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fix executable permission issue of python analysis scripts for post-processing #25
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Having just closed #4, the suggestions made there would fix this issue? |
adcroft
added a commit
that referenced
this issue
Oct 23, 2017
- Merging PR from NCAR onto MOM6:dev/master - No answer or output changes - NOAA-GFDL/MOM6@b85463d Merge branch 'NCAR-dev/ncar' into dev/master - NOAA-GFDL/MOM6@398bf5c Merge pull request #32 from gustavo-marques/delete_unecessary_changes - NOAA-GFDL/MOM6@0e92dfa Delete unecessary changes - NOAA-GFDL/MOM6@ba919f9 Merge pull request #31 from gustavo-marques/remove_surf_forcing - NOAA-GFDL/MOM6@63c7786 Removes dependencies from modules in coupled_driver - NOAA-GFDL/MOM6@8efe390 Makes ocn_comp_mct independent of MOM_surface_forcing - NOAA-GFDL/MOM6@f955f3f Merge pull request #30 from gustavo-marques/issue29 - NOAA-GFDL/MOM6@01bcdec Changes the path of restart files - NOAA-GFDL/MOM6@725df7d Fix calculation of SSH slopes - NOAA-GFDL/MOM6@32916a0 Merge pull request #28 from gustavo-marques/fix_latent_heat_flux - NOAA-GFDL/MOM6@eda526e Revert temporary changes in ocean_model_MOM.F90 - NOAA-GFDL/MOM6@a748f96 Commented SSH slopes using PLM - NOAA-GFDL/MOM6@4328d92 Merge pull request #27 from alperaltuntas/fixRestartTiming - NOAA-GFDL/MOM6@8c67204 Adds option to pass latent heat flux via IOB - NOAA-GFDL/MOM6@e734271 Fixed initial time for cont'd runs. Implemented ocn.log file - NOAA-GFDL/MOM6@64905d5 Merge pull request #26 from gustavo-marques/read_restart - NOAA-GFDL/MOM6@f14d664 Reads a restart file using the ocn rpointer file - NOAA-GFDL/MOM6@2733fd2 writes name of restart file in ocn rpointer file - NOAA-GFDL/MOM6@5ecf3bc Writes restart files using CESM convention - NOAA-GFDL/MOM6@69f5ac7 Separates ocn_comp_mct from ocean_model_mod - NOAA-GFDL/MOM6@d043f87 Deletes public declaration for get_state_pointers - NOAA-GFDL/MOM6@09fa6c3 Deletes get_state_pointers from ocean_model_MOM, its no longer needed there - NOAA-GFDL/MOM6@5a9693f Merge pull request #25 from adcroft/extend-restart-options - NOAA-GFDL/MOM6@aa62808 Allows coupled driver to specify restart file - NOAA-GFDL/MOM6@07d0f36 Fix initialization of namelist parameters - NOAA-GFDL/MOM6@a96c4dd Doxygenized MOM_get_input.F90 - NOAA-GFDL/MOM6@611cfca Merge branch 'dev/master' into dev/ncar - NOAA-GFDL/MOM6@1d5b15a Merge pull request #24 from gustavo-marques/isomip_fixes - NOAA-GFDL/MOM6@44bd09b Corrects axis types for outputs in the ice_shelf module - NOAA-GFDL/MOM6@67c6668 Fixes inequality sign to avoid division by zero
marshallward
added a commit
that referenced
this issue
Apr 14, 2021
- NOAA-GFDL/MOM6@fc75e0fa4 Merge pull request #1370 from Hallberg-NOAA/F_case_file_output - NOAA-GFDL/MOM6@e8e8abab9 Merge remote-tracking branch 'hallberg/F_case_file_output' into F_case_file_output - NOAA-GFDL/MOM6@96f1d1e89 Use allocatable types in write_ocean_geometry_files - NOAA-GFDL/MOM6@983824a69 Merge branch 'dev/gfdl' into F_case_file_output - NOAA-GFDL/MOM6@5fe51b18e Merge pull request #1369 from Hallberg-NOAA/SIS2_IO_upgrades - NOAA-GFDL/MOM6@0eb47b25a +More consistent treatment of input_filename = 'F' - NOAA-GFDL/MOM6@03b997b88 +Enhanced support for novel axes in MOM_io - NOAA-GFDL/MOM6@7ec08cd9b Merge pull request #1365 from marshallward/corad_vec_v2 - NOAA-GFDL/MOM6@dc66dd8a7 Merge branch 'dev/gfdl' into corad_vec_v2 - NOAA-GFDL/MOM6@c5c74419d Merge pull request #1364 from jkrasting/downsampled_diag_fix - NOAA-GFDL/MOM6@a5fb36503 