title: Bandwidth-optimal random shuffling for GPUs

authors: Mitchell, Rory

subjects: computer science

abstract: Linear-time algorithms that are traditionally used to shuffle data on CPUs, such as the method of Fisher-Yates, are not well suited to implementation on GPUs due to inherent sequential dependencies, and existing parallel shuffling algorithms are unsuitable for GPU architectures because they incur a large number of read/write operations to high latency global memory. To address this, we provide a method of generating pseudo-random permutations in parallel by fusing suitable pseudo-random bijective functions with stream compaction operations. Our algorithm, termed “bijective shuffle” trades increased per-thread arithmetic operations for reduced global memory transactions. It is work-efficient, deterministic, and only requires a single global memory read and write per shuffle input, thus maximising use of global memory bandwidth. To empirically demonstrate the correctness of the algorithm, we develop a statistical test for the quality of pseudo-random permutations based on kernel space embeddings. Experimental results show that the bijective shuffle algorithm outperforms competing algorithms on GPUs, showing improvements of between one and two orders of magnitude and approaching peak device bandwidth.

text: Bandwidth-optimal random shuffling for GPUs Linear-time algorithms that are traditionally used to shuffle data on CPUs, such as the method of Fisher-Yates, are not well suited to implementation on GPUs due to inherent sequential dependencies, and existing parallel shuffling algorithms are unsuitable for GPU architectures because they incur a large number of read/write operations to high latency global memory. To address this, we provide a method of generating pseudo-random permutations in parallel by fusing suitable pseudo-random bijective functions with stream compaction operations. Our algorithm, termed “bijective shuffle” trades increased per-thread arithmetic operations for reduced global memory transactions. It is work-efficient, deterministic, and only requires a single global memory read and write per shuffle input, thus maximising use of global memory bandwidth. To empirically demonstrate the correctness of the algorithm, we develop a statistical test for the quality of pseudo-random permutations based on kernel space embeddings. Experimental results show that the bijective shuffle algorithm outperforms competing algorithms on GPUs, showing improvements of between one and two orders of magnitude and approaching peak device bandwidth.

year: 2022

title: Vegetation dieback as a proxy for temperature within a wet pyroclastic density current: A novel experiment and observations from the 6th of August 2012 Tongariro eruption

authors: Efford, Jackson Tai

subjects: wet pyroclastic density current

abstract: The 6th of August 2012 eruption of Te Maari (Mt Tongariro, New Zealand) generated wet pyroclastic density currents (PDCs) which caused widespread dieback of vegetation (singed, brown foliage) in their path. An absence of significant charcoal formation suggests that PDC temperatures were mostly below 250 °C. Textural evidence for liquid water being present in the matrices during emplacement (vesicles) suggests that temperatures were b100 °C. We determined a probable minimum PDC temperature using an experiment replicating the critical temperatures required to induce foliar browning in seven species affected by the eruption. In locations where all species exhibited browned foliage (or were defoliated), temperatures were probably ≥64 °C assuming a PDC duration of 60 s. In the more distal areas, where only the most susceptible species were browned while others remained healthy and unaffected, temperatures were probably around 51–58 °C. These results have relevance to volcanic hazard mitigation and risk assessment, especially on the popular Tongariro Alpine Crossing.

text: Vegetation dieback as a proxy for temperature within a wet pyroclastic density current: A novel experiment and observations from the 6th of August 2012 Tongariro eruption The 6th of August 2012 eruption of Te Maari (Mt Tongariro, New Zealand) generated wet pyroclastic density currents (PDCs) which caused widespread dieback of vegetation (singed, brown foliage) in their path. An absence of significant charcoal formation suggests that PDC temperatures were mostly below 250 °C. Textural evidence for liquid water being present in the matrices during emplacement (vesicles) suggests that temperatures were b100 °C. We determined a probable minimum PDC temperature using an experiment replicating the critical temperatures required to induce foliar browning in seven species affected by the eruption. In locations where all species exhibited browned foliage (or were defoliated), temperatures were probably ≥64 °C assuming a PDC duration of 60 s. In the more distal areas, where only the most susceptible species were browned while others remained healthy and unaffected, temperatures were probably around 51–58 °C. These results have relevance to volcanic hazard mitigation and risk assessment, especially on the popular Tongariro Alpine Crossing.

