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POBASH scripts for generating inputs to parallel C++ jobs
 

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    <p>I'm an amateur C++ programmer trying to learn about basic shell scripting. I have a complex C++ program that currently reads in different parameter values from <code>Parameters.h</code> and then executes one or more simulations with each parameter value sequentially. These simulations take a long time to run. Since I have a cluster available, I'd like to effectively parallelize this job, running the simulations for each parameter value on a separate processor. I'm assuming it's easier to learn shell scripting techniques for this purpose than OpenMPI. My cluster runs on the LSF platform.</p> <p>How can I write my input parameters in Bash so that they are distributed among multiple processors, each executing the program with that value? I'd like to avoid interactive submission. Ideally, I'd have the inputs in a text file that Bash reads, and I'd be passing two parameters to each job: an actual parameter value and a parameter ID.</p> <p>Thanks in advance for any leads and suggestions.</p> <hr> <p><strong>my solution</strong></p> <p>GNU Parallel does look slick, but I ended up (with the help of an IT admin) writing a simple bash script that echos to screen three inputs (a treatment identifier, treatment/parameter value, and a simulation identifier):</p> <p><pre><code>#!/bin/bash j=1 for treatment in <code>cat treatments.txt</code>; do for experiment in <code>cat simulations.txt</code>; do bsub -oo <code>tr_${j}_sim_${experiment}_screen</code> -eo <code>tr_${j}_sim_${experiment}_err</code> -q short_serial "echo \"$j $treatment $experiment\" | ./a.out" done let j=$j+1 done </pre></code></p> <p>The file <code>treatments.txt</code> contains a list of the values I'd like to vary, <code>simulations.txt</code> contains a list of all the simulation identifiers I'd like to run (currently just 1,...,s, where s is the total number of simulations I want for each treatment), and the treatments are indexed 1...<code>j</code>.</p>
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    1. CODoes having a `Parameters.h` file mean that the input values are hard-coded and compiled in the executable? Or does you program parse that file at runtime?
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    2. COCurrently, the input values are hard-coded as const double TREATMENTS[ NUM_TREATMENTS ] = { ... };, but I could of course read them in as inputs during runtime.
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