Merge branch 'dev/gfdl' into downsampled_diag_fix - NOAA-GFDL/MOM6@d485a5123 Merge pull request #1363 from Hallberg-NOAA/SIS2_infra_support - NOAA-GFDL/MOM6@b413f25c5 Merge branch 'SIS2_infra_support' of github.com:Hallberg-NOAA/MOM6 into SIS2_infra_support - NOAA-GFDL/MOM6@358da7cc4 Corrected comments describing CT_copy_data - NOAA-GFDL/MOM6@ad0bc3c41 Merge branch 'dev/gfdl' into SIS2_infra_support - NOAA-GFDL/MOM6@fae570d0a Merge branch 'main' into main_to_gfdl - NOAA-GFDL/MOM6@5f063044c Fixed downsampling summation for more diag types - NOAA-GFDL/MOM6@c549ae9d9 Merge pull request #1358 from NOAA-GFDL/dev-gfdl-main-candidate-2021-03-26 - NOAA-GFDL/MOM6@ad372fdc2 Merge branch 'dev/gfdl' into SIS2_infra_support - NOAA-GFDL/MOM6@d1dc6b5ba Coriolis: Improved coradcalc vectorization - NOAA-GFDL/MOM6@2b6d3e115 Merge pull request #1362 from marshallward/horvisc_diag_to_stack - NOAA-GFDL/MOM6@9792b2346 Fixed downsampling for x:sum y:point z:point diags - NOAA-GFDL/MOM6@665cd9a3b Merge branch 'dev/gfdl' into horvisc_diag_to_stack - NOAA-GFDL/MOM6@b6c7fdb02 change default value of use_mommesh as true - NOAA-GFDL/MOM6@6d4a48390 Merge pull request #1360 from Hallberg-NOAA/fewer_timelevels - NOAA-GFDL/MOM6@3c1cb2efd +Add MOM_domains interfaces needed by SIS2 - NOAA-GFDL/MOM6@cfa59aab1 +Add coupler_types interfaces needed by SIS2 - NOAA-GFDL/MOM6@97f111779 Merge branch 'dev/gfdl' into fewer_timelevels - NOAA-GFDL/MOM6@813fc7975 Merge pull request #1359 from Hallberg-NOAA/FMS2_io_writes - NOAA-GFDL/MOM6@2ffea27be MOM_hor_visc: Variables moved to stack - NOAA-GFDL/MOM6@4fd380747 Merge branch 'dev/gfdl' into FMS2_io_writes - NOAA-GFDL/MOM6@c62d51f9d Remove inappropriate timelevel arguments - NOAA-GFDL/MOM6@13f1e70f5 Merge pull request #1356 from GEOS-ESM/bugfix/sanAkel/output-b-grid-currents - NOAA-GFDL/MOM6@6c2b944e2 Merge branch 'dev/gfdl' into bugfix/sanAkel/output-b-grid-currents - NOAA-GFDL/MOM6@67b03e324 Merge pull request #1353 from Hallberg-NOAA/less_checksums - NOAA-GFDL/MOM6@5669d4360 Merge branch 'dev/gfdl' into less_checksums - NOAA-GFDL/MOM6@b044be8ee Merge branch 'dev/gfdl' into FMS2_io_writes - NOAA-GFDL/MOM6@fe9b2a106 Merge pull request #1352 from Hallberg-NOAA/FMS2_io - NOAA-GFDL/MOM6@f6105cb22 Merge branch 'dev/gfdl' into FMS2_io - NOAA-GFDL/MOM6@95ad9372b Fix distributed reads of checksums using FMS2_io - NOAA-GFDL/MOM6@81c48cbf6 Merge pull request #5 from marshallward/FMS2_io_writes - NOAA-GFDL/MOM6@ba643bde2 Explicit domain decomposition of horizontal axes - NOAA-GFDL/MOM6@7bdecbc62 Add missing ".nc" to FMS2 output filenames - NOAA-GFDL/MOM6@fad7e0d4a Merge branch 'dev/gfdl' into bugfix/sanAkel/output-b-grid-currents - NOAA-GFDL/MOM6@17afc2b5e A call to pass_vector(...) is needed to correctly do a halo exchange before getting currents in A- or B-grid staggering. Now added. - NOAA-GFDL/MOM6@3fe07d4c6 +Move FMS2 read helper routines into MOM_io_infra - NOAA-GFDL/MOM6@2579d0771 Merge pull request #4 from gustavo-marques/less_checksums_mct_nuopc - NOAA-GFDL/MOM6@66ac81057 Only write checksums from root PE MCT/NUOPC caps - NOAA-GFDL/MOM6@84d5e2176 +FMS2 reads for ints & MOM_read_data_fms2 cleanup - NOAA-GFDL/MOM6@4843c6c4d Merge branch 'dev/gfdl' into FMS2_io - NOAA-GFDL/MOM6@03e174e14 Removed FMS2 MOM_axis and MOM_write_field_fms2 - NOAA-GFDL/MOM6@255233ba3 Added code to write via FMS2 interfaces - NOAA-GFDL/MOM6@0fdc5c438 Correct warnings from categorize_axis - NOAA-GFDL/MOM6@f89ddeaa8 +Add edge_axis argument to write_metadata_axis - NOAA-GFDL/MOM6@ee0152f26 +Separate MOM_interp_infra