Custom Query (126 matches)
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| #169 | fixed | Field with attribute "once" is not correctly showed in workflow graphe | yushan | yushan | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| #189 | fixed | Hangs when attempting to use pools and services with XIOS3 generic_testcase | ymipsl | acc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Description |
A first attempt to use the new pools and service with XIOS3 (trunk) results in a deadlock which hangs until the job times out. This is reproducible with minimal changes to the generic_testcase example. Changes are based on the example given in: https://forge.ipsl.jussieu.fr/ioserver/raw-attachment/wiki/WikiStart/Coupling%20workshop-CW2023.pdf which is still the closest material that I can find to any documentation on the new concepts. Based on XIOS3 trunk@2540 with these changes:
XIOS3 has been compiled with intel compilers and intel mpi on an icelake cluster. generic_testcase.exe tests successfully with this setup using traditional, XIOS2 configuration and run with: mpiexec.hydra -print-rank-map -ppn 1 -np 13 ../bin/generic_testcase.exe but hangs (seemingly after setting up contexts) when attempted with these xml changes. alisting of the xios_client and xios-server logs is attached. It appears to be trying to work as intended but hangs. Excited by the prospect of taking control over the distribution of resources but failing miserably at this first attempt. Am I missing a key ingredient? If there isn't an obvious error then what is the best way to dig deeper? |
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| #191 | fixed | Request for information on netcdf4 chunking controls | ymipsl | acc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Description |
XIOS3 is likely to create more opportunities for single file output even from larger configurations. Without the need to post-process output, users will look to control chunking choices. There are attributes that can be set in the XML but the net result isn't obvious. This is a request for a clearer explanation of the algorithm that is used and clarification of the inheritance levels of these attributes. My confusion is best illustrated with an example. For a eORCA025 configuration (x=1440, y=1206, z=75), the default settings give chunksizes of: uos:_ChunkSizes = 1, 1206, 1440 ; uo:_ChunkSizes = 1, 3, 1206, 1440 ; for xyt and xyzt fields respectively in all output files. This is consistent with a default chunking_blocksize_target=20MB But the user may wish to have more chunks in the horizontal without increasing the vertical chunk factor. Here is what I've tried: grep chunk *.xml axis_def_nemo.xml: <axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" chunking_weight="12.0" /> axis_def_nemo.xml: <axis id="deptht300" axis_ref="deptht" chunking_weight="12.0" > axis_def_nemo.xml: <axis id="depthu" long_name="Vertical U levels" unit="m" positive="down" chunking_weight="12.0" /> axis_def_nemo.xml: <axis id="depthv" long_name="Vertical V levels" unit="m" positive="down" chunking_weight="12.0" /> axis_def_nemo.xml: <axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" chunking_weight="12.0" /> axis_def_nemo.xml: <axis id="ncatice" long_name="Ice category" unit="1" chunking_weight="1.0" /> domain_def_nemo.xml: <domain id="grid_T" long_name="grid T" chunking_weight_i="1.0" chunking_weight_j="1.0" /> domain_def_nemo.xml: <domain id="grid_T_inner" long_name="grid T inner" chunking_weight_i="1.0" chunking_weight_j="1.0"/> domain_def_nemo.xml: <domain id="grid_U" long_name="grid U" chunking_weight_i="1.0" chunking_weight_j="1.0"/> domain_def_nemo.xml: <domain id="grid_U_inner" long_name="grid U inner" chunking_weight_i="1.0" chunking_weight_j="1.0"/> domain_def_nemo.xml: <domain id="grid_V" long_name="grid V" chunking_weight_i="1.0" chunking_weight_j="1.0"/> domain_def_nemo.xml: <domain id="grid_V_inner" long_name="grid V inner" chunking_weight_i="1.0" chunking_weight_j="1.0"/> domain_def_nemo.xml: <domain id="grid_W" long_name="grid W" chunking_weight_i="1.0" chunking_weight_j="1.0"/> domain_def_nemo.xml: <domain id="grid_W_inner" long_name="grid W inner" chunking_weight_i="1.0" chunking_weight_j="1.0"/> domain_def_nemo.xml: <domain id="grid_F" long_name="grid F" chunking_weight_i="1.0" chunking_weight_j="1.0"/> domain_def_nemo.xml: <domain id="grid_F_inner" long_name="grid F inner" chunking_weight_i="1.0" chunking_weight_j="1.0"/> field_def_nemo-ice.xml: <field_group id="SBC" chunking_blocksize_target="3.0" > <!-- time step automatically defined based on nn_fsbc --> field_def_nemo-oce.xml: <field_group id="all_ocean" chunking_blocksize_target="3.0"> where the the field_group definitions are placed around all other field_group and field definitions in the respective field_def xmls. This almost works but has inconsistent results: grid_T and grid_W files: monthly means: xyt : _ChunkSizes = 1, 603, 720 ; xyzt: _ChunkSizes = 1, 3, 603, 480 ; 5 day means: xyt : _ChunkSizes = 1, 603, 720 ; grid_U and grid_V files: monthly means: xyt : _ChunkSizes = 1, 1206, 1440 ; xyzt: _ChunkSizes = 1, 1, 1206, 1440 ; 5 day means: xyt : _ChunkSizes = 1, 603, 720 ; icemod files: monthly means: xyt : _ChunkSizes = 1, 603, 720 ; xynt: _ChunkSizes = 1, 3, 603, 480 ; 5 day means: xyt : _ChunkSizes = 1, 603, 720 ; and was largely arrived at by trial and error. How exactly are the various chunking weights used to arrive at the final sizes? Any clues as to why the grid_U and grid_V chunks should end up different for the monthly means? Is my assumption, that setting the chunking_blocksize_target in an empcompassing field_group means it will be inherited by all the fields, correct? |
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