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Some \"_\" formatting was changed to simply \"_\" where the backslash wasn't needed in ug_implementation.rst.\r\n\r\nSeveral namelist settings were tested to make sure the model would abort with identical filenames including the case where a time averaged file with output at each timestep conflicts with an instantaneous history stream of lower output frequency.","shortMessageHtmlLink":"Add checks that individual history streams have unique filenames (#943)"}},{"before":"22097493a8600c9ca7b20960ed1df9af67308084","after":"12dd204349090058a66715163932ae3243f9632c","ref":"refs/heads/main","pushedAt":"2024-03-22T22:48:20.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"apcraig","name":"Tony Craig","path":"/apcraig","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8182814?s=80&v=4"},"commit":{"message":"Port to Carpenter intel and gnu with intel mpi instead of cray-mpich (#942)","shortMessageHtmlLink":"Port to Carpenter intel and gnu with intel mpi instead of cray-mpich (#…"}},{"before":"740f2a65e055e37bebc81aa25675ebc2a65d735d","after":"22097493a8600c9ca7b20960ed1df9af67308084","ref":"refs/heads/main","pushedAt":"2024-03-20T19:13:48.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"apcraig","name":"Tony Craig","path":"/apcraig","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8182814?s=80&v=4"},"commit":{"message":"Add a new diagnostic variable dvsdtd. 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(#940)"}},{"before":"9f30120897f7e27178c7e99357efd47d09923bee","after":"740f2a65e055e37bebc81aa25675ebc2a65d735d","ref":"refs/heads/main","pushedAt":"2024-02-29T20:32:52.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"apcraig","name":"Tony Craig","path":"/apcraig","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8182814?s=80&v=4"},"commit":{"message":"Port to Carpenter (#939)\n\nPort CICE to Carpenter for intel, cray, and gnu compilers with mpich. Will add weekly testing on Carpenter, Onyx was recently decommissioned.\r\n\r\nDuring development,\r\n\r\n- It was discovered that the serial compilers and parallel compilers produce different results. This was reported to sys admins. Serial compilation is done with the parallel compilers to ensure bit-for-bit results with serial and mpi comm versions.\r\n- It was discovered that the openmpi and intel mpi options are not working properly. This was reported to sys admins. All testing is done with mpich for now.","shortMessageHtmlLink":"Port to Carpenter (#939)"}},{"before":"1a530ec749028c7abbab44b3c83b9f9d9475ad60","after":"9f30120897f7e27178c7e99357efd47d09923bee","ref":"refs/heads/main","pushedAt":"2024-02-28T21:20:49.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"apcraig","name":"Tony Craig","path":"/apcraig","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8182814?s=80&v=4"},"commit":{"message":"Set 'idate0' and 'use_leap_years' in nuopc cap (#936)\n\nSet idate0 in nuopc cap, so that the history \"time:units\" attribute in netcdf output is consistent with other model components.\r\n\r\nSet use_leap_years in nuopc cap, so that netcdf output \"time:calendar\" is set correctly in history output\r\n\r\nCo-authored-by: Denise Worthen ","shortMessageHtmlLink":"Set 'idate0' and 'use_leap_years' in nuopc cap (#936)"}},{"before":"64177e3e5658711f5f19030ddfcc6927f1dbda5d","after":"1a530ec749028c7abbab44b3c83b9f9d9475ad60","ref":"refs/heads/main","pushedAt":"2024-02-28T21:17:00.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"apcraig","name":"Tony Craig","path":"/apcraig","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8182814?s=80&v=4"},"commit":{"message":"Typo in nmode0 in PIO for CESM_COUPLED (#938)\n\nFor CESMCOUPLED, the pio_iotype is set though CMEPS. For completeness, we also need to check the ioformat set through CMEPS. ioformat is used to set the nmode0. nmode0 and clobber combine to set the nmode flag for pio_createfile / pio_openfile operations. Due a typo nmode0 was not being set for netcdf4 iotypes (before this change).","shortMessageHtmlLink":"Typo in nmode0 in PIO for CESM_COUPLED (#938)"}},{"before":"aca835755aa82ead50040ea7e43ec63619667054","after":"64177e3e5658711f5f19030ddfcc6927f1dbda5d","ref":"refs/heads/main","pushedAt":"2024-02-23T00:46:22.