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Revision 1.2 - (download) (as text) (annotate)
Tue Feb 5 05:47:32 2008 UTC (12 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.1: +0 -2 lines
Removed obsolete use clauses.

#!/usr/bin/perl -w

=head1 Attribute Time Test

This simple script tests the performance on the attribute server in
multiple-PEG queries. Each test takes a PEG set and computes
the mean time required to run the attribute request by running
multiple trials. The user can specify a single test, multiple
tests with different sizes, or multiple tests with a single size.

The currently-supported command-line options are as follows.

=over 4

=item user

Name suffix to be used for log files. If omitted, the PID is used.

=item trace

Numeric trace level. A higher trace level causes more messages to appear. The
default trace level is 2. Tracing will be directly to the standard output
as well as to a C<trace>I<User>C<.log> file in the FIG temporary directory,
where I<User> is the value of the B<user> option above.

=item sql

If specified, turns on tracing of SQL activity.

=item background

Save the standard and error output to files. The files will be created
in the FIG temporary directory and will be named C<err>I<User>C<.log> and
C<out>I<User>C<.log>, respectively, where I<User> is the value of the
B<user> option above.

=item h

Display this command's parameters and options.

=item phone

Phone number to message when the script is complete.

=item count

Number of pegs to test. The default is 100.

=item trials

Number of trials. The default is 50.

=item tests

Number of separate PEG sets to test.

=item increment

Number of PEGs to add for each test. If this is 0, every test will be for the
same number of PEGs.



use strict;
use Tracer;
use Cwd;
use File::Copy;
use File::Path;
use FIG;
use Time::HiRes qw(time);

# Get the command-line options and parameters.
my ($options, @parameters) = StandardSetup([qw(FIG) ],
                                              trace => [2, "tracing level"],
                                              count => [100, "number of PEGs per trial"],
                                              trials => [50, "number of trials"],
                                              tests => [1, "number of PEG sets to test"],
                                              increment => [100, "number of PEGs to add between tests"],
                                              phone => ["", "phone number (international format) to call when load finishes"],
# Set a variable to contain return type information.
my $rtype;
# Insure we catch errors.
eval {
    # Get a FIG object.
    my $fig = FIG->new();
    # Do one test at a time.
    for (my $test = 1; $test <= $options->{tests}; $test++) {
        # Compute the number of PEGs for this test.
        my $pegCount = $options->{count} + $options->{increment}*($test - 1);
        Trace("Preparing test $test for $pegCount PEGs.") if T(3);
        # Now get the genomes.
        my %genomes = map { $_ => 1 } $fig->genomes();
        # This gives us the genomes in a mixed-up order.
        my @genomeList = keys %genomes;
        # Compute the number of PEGs per genome. We allow for the possibility of some genomes
        # not having enough, so it's not a straight division.
        my $pegsPerGenome = int(4 * $pegCount / scalar(@genomeList));
        $pegsPerGenome = 10 if $pegsPerGenome < 10;
        # Now we accumulate the PEGs in a hash.
        my %pegs = ();
        Trace("Accumulating PEGs at a rate of $pegsPerGenome per genome.") if T(2);
        # Loop until we have enough PEGs.
        while (scalar(keys %pegs) < $pegCount && scalar(@genomeList)) {
            # Get a genome.
            my $genome = pop @genomeList;
            Trace("Pulling PEGs from $genome.") if T(3);
            # Get some of its pegs in subsystems.
            my @newPegs = $fig->assigned_pegs_in_subsystems($genome);
            for (my $i = 0; $i <= $#newPegs && $i <= $pegsPerGenome; $i++) {
                $pegs{$newPegs[$i]} = 1;
        # Get the PEGs into a list and reduce it to the correct size.
        my @keyList = keys %pegs;
        while (scalar(@keyList) > $pegCount) {
            pop @keyList;
        my $count = scalar(@keyList);
        Trace("$count PEGs accumulated.") if T(2);
        # Now we have our pegs. Try the retrieval and time it.
        my $seconds = 0;
        for (my $i = 0; $i < $options->{trials}; $i++) {
            my @attrs;
            my $now = time();
            @attrs = $fig->get_attributes(\@keyList, "evidence_code");
            $seconds += time() - $now;
        my $actualTime = $seconds / $options->{trials};
        Trace("$count pegs processed in $actualTime seconds.") if T(2);
    Trace("Tests complete.") if T(2);
if ($@) {
    Trace("Script failed with error: $@") if T(0);
    $rtype = "error";
} else {
    Trace("Script complete.") if T(2);
    $rtype = "no error";
if ($options->{phone}) {
    my $msgID = Tracer::SendSMS($options->{phone}, "Attribute Time Test terminated with $rtype.");
    if ($msgID) {
        Trace("Phone message sent with ID $msgID.") if T(2);
    } else {
        Trace("Phone message not sent.") if T(2);


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