOKKOS Package bugfix: Workaround for issue #1037
 2018-08-08 08:42:21 -06:00
Steve Plimpton ff87cdb8f4
Merge pull request #1041 from rbberger/fix_gpu_segfault 
Add extra check for OpenCL timers
 2018-08-08 08:41:32 -06:00
Steve Plimpton a3fad229ab
Merge pull request #1040 from lammps/natom 
enable more correct natoms computation when atoms are lost
 2018-08-08 08:41:15 -06:00
Steve Plimpton fac5e29f48
Merge pull request #994 from danicholson/user-uef-image-flags 
USER-UEF support for image flags
 2018-08-08 08:40:56 -06:00
Axel Kohlmeyer 64e152bced add some notes about GPU-direct support requirements to the manual 2018-08-08 14:25:49 +02:00
Axel Kohlmeyer 5d87e0c651 add wrapper for MPI implementation specific GPU-direct detection 
this adds a local wrapper function have_gpu_direct(), that informs about
the support for GPU-direct, if possible and add a warning message in case
it cannot be detected or is not available and using more than 1 MPI rank.
 2018-08-08 13:57:41 +02:00