Compile geometry extension with OpenMP. #1349
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cxhernandez
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Sep 6, 2018
v1.9.2 (July 30, 2018) --------------------- We're pleased to announce the release of MDTraj 1.9.2. This version has a number of bug fixes and improvements for trajectory parsing and conversion. - Fix bug in TINKER ARC reader (#1371) - Improved mdconvert error message (#1368) - Striding relative to current position in XTC and TRR (#1364) - Return last successful read frame for DCD (#1358) - Handle stride like numpy for DCDs (#1352) - Fix pickling of virtual site's element field (#1350) - Compile geometry extension with OpenMP (#1349) - Ensure correct dtype in neighborlist box vectors (#1344) - Added support for prm7 topology file extension (#1334) - Added efficient stride handling fo TRR (#1332) - Use byte offsets between frames for stride of XTCs (#1331) - Updated the calculation of chi5 (#1322, #1323) - Added testing against conda-forge channel (#1310) - Port [OpenMM bond order](openmm/openmm#1668) representation into MDTraj. Implements the `Bond` class to Topology and updates the Mol2 reader to use bond_order field (#1308)
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Adding OpenMP compiler flags to the geometry extension, fixes #1335.
Should this also be done for
format_extensions? If you grep many of the.cfiles built by cython, there is an#ifdef _OPENMP/#endifblock, but I don't see where parallelism is actually used... maybe someone more familiar with that code could comment? (@Lnaden @mpharrigan @marscher)