year: 2014

title: Lake Rotokakahi water quality modelling

authors: Jones, Hannah Frances Emily

abstract: Lake Rotokakahi is an iwi-owned lake, administered by the Lake Rotokakahi Board of Control. The lake has a surface area of 4.4 km2, a mean depth of 17.5 m, and a catchment of 19.7 km2 of which most is in exotic forest (46.5%), with some pasture (27.8%) and regenerating native forest and scrub (25.7%). Lake Rotokakahi has only one permanent surface inflow and it is assumed that the lake must be predominantly groundwater fed. The lake outflow, Te Wairoa Stream, flows into Lake Tarawera. Monitoring indicates that water quality has recently declined in the lake, with a shift from a mesotrophic state in the 1990's, to currently being classified as eutrophic. Increased algal biomass has reduced water clarity and in May 2011 the first ever recorded algae bloom of a toxic cyanobacterium species resulted in a fish kill in Te Wairoa Stream. With the majority of the catchment in either exotic or native forest, the cause for the decline in water quality is unclear. However there is some concern that forestry harvesting operations may lead to increased surface runoff of sediment and associated phosphorus in ephemeral streams that feed into the lake. The objective of this study was to setup a water quality model for Lake Rotokakahi, which in the future may provide a decisionsupport tool for lake managers.
The model used, DYRESM-CAEDYM, is a one-dimensional (1D) coupled hydrodynamic-water quality model that has been widely used in New Zealand and overseas. Methodology for deriving model forcing data (e.g. meteorological data, inflow volumes and nutrient loads), including the application of catchment and lake water balances, is described in this report. The catchment water balance indicates that groundwater and rainfall account for 37% and 42%, respectively, of the total inflow volume to the lake, with surface and ephemeral inflows contributing a smaller proportion (c. 20% combined). Furthermore, it appears that groundwater contributes a significant proportion (c. 60 - 70%) of the total nutrient loads, although surface and ephemeral inflows also contribute a significant proportion (34%) of the total phosphorus load. It should be noted that the catchment water balance is based on a very limited dataset, and therefore subject to significant uncertainty. 
We simulated the period July 2009 to June 2012 with DYRESM-CAEDYM. Model performance statistics indicated reasonable simulation of water quality for the calibration period, but did not satisfactorily capture the magnitude and dynamics of chlorophyll a and some nutrient species over an independent model validation period. There may be a number of reasons for the poor model performance over the validation period. For example, it may be that zooplankton and/or freshwater mussels (kakahi), which were not included in the model configuration, may exert significant grazing pressure on the phytoplankton populations at certain times. Furthermore, the significant uncertainty in the catchment water and nutrient loads most likely will have affected model performance. Nutrient concentrations are routinely monitored only in the surface inflow. There are no measurements of nutrient and sediment loads in ephemeral streams, and there is very limited data on groundwater nutrient concentrations.
In its current form, the DYRESM-CAEDYM model is not suitable for scenario testing of lake management options. It is recommended that effort is directed at quantification of ephemeral and groundwater inflows and their associated nutrient and (particularly for ephemeral inflows) sediment loads. This may be particularly important for ephemeral inflows located close to the lake that may be influenced by forestry harvesting operations. Recent increases in measured total phosphorus and phosphate concentrations in the surface inflow and in the lake, combined with the degradation of water quality that has already occurred over the last 20 years, provides further impetus for addressing this critical information gap. Were new data to  become available, opportunities exist for improving the performance of the current model and for developing a three-dimensional coupled hydrodynamic-water quality model (e.g. ELCOM-CAEDYM) with representation of kakahi and/or zooplankton, which may be able to resolve questions pertinent to the functioning of the lake, and to lake and catchment management.

