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vine manual spelling errors (#4091)
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doc/manuals/taskvine/index.md

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@@ -18,7 +18,7 @@ worker processes. The application generates a large number of small
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tasks, which are distributed to workers.
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As tasks access external data sources and produce their own outputs,
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more and more data is pulled into local storage on cluster nodes.
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This data is used to accelerate future tasks and avoid re-computing exisiting results.
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This data is used to accelerate future tasks and avoid re-computing existing results.
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The application gradually grows "like a vine" through
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the cluster.
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@@ -489,14 +489,14 @@ additional setup, depending on the language in use:
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#### Python Setup
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If you installed via Conda, then no further setup is needed.
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If you installed via conda, then no further setup is needed.
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If you are running a Python application and did *not* install via Conda,
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If you are running a Python application and did *not* install via conda,
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then you will need to set the `PYTHONPATH` to point to the cctools
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installation, like this:
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```sh
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# Note: This is only needed if not using Conda:
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# Note: This is only needed if not using conda:
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$ PYVER=$(python -c 'import sys; print("%s.%s" % sys.version_info[:2])')
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$ export PYTHONPATH=${HOME}/cctools/lib/python${PYVER}/site-packages:${PYTHONPATH}
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```
@@ -699,7 +699,7 @@ We can also create a factory directly in python. Creating a factory object does
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immediately launch it, so this is a good time to configure the resources,
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number of workers, etc. Factory objects function as Python context managers, so
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to indicate that a set of commands should be run with a factory running, wrap
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them in a with statement. The factory will be cleaned up automtically at the
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them in a with statement. The factory will be cleaned up automatically at the
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end of the block. As an example:
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```python
@@ -793,7 +793,7 @@ If peer transfers have been disabled, they may be re-enabled accordingly:
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```
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Transfers between workers may be impacted by transient issues which may cause intermittent transfer failures. In these situations we take note of the
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failure that occured, and avoid using the same worker as a source for a period of time. This time period has a default value of 15 seconds.
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failure that occurred, and avoid using the same worker as a source for a period of time. This time period has a default value of 15 seconds.
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It may be changed by the user using `vine_tune` with the parameter `transient-error-interval`.
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### MiniTasks
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```
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##### Apptainer Execution Cpntext From a Mini Task
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##### Apptainer Execution Context From a Mini Task
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In the previous section we manually built the directory structure needed for
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the execution context. This is not very flexible, as we need to create one such
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```
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This password will be particular to your application, and only managers and
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workers with the same password will be able to interoperator.
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workers with the same password will be able to interoperate.
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Then, modify your manager program to use the password:
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=== "Python"
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sandbox, which means that the command line of the tasks does not need to
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change.
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Note this feature is specifically designed for specifying and distingushing
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Note this feature is specifically designed for specifying and distinguishing
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input file names for different platforms and architectures. Also, this is
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different from the $VINE_SANDBOX shell environment variable that exports
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the location of the working directory of the worker to its execution
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all apply to `PythonTask` as well.
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When running a Python function remotely, it is assumed that the Python interpreter
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and libraries available at the worker correspond to the appropiate python environment for the task.
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and libraries available at the worker correspond to the appropriate python environment for the task.
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If this is not the case, an environment file can be provided with t.set_environment:
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=== "Python"
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The **treeReduce** function combines an array using a given function by
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breaking up the array into chunk_sized chunks, computing the results, and returning
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the results to a new array. It then does the same process on the new array until there
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only one element left and then returns it. The given fucntion must accept an iterable,
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and must be an associative fucntion, or else the same result cannot be gaurenteed for
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only one element left and then returns it. The given function must accept an iterable,
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and must be an associative function, or else the same result cannot be guaranteed for
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different chunk sizes. Again, cheaper functions work better with larger chunk_sizes,
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more expensive functions work better with smaller ones. Errors will be placed in results.
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Also, the minimum chunk size is 2, as going 1 element at time would not reduce the array
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The only caveat is when using `vine_submit_workers -T uge`, as there are many
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differences across systems that the script cannot manage. For `
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vine_submit_workers -T uge` you have to set **both** the resources used by the
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worker (i.e., with `--cores`, etc.) and the appropiate computing node with the `
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worker (i.e., with `--cores`, etc.) and the appropriate computing node with the `
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-p ` option.
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For example, say that your local UGE installation requires you to set the
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$ vine_submit_workers -T uge --cores 4 -p "-pe smp 4" MACHINENAME 9123
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```
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If you find that there are options that are needed everytime, you can compile
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If you find that there are options that are needed every time, you can compile
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CCTools using the ` --uge-parameter `. For example, at Notre Dame we
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automatically set the number of cores as follows:
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A TaskVine manager produces several logs: `debug`, `taskgraph`, `performance`,
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and `transactions`. These logs are always enabled, and appear in the current
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working directory in the sudirectories:
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working directory in the subdirectories:
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```sh
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vine-run-info/YYYY-mm-ddTHH:MM:SS/vine-logs
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```
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The script `vine_graph_log` is a wrapper for `gnuplot`, and with it you
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can plot some of the statistics, such as total time spent transfering tasks,
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can plot some of the statistics, such as total time spent transferring tasks,
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number of tasks running, and workers connected. For example, this command:
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```sh
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### Other Tools
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`vine_plot_compose` visualizes workflow executions in a variety of ways, creating a composition of multiple plots in a single visualiztion. This tool may be useful in
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`vine_plot_compose` visualizes workflow executions in a variety of ways, creating a composition of multiple plots in a single visualization. This tool may be useful in
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comparing performance across multiple executions.
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```sh
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This subsection describes the communication patterns between a library and a worker, agnostic of programming languages a library is implemented in.
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Upon library startup, it should send to its worker a json object as a byte stream.
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The json object should have the following keys and associated values' types: `{"name": type-string, "taskid": type-int, "exec\_mode": type-string}`.
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Upon library startup, it should send to its worker a JSON object as a byte stream.
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The JSON object should have the following keys and associated values' types: `{"name": type-string, "taskid": type-int, "exec\_mode": type-string}`.
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`"name"` should be the name of the library.
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`"taskid"` should be the library' taskid as assigned by a taskvine manager.
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`"exec\_mode"` should be the function execution mode of the library.

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