Add option to cache integer data sets to disk#641

Merged

drroe merged 48 commits intoAmber-MD:masterfrom

drroe:datasetcache

Mar 12, 2019

Commits on Sep 28, 2018

DRR - Cpptraj: Test splitting DataSet_integer into memory and disk-cached versions.
Daniel R. Roe
committed
DRR - Cpptraj: Use switch statement to allocate sets instead of array, lets us introduce transparent disk caching of data sets.
Daniel R. Roe
committed
DRR - Cpptraj: Update dependencies
Daniel R. Roe
committed
DRR - Cpptraj: Get rid of DataSet_integer iterators for now - could be tricky to do with disk caching.
Daniel R. Roe
committed
DRR - Cpptraj: Change reference operator to SetElement to allow disk caching to work properly
Daniel R. Roe
committed
DRR - Cpptraj: Finish initial disk cache class for integer data set.
Daniel R. Roe
committed

Commits on Oct 1, 2018

DRR - Cpptraj: Add utility for making temporary file names that doesnt rely on tmpnam
Daniel R. Roe
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DRR - Cpptraj: Should be pure virtual.
Daniel R. Roe
committed
DRR - Cpptraj: Ensure actual temp file is removed as well.
Daniel R. Roe
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DRR - Cpptraj: Ensure definitions are ended
Daniel R. Roe
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DRR - Cpptraj: Add usediskcache command
Daniel R. Roe
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DRR - Cpptraj: Replace non-const bracket operator with SetElement
Daniel R. Roe
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DRR - Cpptraj: Add the 'onlycols' option to 1d standard data file reads.
Daniel R. Roe
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DRR - Cpptraj: Add 'title' option for gnuplot output
Daniel R. Roe
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DRR - Cpptraj: Add lifetime test with data set caching
Daniel R. Roe
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DRR - Cpptraj: Add onlycols test for 1d standard data read
Daniel R. Roe
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Commits on Oct 2, 2018

DRR - Cpptraj: When integer values are detected in standard data file read, allocate integer data set.
Daniel R. Roe
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DRR - Cpptraj: Clean up some functions
Daniel R. Roe
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DRR - Cpptraj: Protect with ifdefs
Daniel R. Roe
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DRR - Cpptraj: Revision bump. Disk caching should be fully backwards compatible.
Daniel R. Roe
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DRR - Cpptraj: Improve code docs.
Daniel R. Roe
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Commits on Oct 30, 2018

Merge branch 'master' into datasetcache
Daniel R. Roe
committed

Commits on Dec 20, 2018

Merge branch 'master' into datasetcache
Daniel R. Roe
committed

Commits on Jan 16, 2019

Commits on Feb 26, 2019

Commits on Feb 28, 2019

DRR - Cpptraj: Start implementing SizeInBytes [ci skip]
drroe
committed

Commits on Mar 12, 2019