text: Lake Rotokakahi water quality modelling Lake Rotokakahi is an iwi-owned lake, administered by the Lake Rotokakahi Board of Control. The lake has a surface area of 4.4 km2, a mean depth of 17.5 m, and a catchment of 19.7 km2 of which most is in exotic forest (46.5%), with some pasture (27.8%) and regenerating native forest and scrub (25.7%). Lake Rotokakahi has only one permanent surface inflow and it is assumed that the lake must be predominantly groundwater fed. The lake outflow, Te Wairoa Stream, flows into Lake Tarawera. Monitoring indicates that water quality has recently declined in the lake, with a shift from a mesotrophic state in the 1990's, to currently being classified as eutrophic. Increased algal biomass has reduced water clarity and in May 2011 the first ever recorded algae bloom of a toxic cyanobacterium species resulted in a fish kill in Te Wairoa Stream. With the majority of the catchment in either exotic or native forest, the cause for the decline in water quality is unclear. However there is some concern that forestry harvesting operations may lead to increased surface runoff of sediment and associated phosphorus in ephemeral streams that feed into the lake. The objective of this study was to setup a water quality model for Lake Rotokakahi, which in the future may provide a decisionsupport tool for lake managers.
The model used, DYRESM-CAEDYM, is a one-dimensional (1D) coupled hydrodynamic-water quality model that has been widely used in New Zealand and overseas. Methodology for deriving model forcing data (e.g. meteorological data, inflow volumes and nutrient loads), including the application of catchment and lake water balances, is described in this report. The catchment water balance indicates that groundwater and rainfall account for 37% and 42%, respectively, of the total inflow volume to the lake, with surface and ephemeral inflows contributing a smaller proportion (c. 20% combined). Furthermore, it appears that groundwater contributes a significant proportion (c. 60 - 70%) of the total nutrient loads, although surface and ephemeral inflows also contribute a significant proportion (34%) of the total phosphorus load. It should be noted that the catchment water balance is based on a very limited dataset, and therefore subject to significant uncertainty. 
We simulated the period July 2009 to June 2012 with DYRESM-CAEDYM. Model performance statistics indicated reasonable simulation of water quality for the calibration period, but did not satisfactorily capture the magnitude and dynamics of chlorophyll a and some nutrient species over an independent model validation period. There may be a number of reasons for the poor model performance over the validation period. For example, it may be that zooplankton and/or freshwater mussels (kakahi), which were not included in the model configuration, may exert significant grazing pressure on the phytoplankton populations at certain times. Furthermore, the significant uncertainty in the catchment water and nutrient loads most likely will have affected model performance. Nutrient concentrations are routinely monitored only in the surface inflow. There are no measurements of nutrient and sediment loads in ephemeral streams, and there is very limited data on groundwater nutrient concentrations.
In its current form, the DYRESM-CAEDYM model is not suitable for scenario testing of lake management options. It is recommended that effort is directed at quantification of ephemeral and groundwater inflows and their associated nutrient and (particularly for ephemeral inflows) sediment loads. This may be particularly important for ephemeral inflows located close to the lake that may be influenced by forestry harvesting operations. Recent increases in measured total phosphorus and phosphate concentrations in the surface inflow and in the lake, combined with the degradation of water quality that has already occurred over the last 20 years, provides further impetus for addressing this critical information gap. Were new data to  become available, opportunities exist for improving the performance of the current model and for developing a three-dimensional coupled hydrodynamic-water quality model (e.g. ELCOM-CAEDYM) with representation of kakahi and/or zooplankton, which may be able to resolve questions pertinent to the functioning of the lake, and to lake and catchment management.

year: 2014