XIOS Integration (MVP) #265
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CMake progress is good but needs some tidying. E.g. Proof of concept build is working. |
This was referenced Sep 18, 2023
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…unication, presume xios was anticipating further setup)
…it round but not necessary to proceed.
…es appropriately (ifcore already available, don't search)
nextsim build fails due to incorrect order of libraries -lxios needs to come before -lnetcdf also for gnu compiler we need -lgfortran and for intel compiler we need -lifcore TODO: Findxios in conjuction with the CMakeLists.txt needs fixing still so that it can work when xios is not installed.
I have manually changed lib ifcore to lgfortran. This will need to fixed properly for intel and gnu compiler and not hard-coded. this is a temporary fix. The order of libs is also incorrect for XIOS_LIBRARY_LIST. xios depends on netcdf so it should come second. There was an erroneous ::Xios for the constructor when creating xios_handler.
I have updated the ubuntu install and setup for XIOS and nextsimdg I have removed unnecessary packages and hopefully xios will now build.
TomMelt
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This was referenced Oct 5, 2023
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I have updated and simplified the Xios class We have methods to get/set common variables: * Calendar origin * Calendar start * Calendar timestep There are some initialization method and an isInitialized function to verify. I have simplified the string conversion string for datetime
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this PR has got stale due to significant changes since the beginning of XIOS project. This PR will be superseded by #496 . |
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Nextsim XIOS Integration
Closes #218
This is a master pull request tracking the integration of XIOS for File I/O into Nextsim DG. Some of the sub-components are being tracked by separate PRs. See the design document on the Wiki for more information on XIOS Integration.
The core functionality of XIOS is included as part of this PR as the other two components will require it.
Core XIOS functionality
Closes #293
XIOS uses a client-server model. To use XIOS we must first initialize the clients on each process (
cxios_init_client) and subsequently initialize the server (cxios_context_initialize). Here are the necessary steps to be able to setup the XIOS client & server processes.CMakeLists.txtmpi_local) (I am dependent ondoctestwith MPI support)doctestNOTE currently addressing bug in Xios class that affects the
getCalendarTimestepmethod. For now I have implemented a work around (I have now fixed this with #424 but I want to find a better solution for mpi-aware doctests).Once the essentials have been created to begin using XIOS my intention is for the development branches to be structured as follows:
Merge instructions
When development of all XIOS features is ready (#422, #421 and this PR). The plan is to merge them (in reverse order) into this branch, finally merging this branch back into
feat_mar3feat_mar3feature218_xios_io- XIOS Integration (MVP) #265xios-nextsim-data-io- XIOS Nextsim Data IO #422xios-nextsim-sync-data- XIOS Nextsim data synchronization #421Notes on XIOS
XIOSis a third party library which was designed to handle file I/O asynchronouslyXIOSrequires a configuration.xmlfile defining a calendar system to run.xmlor at runtime (see UserGuide for more info)