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Merge latest PIO2 master#407

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jedwards4b merged 214 commits intomasterESMCI/cime:masterfrom jayeshkrishna/pio2/latest_master_081616ESMCI/cime:jayeshkrishna/pio2/latest_master_081616Copy head branch name to clipboardAug 16, 2016

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Commits on Jan 11, 2016

• Merge pull request #4 from NCAR/master

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Commits on Mar 15, 2016

• Merge pull request #5 from NCAR/master

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Commits on Mar 18, 2016

• now duplicate MPI communicators in init_intracomm

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• added comments

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Commits on Mar 29, 2016

• free MPI group

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• Merge pull request #61 from NCAR/ejh_24

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• changes to pioperformance.F90 to support the PIO1 library.

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Commits on Apr 4, 2016

• Changes to pioperformance.F90 to get it to build and run with PIO1. Also adding the hacky makefile I built for my yelowstone work dir to build pioperf against PIO1 as an example and backup.

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• Merge pull request #62 from Katetc/master

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Commits on Apr 15, 2016

• Added a catch for NC_EINVAL errors on file opening (in this case, try plain netcdf before giving up and throwing a total error). This addresses the runtime error in test ERP_Ln9.f19_f19.FW5.yellows…

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Commits on May 4, 2016

• added documentation to iosystem_desc_t

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• changed example data size, added valgrind suppression file

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• changing in pio_file.c to support async

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• change in response to review feedback

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Commits on May 5, 2016

• Merge pull request #64 from NCAR/ejh_doc

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• Merge pull request #65 from NCAR/ejh_example_valgrind

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• Merge pull request #66 from NCAR/ejh_pio_file_async

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• changes to pioc.c to support async, also some temporary copies of code files for async development

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• removed extra index for async ncids

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• Merge pull request #67 from NCAR/ejh_async_files

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• manually merged async changes from ejh_27

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• got non-async build working

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• got async option working

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• got non-async build working again

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Commits on May 6, 2016

• got attribut put working

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Commits on May 9, 2016

• development of async inq functions

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• more inq functions working with async

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Commits on May 10, 2016

• removed some unneeded msg constants

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• added logging

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• rearranged order of functions, started to use LOG in pio_msg

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• cleaning up error handling

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Commits on May 11, 2016

• further async development

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• better error handling

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• continued development of async

  edhartnett

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• added log message

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• further development

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• further development of async

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• further development of async

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• further development of async

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• further development of async

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• further development of async

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Commits on May 12, 2016

• further async development

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• code cleanup

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• further cleanup of async code

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• further cleanup of async code

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• further cleanup of async code

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• further cleanup of async code

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• further cleanup of async code

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• further development of async code

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• further async development

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• further async development

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• further async development

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Commits on May 13, 2016

• added PIOc_inq_type

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• added PIOc_inq_type

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• further development of async get_att

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• now get_att generalized by type

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• now get_att generalized by type

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• now get_att generalized by type

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• got put_att working with async

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• further development of async code

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• further development of async code

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• moved logging code to pioc_support

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Commits on May 14, 2016

• cleaning up call to netcdf layer in PIOc_nc_async

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• cleaning up call to netcdf layer in PIOc_nc_async

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• got inq_format working with async

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• got inq_attname working with async

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• got inq_attid working for async

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• got inq_attid working for async

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• got rename_dim working

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• got rename_var working with async

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• got rename_var working with async

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Commits on May 16, 2016

• Changed Pnetcdf required version to 1.6.1 in documentation.

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• Merge pull request #6 from NCAR/master

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Commits on May 17, 2016

• fixed rename_att function for async

  edhartnett

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• more cleanup

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• continued async development

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• continued async development

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• continued async development

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• continued async development

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• continued async development

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• more async changes

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• more async changes

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• more async changes

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• more async changes

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• more async changes

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• more async changes

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• more async changes

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• more async changes

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• more async changes

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• got redef function working with async

  edhartnett

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• created internal function because pnetcdf does not have inq_type()

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• further development of async code

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• further development of async code

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• Added documentation for the Unit and Performance tests in PIO2. Fixed some of the markup on the Examples page.

