Files changed (1)
-This journal is about my work as a Research Associate with `Dr. Susan Allen`_ in the `Department of Earth, Ocean and Atmospheric Sciences`_ at the `University of British Columbia`_ during our sabbatical which started on 1 July 2013.
+This journal is about my work as a Research Software Engineer with `Dr. Susan Allen`_ in the `Department of Earth, Ocean and Atmospheric Sciences`_ at the `University of British Columbia`_ during our sabbatical which started on 1 July 2013.
-Changed web remote app to by run via Pyramid pserve utility but stum
mbled on entry point issue when I deployed it to the RaspPi.
+Changed web remote app to by run via Pyramid pserve utility but stumbled on entry point issue when I deployed it to the RaspPi.
Updated default namelist.domeain, namelist.lateral, and namelist.dynamics files to contain the present spin-up run values; dt=10s, 5 barotropic time steps per dt, open Johnstone Strait boundary, and lateral eddy diffusion & evd = 20 m2/s.
An email discussion with Masao@westgrid has cleared up what's going on with job run time; L5420 nodes run at about half the speed of X5675 nodes, and our jobs appear to the allocated either all L5420 or all X5675 nodes.
If we specify X5675 nodes only we'll likely wait longer in the queue than if we specify enough walltime for the job to finish on L5420 nodes.
Ran 26oct 1-core run on salish for 3.8 hours and it completed 541 time steps for a run rate of 60.7h per model day; i.e. much slower than multi-core/node runs.
Dug into array bounds error that Nancy found and concluded with Susan that it is a code smell, but not relevant to the boundary condition v-eta mixup issue.
+Created notebook to check 2.5km GEM atmospheric forcing intial test dataset from EC; found that lats/lons do not correspond to our domain location and informed Kao-Shen and Luc of the problem.
Stalled out on merge conflict handling because Jordi wants to include GUI tools but doesn't want to deal with :kbd:`[merge-tools]` config on OS/X; waiting for email thread input from other hg-list members.
-Confirmed that file annoation is the default on OS/X and Ubuntu, provided that the user does not have a merge tools specified in their config; Jordi sees different on Debian and Windows/TortoiseHg.
+Confirmed that file annotation is the default on OS/X and Ubuntu, provided that the user does not have a merge tools specified in their config; Jordi sees different on Debian and Windows/TortoiseHg.
+Resumed checking 2.5km GEM atmospheric forcing intial test dataset from EC; now with correct lats/lons.
Annotated runs with 5-day restart files in spin-up docs, and noted on the whiteboard the 7 runs that would have to be repeated to give us 5-day restart from 28Oct through 1Mar.
+Presented "Software Collaboration Tools and the Salish Sea MEOPAR Project" and it was well received.
+Transferred results of 27dec31dec spin-up run to ocean, and hard linked restart files to collection on jasper.
+Worked on flake8 cleanup of SalishSeaTools.tidetools module, and refactoring plotting functions to return figure objects instead of saving figure image files to disk.
+Met w/ Roman re: undefined references linking failure on orcinus; concluded that it is an FCM issue whereby the object library files is not created, or deleted before linking.
+Continued checking 2.5km GEM atmospheric forcing initial test dataset from EC; atmospheric pressure values are surface rather than sea level that NEMO expects.
+Attended Phys Ocgy seminar where Susan did an extended presentation of her CMOS talk on downwelling canyons.
+Finally succeeded in creating a brittle but repeatable build script for orcinus; how intel and netcdf_hdf5 modules are loaded turns out to matter too.
+Charles told me that when he updated salish to Ubuntu 14.04 a bug that was preventing TORQUE from working was resolved.
+Found that executable needs to be re-built because the version of gfortran and some other libraries has been bumped.
+The -cpp compiler flag is now required to successfully build the IO server, but that causes a failure in a comment in NEMOGCM/EXTERNAL/XMLF90/src/xpath/m_path.f90.
+Got a 5d run on orcinus initiated by :command:`salishsea run` that included gathering of results and deletion of temporary run directory; at job is not required for run directory deletion.
+Worked with Ashley on the next step of refactoring here Pa-Th model: isolation and vectorization of the advection scheme function.
+Added Hal Ritchie's CMOS slide deck, my CMOS slide deck and source files, and a collection of logo image files to private-docs repo.
+Continued checking 2.5km GEM atmospheric forcing initial test dataset from EC; added air temperature and specific humidity.
+Continued checking 2.5km GEM atmospheric forcing initial test dataset from EC; refactored plots to be 2-up, and added precipitation, and thermal & solar radiation.
+Attended MEOPAR boat cruise around Halifax harbour; talked to Rich about Python implementation or wrapper for the new sea water equation of state utilities.
+Gave talk to CCCma Python user's group about version control and Python as a tools and glue language.
+Continued work on analysis_tools notebooks; added section on streamline plots; created new notebook re: plotting velocities and tracers on vertical planes.
+Reviewed 2.5km GEM atmospheric forcing initial test dataset analysis notebook w/ Susan and Nancy and updated comments and actions.