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"apcraig","name":"Tony Craig","path":"/apcraig","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8182814?s=80&v=4"},"commit":{"message":"io: allow disabling coordinates in history files (#935)\n\n* ice_history_shared: add namelist flags for coordinate variables\r\n\r\nUsers might not wish for all 8 coordinate variables to be written to\r\neach history file, so add namelist flags allowing to disable each\r\ncoordinate variable independantly, following the approach used for the\r\nother grid variables. Move the definition of 'ncoord' from each IO\r\nbackend to 'ice_history_shared'. Note that we already 'use' the whole of\r\nice_history_shared in ice_history_write, so we do not need to adjust the\r\nuse statement.\r\n\r\nNote that the code that writes these variables in module\r\n'ice_history_write' in each of the IO backends is not modified, it will\r\nbe adjusted in a following commit.\r\n\r\n* io_{netcdf,pio2}/ice_history_write: define coordinates attributes in a loop\r\n\r\nIn ice_history_write::ice_write_hist, we initialize the 'var_coord' and\r\n'coord_bounds' arrays by manually incrementing 'ind' and initializing\r\neach elements with the corresponding information for each coordinate\r\nvariable. The rest of the code in that subroutine instead uses a loop on\r\n'ncoord', which is a parameter holding the number of coordinates\r\nvariable, along with 'select' statements.\r\n\r\nThe latter approach is more elegant and also more flexible if we change\r\nthe number of coordinates variables. Refactor the code to use a loop and\r\nleverage the integers n_{u,t,n,e}{lon,lat} added in the previous commit,\r\nin both io_netcdf and io_pio2, which have identical code in this part of\r\nthe subroutine.\r\n\r\n* io_{netcdf,pio2}/ice_history_write: use namelist flags for coordinate variables\r\n\r\nIn order to enable the namelist flags for each coordinate variables\r\nadded in the previous commit, adjust the code of the io_netcdf and\r\nio_pio2 backends by checking the value of 'icoord(i)' for each loop on\r\n'ncoord' that calls NetCDF or PIO functions.\r\n\r\nAdd the new flags to the reference namelist.","shortMessageHtmlLink":"io: allow disabling coordinates in history files (#935)"}},{"before":"9e9e5b3fabd88c429c4632baa8235187129e2dd7","after":"aca835755aa82ead50040ea7e43ec63619667054","ref":"refs/heads/main","pushedAt":"2024-02-22T16:55:44.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"apcraig","name":"Tony Craig","path":"/apcraig","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8182814?s=80&v=4"},"commit":{"message":"Update IO formats and add new IO namelist controls (#928)\n\nThis provides new features for CICE IO both thru netCDF and PIO. New namelist are added to control history and restart format, hdf5 compression and chunking, the PIO rearranger, and PIO IO task control. Separate controls are provided for history and restart files. The namelist changes are for\r\n\r\n _history_format, restart_format\r\n history_rearranger, restart_rearranger\r\n history_iotasks, history_root, history_stride, restart_iotasks, restart_root, and restart_stride\r\n history_chunksize, history_deflate, restart_chunksize, restart_deflate._\r\n\r\nIn particular,\r\n\r\n- Update restart_format and history_format options to 'cdf1', 'cdf2', 'cdf5', 'hdf5', 'pnetcdf1', 'pnetcdf2', 'pnetcdf5', 'default'. The old options, 'default', 'pio_netcdf', and 'pio_pnetcdf' are still supported and backwards compatible with lcdf64, but are deprecated and no longer documented. The old options and old namelist lcdf64 are covered by the new options. Support of the old options should be removed in the future. Note that some problems were discovered when opening files with hdf5 format but reading non-hdf5 files with a spack built PIO/netCDF. As a result, the format specified for the restart read is always 'cdf1' which provides flexibility and robustness across software installs, although it may result in serial reads of hdf5 files when a parallel read could be done.