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• Merge pull request #68 from Katetc/master

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Commits on May 18, 2016

• first pass at PIOc_put_vars_tc()

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• Merge branch 'master' into ejh_async2

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• put_vars with async

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Commits on May 23, 2016

• more development of async code

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• more development of async changes

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• further development of async

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• added file for varm functions

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• return error for async use with varm

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Commits on May 24, 2016

• cleaned up put_var1 functions

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• futher cleanup of var1 functions

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Commits on May 26, 2016

• got get_vars working

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• got get_var/vara working

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• got get_var1 working

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Commits on May 27, 2016

• Merge branch 'ejh_async2'

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• response to code review comments

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• clean up

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• turn on async for yellowstone

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• Merge pull request #70 from NCAR/ejh_async3

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• removed use of MPI_Comm_create_group

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Commits on May 28, 2016

• Merge pull request #71 from NCAR/ejh_async4

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Commits on May 29, 2016

• took out log statement that was causing too much output

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Commits on May 30, 2016

• took out logging statement

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Commits on May 31, 2016

• trying to fix problem with put on some platforms

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• took out use of log in fortran test

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Commits on Jun 1, 2016

• fixed error handling of MPI errors on transfer of parameter data to pio_msg

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Commits on Jun 2, 2016

• more log messages to find bug

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Commits on Jun 3, 2016

• added temporary mpi_intercomm_merge() function for MPI_SERIAL builds

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• temporarily turned off pnetcdf in test_intercomm.c

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• more logging statements

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• commented out extra declaration

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Commits on Jun 4, 2016

• changes to fix cdash tests, added logging to fortran

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• turned pnetcdf testing back on for test_intercomm.c

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Commits on Jun 6, 2016

• tryhing to isolate put problem

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• tryhing to isolate put problem

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• tryhing to isolate put problem

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• no longer run test_intercomm for serial builds

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• changed type of num_elems from size_t to PIO_Offset

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Commits on Jun 7, 2016

• more logging to try and get enddef working on caldera

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• now MPI_abort does not overwrite ret_val

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• clean up error handling

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• cleanup of error handling in file functions

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• cleanup of error handling in file functions

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• Merge pull request #72 from NCAR/ejh_test_error_handling

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Commits on Jun 8, 2016

• more logging statements to find bug

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• turned pnetcdf back on in test_intercomm

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• more log messages

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• compensate for poor handling of NULL for stride by pnetcdf

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Commits on Jun 9, 2016

• more logging

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• more logging

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• stopped faking the stride for puts

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Commits on Jun 10, 2016

• more log messages

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• working on put issue

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Commits on Jun 13, 2016

• cleanup

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• more cleanup

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• Merge pull request #74 from NCAR/ejh_cleanup4

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• breaking branch to test cdash building of branches

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• more cleanup

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• more cleanup

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• more cleanup

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• more cleanup

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• Merge pull request #75 from NCAR/ejh_cleanup6

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Commits on Jun 14, 2016

• added logging statement to debug cdash problem

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• Revert "Ejh cleanup6"

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• Merge pull request #76 from NCAR/revert-75-ejh_cleanup6

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Commits on Jun 15, 2016

• documentation and spacing cleanup

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• documentation fix

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• Merge pull request #77 from NCAR/ejh_darray1

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• starting to add darray test

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• cleanout of test_darray

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• development of darray test

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• more work on darray test

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• more work on darray test

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• more work on darray test

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Commits on Jun 16, 2016

• fixing problems when built without logging, took out unneeded msgs

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• put messages back in until async build is the only build

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• getting non-async build to work

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• Merge pull request #78 from NCAR/ejh_darray2

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Commits on Jun 20, 2016

• documentation and spacing changes

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• cleanup and documentation

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Commits on Jun 21, 2016

• Merge pull request #81 from NCAR/ejh_darray3

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• split off pio_darray_async.c

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• added test_darray_async.c for async darray testing

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• added config.h include

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• added some comments

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• more documentation changes

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• more comments, some code cleanup

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• removed some dead code, improved comments

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• minor cleanup

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• more comments

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Commits on Jun 22, 2016

• Merge pull request #84 from NCAR/ejh_darray4

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Commits on Jul 28, 2016

• Merge pull request #7 from NCAR/master

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Commits on Aug 1, 2016

• Fixed doc build for async vs. non-async builds

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• Comment and clean up

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• Merge pull request #87 from NCAR/ejh_docs

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Commits on Aug 3, 2016

• added PIOc_strerror() and test for it

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• changed signature of PIOc_strerror()

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• adding fortran interface to PIOc_strerror()

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• added test for fortran pio_strerror

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Commits on Aug 4, 2016

• Merge pull request #88 from NCAR/ejh_strerr

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Commits on Aug 10, 2016

• removed test that depended on changing netCDF error string

  

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• Merge pull request #91 from NCAR/ejh_fix_test_names

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Commits on Aug 12, 2016

• Merge pull request #8 from NCAR/master

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• Changes required for the new Hobart nag 6.1

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• Merge pull request #92 from Katetc/master

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• Changes required for nightly cdash to work with new Hobart and Nag 6.1

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• Merge pull request #93 from Katetc/master

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Commits on Aug 16, 2016

• Merge branch 'ParallelIO_branch' (PIO2 master)

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