axistype from MOM_io - NOAA-GFDL/MOM6@09173f7dc Only write checksums from root PE for FMS_cap - NOAA-GFDL/MOM6@30b057116 Merge branch 'dev/gfdl' into FMS2_io - NOAA-GFDL/MOM6@91232095d Merge branch 'dev/gfdl' into FMS2_io - NOAA-GFDL/MOM6@aab2ad645 +Add ability to read fields via FMS2 interfaces - NOAA-GFDL/MOM6@23a78d2f6 Clean up in MOM_restart.F90 - NOAA-GFDL/MOM6@c68fedfea +Change arguments to MOM_register_variable_axes - NOAA-GFDL/MOM6@0ba1aa53e +Simplified read_data_fms2 and write_field_fms2 - NOAA-GFDL/MOM6@f2459ec21 Merge branch 'user/jml/add_fms2io_to_MOM_restart' of https://github.com/wrongkindofdoctor/MOM6 into FMS2_io - NOAA-GFDL/MOM6@a07757314 Explicitly set (1x1) io_domain as a default - NOAA-GFDL/MOM6@d4531ca37 Duplicated infra/FMS1 into infra/FMS2 - NOAA-GFDL/MOM6@f806579bc Correct module use statements in infra/FMS1 - NOAA-GFDL/MOM6@2e46ea6d7 removed errant .true. in save_restart call - NOAA-GFDL/MOM6@809b3ac52 added local logical variables to save restart wrapper that are set using the use_fms2 and write_ic flags if present to avoid invalid memory reference error added str_len argument to register_variable_attribute calls - NOAA-GFDL/MOM6@a74c7eaba changed FMS release to 2020.03-beta1 - NOAA-GFDL/MOM6@5c2daa5da converted save_restart and restore_state to interface that call versions of the routines with the fms-io or fms2-io interfaces added module use statments for fms2_io and MOM_io helper routines to MOM_restart added use_fms2=.true. arguments to save_restart and restore_state calls added write_ic=.true. to the save_restart call in MOM.F90 - NOAA-GFDL/MOM6@40047fa50 Merge pull request #66 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@c8695c621 Merge pull request #65 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@0cf3cb9c9 Merge pull request #64 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@de7f95a57 Merge pull request #63 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@50c353935 Merge pull request #62 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@cbdcf8a52 Create hola_tierra.yml - NOAA-GFDL/MOM6@763b17650 Merge pull request #61 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@ff3412651 Merge pull request #60 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@cea55fec4 Merge pull request #59 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@b8eee455f Merge branch 'dev/gfdl' of github.com:NOAA-GFDL/MOM6 into dev/gfdl - NOAA-GFDL/MOM6@46b8f0fd5 Merge pull request #58 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@ff1a27f59 Merge pull request #57 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@496617cb1 Merge pull request #56 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@e9281f40e Merge pull request #55 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@4a5613400 Merge pull request #54 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@86c2a7dfa Merge pull request #53 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@c24535733 Merge pull request #52 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@8d7be6866 Merge pull request #51 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@7adcc9037 Merge pull request #50 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@aff2a13ab Merge pull request #49 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@477d9f85d Merge pull request #48 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@cee0a2166 Merge pull request #47 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@12dccaf8a Merge pull request #46 