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本帖最后由 金鹏 于 2020-6-15 07:35 编辑
core22 0.0.8 released to BETA[size=1.3em]We've now released core22 0.0.8 to BETA, which fixes two issues:
* There was some potential for being stuck in a CORE_RESTART infinite loop if a NaN occurs between step 0 and the first checkpoint interval (5% by default). This has been fixed in core22 0.0.0, which should now auto-download for beta projects (currently 13412-13413, which are also available on INTERNAL via ProjectKey=13412 or 13413). Please check if your core is stuck in an infinite CORE_RESTART loop if it has been running for a few hours and, if so, dump the WU and you'll pick up the new core22 0.0.8.
* We have disabled separate PME streams for NVIDIA hardware by default (to match core22 0.0.5; this was enabled in 0.0.6-0.0.7) until we can further debug why this has issues with some NVIDIA GPUs. core22 0.0.6-0.0.7 could cause CORE_RESTART infinite loop[size=1.3em]There was some potential for being stuck in a CORE_RESTART infinite loop if a NaN occurs between step 0 and the first checkpoint interval (5% by default). This has been fixed in core22 0.0.0, which should now auto-download for beta projects (currently 13412-13413, which are also available on INTERNAL via ProjectKey=13412 or 13413). Please check if your core is stuck in an infinite CORE_RESTART loop if it has been running for a few hours and, if so, dump the WU and you'll pick up the new core22 0.0.8.
Thanks for helping us test the new core22 releases! We're making great progress on including new features to enable more science!
~ The Chodera lab // MSKCC
Re: core22 0.0.6 released for BETA testing![size=1.3em]We've found an issue with core22 0.0.6 and are pushing out 0.0.7 with a critical bugfix now! Stay tuned.
The issue was that the final checkpointState.xml file was not being written and returned when the WU completed successfully. We'll fix our testing process to make sure we don't introduce an issue like this again in future.
Thanks everybody! core22 0.0.6 released for BETA testing![size=1.3em]We've just released core22 0.0.6 for BETA testing!
This core brings with it lots of new features and a key bugfix for AMD cards:
Features
Now built on the most up-to-date release of OpenMM: OpenMM 7.4.2
Average performance (in ns/day) is now printed out to the client log at the end of the WU.
JSON viewer frames are now written every 1% by default, and project managers can now flexibly control the viewer frame interval for each project.
Checkpoints are now written every 5% by default, and project managers can now flexibly control the checkpoint interval independent of the XTC frame write interval for each project.
Checkpoint, XTC, and viewer frame intervals are now written to client log
Adds experimental support for Intel GPUs that we'll be testing soon
Slight performance improvement on some GPUs by enabling separate PME streams by default
Please post here if you notice any issues!
Bugfixes and stability improvements
Issues causing some AMD cards (AMD RX 460/470/480/570/580/590) to fail withCODE: SELECT ALLError invoking kernel sortShortList: clEnqueueNDRangeKernel (-5)was fixed in OpenMM (openmm/openmm#2608) and included in OpenMM 7.4.2
Project managers now have control over force and energy RMSE error checking thresholds, which should allow project managers to reduce RMSE energy and force errors for large projects by setting these thresholds larger.
Fixes bugs in resuming from projects that use CustomIntegrators (like 114xx for the COVID Moonshot) and correctly rewinds globals.csv files to ensure integrity of data when core is paused/resumed
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发表于 2020-6-12 10:22:34
