<li><ahref="nemo/README.md#verification-of-results">Test Case A</a></li>
<li><ahref="nemo/README.md#verification-of-results">Test Case B</a></li>
</ul>
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<td>154,240</td>
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@@ -397,54 +397,6 @@ NAMD is written in C++ and parallelised using Charm++ parallel objects, which ar
- Test Case C: https://repository.prace-ri.eu/ueabs/NAMD/2.2/NAMD_TestCaseC.tar.gz
- Build and Run Instructions : https://repository.prace-ri.eu/git/UEABS/ueabs/-/blob/r2.2-dev/NAMD/README.md
# NEMO <a name="nemo"></a>
NEMO (Nucleus for European Modelling of the Ocean) [22] is mathematical modelling framework for research activities and prediction services in ocean and climate sciences developed by European consortium. It is intended to be tool for studying the ocean and its interaction with the other components of the earth climate system over a large number of space and time scales. It comprises of the core engines namely OPA (ocean dynamics and thermodynamics), SI3 (sea ice dynamics and thermodynamics), TOP (oceanic tracers) and PISCES (biogeochemical process).
Prognostic variables in NEMO are the three-dimensional velocity field, a linear or non-linear sea surface height, the temperature and the salinity.
In the horizontal direction, the model uses a curvilinear orthogonal grid and in the vertical direction, a full or partial step z-coordinate, or s-coordinate, or a mixture of the two. The distribution of variables is a three-dimensional Arakawa C-type grid for most of the cases.
The model is implemented in Fortran 90, with preprocessing (C-pre-processor). It is optimized for vector computers and parallelized by domain decomposition with MPI. It supports modern C/C++ and Fortran compilers. All input and output is done with third party software called XIOS with dependency on NetCDF (Network Common Data Format) and HDF5. It is highly scalable and perfect application for measuring supercomputing performances in terms of compute capacity, memory subsystem, I/O and interconnect performance.
### Test Case Description
The GYRE configuration has been built to model seasonal cycle of double gyre box model. It consists of idealized domain over which seasonal forcing is applied. This allows for studying large number of interactions and their combined contribution to large scale circulation.
The domain geometry is rectangular bounded by vertical walls and flat bottom. The configuration is meant to represent idealized north Atlantic or north pacific basin. The circulation is forced by analytical profiles of wind and buoyancy fluxes.
The wind stress is zonal and its curl changes sign at 22 and 36. It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and a small recirculation gyre in the southern corner. The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile.
A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column. The fresh water flux is also prescribed and varies zonally. It is determined such as, at each time step, the basin-integrated flux is zero.
The basin is initialized at rest with vertical profiles of temperature and salinity uniformity applied to the whole domain. The GYRE configuration is set through the namelist_cfg file.
The horizontal resolution is determined by setting jp_cfg as follows:
`Jpiglo = 30 x jp_cfg + 2`
`Jpjglo = 20 x jp_cfg + 2`
In this configuration, we use default value of 30 ocean levels depicted by jpk=31. The GYRE configuration is an ideal case for benchmark test as it is very simple to increase the resolution and perform both weak and strong scalability experiment using the same input files. We use two configurations as follows:
**Test Case A**:
* jp_cfg = 128 suitable up to 1000 cores
* Number of Days: 20
* Number of Time steps: 1440
* Time step size: 20 mins
* Number of seconds per time step: 1200
**Test Case B**
* jp_cfg = 256 suitable up to 20,000 cores.
* Number of Days (real): 80
* Number of time step: 4320
* Time step size(real): 20 mins
* Number of seconds per time step: 1200
* Web site: <http://www.nemo-ocean.eu/>
* Download, Build and Run Instructions : <https://repository.prace-ri.eu/git/UEABS/ueabs/tree/master/nemo>
# PFARM <a name="pfarm"></a>
PFARM is part of a suite of programs based on the ‘R-matrix’ ab-initio approach to the variational solution of the many-electron Schrödinger
