Mesoscopic simulations of hydrocarbon flow in source shales are challenging, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid-fluid and fluid-solid interactions in nano-to micro-scale shale pores, which are physically and chemically sophisticated, must be captured. To address those challenges, we present a GPU-accelerated package for simulation of flow in nano-to micro-pore networks with a many-body dissipative particle dynamics (mDPD) mesoscale model. Based on a fully distributed parallel paradigm, the code offloads all intensive workloads on GPUs. Other advancements, such as smart particle packing and no-slip boundary condition in complex pore geometries, are also implemented for the construction and the simulation of the realistic shale pores from 3D nanometer-resolution stack images. Our code is validated for accuracy and compared against the CPU counterpart for speedup. In our benchmark tests, the code delivers nearly perfect strong scaling and weak scaling (with up to 512 million particles) on up to 512 K20X GPUs on Oak Ridge National Laboratory's (ORNL) Titan supercomputer. Moreover, a single-GPU benchmark on ORNL's SummitDev and IBM's AC922 suggests that the host-to-device NVLink can boost performance over PCIe by a remarkable 40%. Lastly, we demonstrate, through a flow simulation in realistic shale pores, that the CPU counterpart requires 840 Power9 cores to rival the performance delivered by our package with four V100 GPUs on ORNL's Summit architecture. This simulation package enables quick-turnaround and high-throughput mesoscopic numerical simulations for investigating complex flow phenomena in nano-to micro-porous rocks with realistic pore geometries. Program summaryProgram title: USER MESO 2.5 Licensing provisions: GNU General Public License 3 Programming language: CUDA C/C++ with MPI and OpenMP Nature of problem: Particle-based simulation of multiphase flow and fluid-solid interaction in nano-to micro-scale pore networks of arbitrary pore geometries. Solution method: Fluid particles and solid wall particles are modeled with a many-body dissipative particle dynamics (mDPD) model -a mesoscopic model for coarse-grained fluid and solid molecules. The pore surface wall boundary for arbitrary surface geometries is modeled with a no-slip boundary condition for fluid particles that prevents fluid particles from indefinitely penetrating in the walls. The time evolution of the system is integrated using the Velocity-Verlet algorithm. Restrictions: The code is compatible with NVIDIA GPUs with compute capability 3.0 and above. Unusual features: The code is implemented on GPGPUs with significantly improved speed.Recently we developed an mDPD based nano to micro-scale pore flow model and applied it for multiphase flow simulations in source shale [58]. In that model, realistic shale pore geometries are constructed based on 3D voxel 2/21

Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.