GCHP v11-02

Version Mapping and Status

The table below maps GEOS-Chem versions and status with the compatible versions of the high performance option (GCHP) and unit tester (UT). Unless otherwise specified, all versions appear as git tags within the master branches of the repositories linked to in the table heading.

GCHP	GEOS-Chem	UT	Download Status	Validation History	Notes
hp_v1.1.0	v11-02b	v11-02b	Not yet available	Formal 1-month benchmark in progress (v11-02b)	First formal benchmark of HP option
hp_v1.0.0	v11-01_public	v11-01_public	Recommended	Internal benchmark completed April 2017	Requires GEOS-Chem and UT branches GCHP_master

New Features in this Version

HP v1.1.0

This version will be included in the 1-month benchmark of GEOS-Chem v11-02b. Please see the approval form for the 1-month benchmark simulation v11-02b with high performance option (GCHP) for complete information on validation of this version.

Feature	Submitted by	Type	Status
Features affecting the full-chemistry simulation:
Enable compiling GCHP with the gfortran compiler	Seb Eastham (Harvard)	Structural	Pending benchmark approval
Update handling of the species restart file: Allow omission of advected species from the restart file Add option to skip use of a species restart file and initialize all species concentrations from the species database	Lizzie Lundgren (GCST)	Structural	" "
Apply updates for changes introduced in GEOS-Chem v11-02a Enable usage of day-of-week scale factors Updates to changes in Input_Opt variables	Seb Eastham (Harvard) Lizzie Lundgren (GCST)	Structural	" "

HP v1.0.0

GEOS-Chem with HP v1.0.0 is a preliminary version of the HP option in GEOS-Chem. It did not undergo a formal benchmark review by the GEOS-Chem Steering Committee. Please see GEOS-Chem v11-01 HP validation wiki page for information about the internal benchmark of this version performed by the GCHP Development Team.

Feature	Submitted by	Type	Status
Features affecting the full-chemistry simulation:
Initial version for validation of scientific fidelity	Mike Long (GCST) Seb Eastham (Harvard) Jiawei Zhuang (Harvard) Bob Yantosca (GCST) Lizzie Lundgren (GCST)	General	Internal benchmark complete (April 2017)

In the pipeline

Feature	Submitted by	Type	Status
On hold

Validation

In this section we provide information about the benchmarks and tests that we have done to validate the high performance option of GEOS-Chem v11-02.

1-month and 1-year benchmarks

For complete information about the benchmark simulations used to validate GEOS-Chem v11-02, please see our GEOS-Chem v11-02 benchmark history wiki page.

Unit tests

We currently do not perform unit tests on high performance GEOS-Chem.

Previous HP issues now resolved in GEOS-Chem v11-02

Day-of-week read-in is now possible

Seb Eastham (Harvard) implemented an update in MAPL to allow use of day-of-week scale factors with emissions. He wrote:

Data which varies by day-of-the-week can now be read in. Such data must be contained within a single file, and must have exactly 7 or 84 time entries. If 7 entries, these must correspond to each day of the week, starting with Sunday. If 84, this must be 12 7-day sets, one set for each month. Time information will be largely ignored. This read-in mode can be selected by specifying "D" for the "Cyclic" flag in ExtData.

--Lizzie Lundgren (talk) 20:26, 12 June 2017 (UTC)

Implementation of GFortran compiler options

Seb Eastham (Harvard) implemented updates to enable compilation of the high performance option of GEOS-Chem with GFortran. He wrote:

Modifications to makefiles required for the build process to recognize, and correctly handle, the use of GCC as the only compiler. This set up was tested with GCC 5.4.0. The code was successfully compiled and run with MVAPICH2, and included the bug fixes in the next few commits:

• The species identification routine in gchp_utils fails if "EOF" is reported from read_one_line, but EOF is never set. This has been fixed.
• GC_F_INCLUDE is now only added to the "INC_NETCDF" variable if it is defined. Previously it was added once, and then again if defined, resulting in it being added twice.
• The State_Met field MOLENGTH was being populated even when the array had not been allocated. This behavior resulted in a segfault with GFortran.
• The default LUN for log writing is 700 in the code, but can be overwritten from the input directory. However, if the user selects LUN 6, this can cause problems, as units 5 and 6 are reserved for STDIN and STDOUT. ifort seemed to be able to cope but GFortran would die with mysterious errors. To prevent this, the code now stops if the user tries to select either of these LUNs.

--Lizzie Lundgren (talk) 20:31, 12 June 2017 (UTC)

Relax restart file requirements

Lizzie Lundgren (GCST) implemented two updates to allow more flexibility in the use of restart files.

1. Remove the requirement of including all advected species in the restart file: MAPL now changes the internal state RESTART attribute per species from initial category MAPL_RestartOptional to new category MAPL_RestartBootstrap if species are bootstrapped (default values used) rather than initialized from the restart file. This enables a later step of over-writing only the bootstrapped species with background concentration values stored in the species database, ultimately allowing the user to omit species from the restart file.
2. Remove the requirement of using a restart file: If the user now enters '+none' for GIGCchem_INTERNAL_RESTART_FILE in the GCHP.rc config file, then new RESTART category MAPL_RestartSkipInitial is set for all species during initialization of the internal state. This has the same effect as using existing category MAPL_RestartSkip except that (1) background values from the species database are retrieved to overwrite default values set in MAPL, and (2) species are written to the output checkout point.

--Lizzie Lundgren (talk) 20:53, 12 June 2017 (UTC)

Outstanding HP issues not yet resolved in GEOS-Chem v11-02

TBD