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@7dbca83ff Merge pull request #44 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@162ca970b Merge pull request #43 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@abaf004cb Merge pull request #42 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@075ab81e5 Merge pull request #41 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@e072bc7cc Merge in latest dev/gfdl updates (#40) - NOAA-GFDL/MOM6@cae4cfd05 Merge branch 'dev/gfdl' of github.com:wrongkindofdoctor/MOM6 into dev/gfdl - NOAA-GFDL/MOM6@ece60c11e Merge branch 'NOAA-GFDL-dev/gfdl' into dev/gfdl - NOAA-GFDL/MOM6@3e27e4793 Merge branch 'dev/gfdl' of git://github.com/NOAA-GFDL/MOM6 into NOAA-GFDL-dev/gfdl - NOAA-GFDL/MOM6@59109032e Merge pull request #38 from wrongkindofdoctor/revert-37-dev/gfdl - NOAA-GFDL/MOM6@3c15a0c11 Revert "Merge in dev/gfdl updates (#37)" - NOAA-GFDL/MOM6@855d7069d Merge in dev/gfdl updates (#37) - NOAA-GFDL/MOM6@2c32568b7 merge in latest dev/gfdl updates (#36) - NOAA-GFDL/MOM6@09bcebcfe Merge pull request #35 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@124a071e4 Merge pull request #33 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@a427676bd Merge pull request #32 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@0b874f32c Merge pull request #31 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@a5386da98 Merge pull request #30 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@5b2852cde Merge pull request #28 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@22c586562 Merge pull request #27 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@f9b5a7fca Merge pull request #26 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@577208343 Merge pull request #25 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@5589d8cc3 Merge pull request #24 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@aa11e1f66 Merge pull request #23 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@b5e5c48a6 Merge pull request #22 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@911d0a240 Merge pull request #21 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@601eb679c Merge pull request #20 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@b4fd53be9 Merge pull request #19 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@f6879f425 Merge pull request #18 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@139ab1fc0 Merge pull request #17 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@a0c80dcf3 Merge pull request #16 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@42cca4f46 Merge pull request #15 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@a1c556b7f Merge pull request #14 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@f5bc54b67 Merge pull request #13 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@6ffc8976f Merge pull request #12 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@30d35a3c6 Merge pull request #11 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@1304880fb Merge pull request #10 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@522069b31 Merge pull request #9 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@1bbc8de13 Merge pull request #8 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@9aa2aaeb1 Merge pull request #7 from NOAA-GFDL/dev/gfdl - NOAA-GFDL/MOM6@b7f50fcbf Merge remote-tracking branch 'GFDL_MOM6/dev/gfdl' into dev/gfdl merge in latest MOM updates * GFDL_MOM6/dev/gfdl: (220 commits) Update cache dir for /lustre/f2 Update cache dir for /lustre/f2 