@@ -127,7 +127,7 @@ shoud be allocated on the same socket.
**A) `GluCl Ion Channel`**
The ion channel system is the membrane protein GluCl, which is a pentameric chloride channel embedded in a lipid bilayer. The GluCl ion channel was embedded in a DOPC membrane and solvated in TIP3P water. This system contains 142k atoms, and is a quite challenging parallelisation case due to the small size. However, it is likely one of the most wanted target sizes for biomolecular simulations due to the importance of these proteins for pharmaceutical applications. It is particularly challenging due to a highly inhomogeneous and anisotropic environment in the membrane, which poses hard challenges for load balancing with domain decomposition.
The ion channel system is the membrane protein GluCl, which is a pentameric chloride channel embedded in a lipid bilayer. The GluCl ion channel was embedded in a DOPC membrane and solvated in TIP3P water. This system contains 142k atoms, and is a quite challenging parallelisation case due to the small size. However, it is likely one of the most wanted target sizes for biomolecular simulations due to the importance of these proteins for pharmaceutical applications. It is particularly challenging due to a highly inhomogeneous and anisotropic environment in the membrane, which poses hard challenges for load balancing with domain decomposition. This test case was used as the “Small” test case in previous PRACE-2IP-5IP projects. It is reported to scale efficiently up to 300 - 1000 cores on recent x86 based systems.
Download test Case A [https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseA.tar.xz](https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseA.tar.xz)
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@@ -136,14 +136,14 @@ Download test Case A [https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_T
A model of cellulose and lignocellulosic biomass in an aqueous solution
This system of 3.3 million atoms is inhomogeneous.
Reaction-field electrostatics are used instead of PME and therefore scales well.
Reaction-field electrostatics are used instead of PME and therefore scales well. This test case was used as the “Large” test case in previous PRACE-2IP-5IP projects. It is reported in previous PRACE projects to scale efficiently on 10000+ recent x86 cores.
Download test Case B [https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseB.tar.xz](https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseB.tar.xz)
**C) `STMV 8M` **
This is a `2 x 2 x 2` replica of the STMV (Satellite Tobacco Mosaic Virus). It is a converted to GROMACS case of
the corresponding NAMD benchmark. It contains 8.5 million atoms and uses PME for electrostatics.
the corresponding NAMD benchmark. It contains 8.5 million atoms and uses PME for electrostatics. It is reported to scale efficiently on more than 10000 recent x86 cores.
Download test Case C [https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseC.tar.xz](https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseC.tar.xz)