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MOLA automates several tasks including: ligand preparation, docking jobs distribution and results analysis.
I/O saturation was most apparent at the end of the initial wave of docking jobs when multiple log files are simultaneously written to disk and grid maps for the next docking jobs are loaded.
Using MPI and OpenMP, AutoDock 4.2 was parallelized for use on MPI-enabled systems and to multithread the execution of individual docking jobs.
An assessment script monitors the overall progress of the docking jobs and, should runtime limits be exceeded, it notifies the user that a restart is required.
Extending on these previous approaches, we had three goals for parallelization of AD4: 1) enable parallel execution of AD4 across multiple HPC architectures, 2) reduce I/O, and 3) parallelize the execution of individual docking jobs.
When profiling is enabled, a.csv file is updated as each docking finishes, so a user can monitor the progress of individual docking jobs and be made aware of any performance issues while the program is running.
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We assigned one docking job to each node and then distributed the calculations of ligand rotation by thread parallelization with CPU cores and GPUs.
These are not the tough, blue-collar dock jobs depicted in the Marlon Brando film "On the Waterfront," but rather clerical jobs usually paying nearly $120,000 a year.
As manufacturing and dock jobs went, the children of the old East Enders had found jobs in the City and the used car lots of the Southend Arterial Road.
Many blue-collar workers often Alioto supporters lost their jobs as large corporations with service industry positions replaced factory and dry dock jobs.
Cuney established his own business of stevedores and a union of black dockworkers to break the white monopoly on dock jobs.
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