\r\n- Deprecate lcdf64 namelist. This namelist is no longer needed and is covered by the new restart_format and history_format options. The namelist still exists and is backwards compatible with the old 'default', 'pio_netcdf', and 'pio_pnetcdf' format options, but is no longer documented. This should be removed in the future.\r\n- Add new namelist to control PIO pe/task setup (iotasks, root, stride) for history and restart. These settings control the PIO IO tasks. The root, stride, and iotasks are consistent with the MPI communicator. root=0 is the first MPI task. These control PIO IO performance and are usually a function of things like the IO and node hardware. See PIO for more information. CICE computes PIO iotask, root, and stride defaults for cases where -99 is passed in for some or all of these namelist. Those defaults are somewhat constrained by a bug in PIO, https://github.com/NCAR/ParallelIO/issues/1986. The current implementation avoids the bug by limiting the iotasks for some MPI task counts. This is noted in ice_pio.F90.\r\n- Add new namelist to control PIO rearranger (rearranger) for history and restart. Supports 'box', 'subset', and 'default'. These control how PIO rearrangment is carried out. default is equivalent to box and the box generally performs better. See PIO for more information.\r\n- Add new namelist to support hdf5 compression and chunking (deflate, chunksize) for history and restart. The deflate controls file compression and is an integer between 0 and 9 where 0 means no compression and 9 is maximum compression. Generally, the higher the number, the slower the IO and the smaller the file, but the optimal setting depends on the contents of the file. Chunksize provides a performance control for the hdf5 parallel writes. It is a 2d array and is associated with the size of the piece of the array written by hdf5. hdf5 can be read and written in parallel, but that depends on how netCDF and PIO are built. Note that prior version of PIO, including PIO1, do not support the hdf5 compression and chunking thru the PIO interface.\r\n- Add new namelist settings (set_nml files) and update the io_suite to cover the new IO options. Remove old namelist settings associated with the deprecated format options and the lcdf64 namelist. These deprecated feature are no longer tested.\r\n- Update documentation to add new namelist and IO features.\r\n- Update the nuopc/cmeps driver code to support the new features.\r\n- Update the default ice_in to add the new namelist.\r\n- Update the derecho netcdf module to a version that supports hdf5.\r\n- Clean up some code formatting (indentation)\r\n\r\n---------\r\n\r\nCo-authored-by: Anton Steketee ","shortMessageHtmlLink":"Update IO formats and add new IO namelist controls (#928)"}},{"before":"095e62a9342df74261b90fcb7a20d2ecdae2c5bc","after":"9e9e5b3fabd88c429c4632baa8235187129e2dd7","ref":"refs/heads/main","pushedAt":"2024-02-19T19:08:37.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"apcraig","name":"Tony Craig","path":"/apcraig","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8182814?s=80&v=4"},"commit":{"message":"ug_testing.rst: also mention checking the base suite results (#934)\n\nIn the \"End-To-End Testing Procedure\" section of the user guide, we\r\ninstruct users to run a base suite and a test suite, but only mention\r\nchecking the results of the test suite.\r\n\r\nAlso mention checking the results of the base suite first, to make sure\r\neverything passes before checking the test suite.\r\n\r\nSuggested-by: Jean-Francois Lemieux ","shortMessageHtmlLink":"ug_testing.rst: also mention checking the base suite results (#934)"}},{"before":"1a00e5e4e967c8429a7753ac3597f9c1476cf6b7","after":"095e62a9342df74261b90fcb7a20d2ecdae2c5bc","ref":"refs/heads/main","pushedAt":"2024-02-12T22:49:03.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"apcraig","name":"Tony Craig","path":"/apcraig","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8182814?s=80&v=4"},"commit":{"message":"Update PULL_REQUEST_TEMPLATE to request detailed information (#931)\n\nUpdate PULL_REQUEST_TEMPLATE to request detailed information about changes associated with the PR. 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