Calculate height-related diagnostics in Z Set coord_adapt and coord_slight parameters in H Corrected comments in build_zlike_column +Pass max_depth to initialize_regridding in Z Corrected comments in build_sigma_column Combined scaling factors in build_adapt_column Clarified comments in Idealized_Hurricane +Recast MOM_diag_to_Z to work in units of Z +Recast MOM_ALE_sponge to work in units of Z +Added m_to_Z arg to horiz_interp_and_extrap_tracer Find energetic_PBL column height changes in Z +Find diapyc_energy_req column height changes in Z Use local variables to rescale in MOM_Point_Accel Recast MOM_sum_output to work in units of Z Simplify MOM_diagnostics code +Rescale depth inside of MEKE_lengthScales_0d +Add conversion argument to register_static_field Rescale values reported by PointAccel ... - NOAA-GFDL/MOM6@975262dc9 Merge pull request #5 from NOAA-GFDL/dev/gfdl
marshallward
added a commit
that referenced
this issue
Dec 10, 2021
- NOAA-GFDL/MOM6@ec553aa93 +Obsolete ETA_TOLERANCE_AUX - NOAA-GFDL/MOM6@3f46b6a7f +Set find_salt_root if SHELF_THREE_EQN = .False. - NOAA-GFDL/MOM6@8b5c1c87f Deallocate eta_PF_start to avoid a memory leak - NOAA-GFDL/MOM6@833cd3010 +Remove clocks inside of j-loops - NOAA-GFDL/MOM6@e2c81e916 +Rescale forcing arguments and revise ctrl_forcing (#25) - NOAA-GFDL/MOM6@5f21667f0 +Rescale fluxes%net_mass_src and other diagnostics (#23) - NOAA-GFDL/MOM6@c0be5d3d3 Use post_product_u for momentum budget diagnostics - NOAA-GFDL/MOM6@e756a69d5 +Add post_product_[uv] and post_product_sum_[uv] - NOAA-GFDL/MOM6@649485287 Code cleanup in drivers/solo_driver forcing files - NOAA-GFDL/MOM6@d7167453e Testing: Codecov uploader update - NOAA-GFDL/MOM6@ceb181f22 Fix out-of-bounds k index in PPM flux - NOAA-GFDL/MOM6@f67e03064 Cleaned up whitespace leftover from porous topomerge. - NOAA-GFDL/MOM6@a0248ef23 Minor code cleanup in drivers/FMS_cap - NOAA-GFDL/MOM6@e218478b9 Expanded comments describing src/core code (#13) - NOAA-GFDL/MOM6@359743314 Bug fix for reading First_direction from restart - NOAA-GFDL/MOM6@13a1cde09 +Rescaled flux arguments to tracer_vertdiff() - NOAA-GFDL/MOM6@111b3e7e6 +Eliminate forcing%netSalt - NOAA-GFDL/MOM6@6c01c8d65 (*)Refactored and fixed pseudo_salt_tracer code
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When an experiment starts on gaea the whole mom6/ directory (minus .datasets) is g-copied to gfdl /nbhome/$USER for PP.
But gcp does not preserve the (x-) permissions of the files. Hence when analysis scripts are called we get a permissions error like this:
/nbhome/Bonnie.Samuels/ulm_vanilla_dev_awg_mom6_2015.04.20/CM4_c96L48_am4f4_2000/mom6/tools/analysis/EddyKineticEnergy.py -g 00050101.ocean_static.nc -o /nbhome/Bonnie.Samuels/ulm_vanilla_dev_awg_mom6_2015.04.20/CM4_c96L48_am4f4_2000/refineDiag_ocean_annual/ocean_00050101/EddyKineticEnergy -l 00050101 00050101.ocean_daily.nc
/nbhome/Bonnie.Samuels/ulm_vanilla_dev_awg_mom6_2015.04.20/CM4_c96L48_am4f4_2000/mom6/tools/analysis/EddyKineticEnergy.py: Permission denied.
I suggest to add a "python " keyword before calling a python script in any caller shell script to avoid this.
The list of existing caller scripts is:
mom6/tools/analysis/MOM6_refineDiag.csh
mom6/ice_ocean_SIS/OM4_025/ocn_annual.frepp
mom6/ice_ocean_SIS/OM4_025/ocn_annual_z.frepp
mom6/ice_ocean_SIS/OM4_025/ocn_monthly.frepp
The workaround to this issue before it is solved is to do the following as part of the pp.starter (this is how the issue is currently avoided)
chmod -R +x mom6/
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