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Jan Eitzinger 2019-04-29 10:21:48 +02:00
parent dee638f4d7
commit c92ebc4149
6 changed files with 817 additions and 1 deletions
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2
LICENSE
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MIT License MIT License
Copyright (c) 2019 Copyright (c) 2019 RRZE, University Erlangen-Nuremberg
Permission is hereby granted, free of charge, to any person obtaining a copy Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal of this software and associated documentation files (the "Software"), to deal

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acImportPBS.pl Executable file
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#!/usr/bin/env perl
# =======================================================================================
#
# Author: Jan Eitzinger (je), jan.eitzinger@fau.de
# Copyright (c) 2019 RRZE, University Erlangen-Nuremberg
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
# =======================================================================================
use strict;
use warnings;
use utf8;
use Data::Dumper;
use DateTime::Format::Strptime;
use DBI;
if ( $#ARGV < 1 ){
die "Usage: $0 <DBFile> <importDIR>\n";
}
my $database = $ARGV[0];
my $basedir = $ARGV[1];
my %attr = (
PrintError => 1,
RaiseError => 1
);
my $dbh = DBI->connect(
"DBI:SQLite:dbname=$database", "", "", \%attr);
my $dateParser =
DateTime::Format::Strptime->new(
pattern => '%m/%d/%Y %H:%M:%S',
time_zone => 'Europe/Berlin',
on_error => 'undef'
);
my $sth_insert_job = $dbh->prepare(qq{
INSERT INTO job
(job_id, user_id, project_id, cluster_id,
start_time, stop_time, duration, walltime,
job_state, num_nodes, node_list, has_profile)
VALUES (?,?,?,?,?,?,?,?,?,?,?,?)
});
my $sth_select_job = $dbh->prepare(qq{
SELECT id, user_id, job_id, cluster_id,
start_time, stop_time, duration, num_nodes
FROM job
WHERE job_id=?
});
my %JOBCACHE;
while( defined( my $file = glob($basedir . '/*' ) ) ) {
print "Processing $file ...";
open(my $fh, "<","$file");
while ( my $record = <$fh> ) {
if ( $record =~ /(.*);([A-Z]);(.*?);(.*)/ ) {
my $dt = $dateParser->parse_datetime($1);
my $timestamp = $dt->epoch;
my $job_state = $2;
my $job_id = $3;
my $jobinfo = $4;
my @data = split(/ /, $jobinfo);
my $queue;
my $user_id;
my $project_id;
my $start_time;
my $stop_time;
my $walltime;
my @nodes;
my $num_nodes;
my $node_list;
foreach my $prop ( @data ) {
if ( $prop =~ /user=(.*)/ ) {
$user_id = $1;
} elsif ( $prop =~ /group=(.*)/ ) {
$project_id = $1;
} elsif ( $prop =~ /start=(.*)/ ) {
$start_time = $1;
} elsif ( $prop =~ /end=(.*)/ ) {
$stop_time = $1;
} elsif ( $prop =~ /queue=(.*)/ ) {
$queue = $1;
} elsif ( $prop =~ /Resource_List\.walltime=([0-9]+):([0-9]+):([0-9]+)/ ) {
$walltime = $1 * 3600 + $2 * 60 + $3;
} elsif ( $prop =~ /exec_host=(.*)/ ) {
my $hostlist = $1;
my @hosts = split(/\+/, $hostlist);
foreach my $host ( @hosts ) {
if ( $host =~ /(.*?)\/0/) {
push @nodes, $1;
}
}
$num_nodes = @nodes;
$node_list = join(',', @nodes);
}
}
if ( $job_state eq 'S' ) {
$JOBCACHE{$job_id} = {
'user_id' => $user_id,
'project_id' => $project_id,
'start_time' => $start_time,
'walltime' => $walltime,
'num_nodes' => $num_nodes,
'node_list' => $node_list
};
} elsif ( $job_state eq 'E' ) {
delete $JOBCACHE{$job_id};
} elsif ( $job_state eq 'D' or $job_state eq 'A' ) {
my $job;
if (exists $JOBCACHE{$job_id}){
$job = $JOBCACHE{$job_id};
} else {
next;
}
# print Dumper($job);
$user_id = $job->{'user_id'};
$project_id = $job->{'project_id'};
$start_time = $job->{'start_time'};
$stop_time = $timestamp;
$walltime = $job->{'walltime'};
$num_nodes = $job->{'num_nodes'};
$node_list = $job->{'node_list'};
delete $JOBCACHE{$job_id};
}
if ( $job_state eq 'E' or
$job_state eq 'D' or
$job_state eq 'A' )
{
my $duration = $stop_time - $start_time;
# check if job already exists
my @row = $dbh->selectrow_array($sth_select_job, undef, $job_id);
if ( @row ) {
print "Job $job_id already exists!\n";
} else {
$sth_insert_job->execute(
$job_id,
$user_id,
$project_id,
"emmy",
$start_time,
$stop_time,
$duration,
$walltime,
$job_state,
$num_nodes,
$node_list,
0);
}
}
}
}
close $fh or die "can't close file $!";
print " done\n";
}
$dbh->disconnect;

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acImportSlurm.pl Executable file
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#!/usr/bin/env perl
# =======================================================================================
#
# Author: Jan Eitzinger (je), jan.eitzinger@fau.de
# Copyright (c) 2019 RRZE, University Erlangen-Nuremberg
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
# =======================================================================================
use strict;
use warnings;
use utf8;
use Data::Dumper;
use DateTime::Format::Strptime;
use DBI;
if ( $#ARGV < 1 ){
die "Usage: $0 <DBFile> <importDIR>\n";
}
my $database = $ARGV[0];
my $basedir = $ARGV[1];
my %attr = (
PrintError => 1,
RaiseError => 1
);
my $dbh = DBI->connect(
"DBI:SQLite:dbname=$database", "", "", \%attr);
my $dateParser =
DateTime::Format::Strptime->new(
pattern => '%Y-%m-%dT%H:%M:%S',
time_zone => 'Europe/Berlin',
on_error => 'undef'
);
sub parse_nodelist {
my $nodestr = shift;
my @nodes;
if ( $nodestr =~ /([a-z]+)\[(.*)\]/) {
my $prefix = $1;
my $list = $2;
my @listitems = split(',', $list);
foreach my $item ( @listitems ){
if ( $item =~ /([0-9]+)-([0-9]+)/ ){
foreach my $nodeId ( $1 ... $2 ){
push @nodes, $prefix.$nodeId;
}
} else {
push @nodes, $prefix.$item;
}
}
return join(',', @nodes);
} else {
return $nodestr;
}
}
my $sth_insert_job = $dbh->prepare(qq{
INSERT INTO job
(job_id, user_id, project_id, cluster_id,
start_time, stop_time, duration, walltime,
job_state, num_nodes, node_list, has_profile)
VALUES (?,?,?,?,?,?,?,?,?,?,?,?)
});
my $sth_select_job = $dbh->prepare(qq{
SELECT id, user_id, job_id, cluster_id,
start_time, stop_time, duration, num_nodes
FROM job
WHERE job_id=?
});
my %JOBCACHE;
my $dt;
while( defined( my $file = glob($basedir . '/*' ) ) ) {
print "Processing $file ...";
open(my $fh, "<","$file");
my $columns = <$fh>;
while ( my $record = <$fh> ) {
my @fields = split(/\|/, $record);
if ( $fields[1] =~ /^[0-9]+$/) {
my $cluster_id = $fields[0];
my $job_id = $fields[1];
my $user_id = $fields[2];
my $project_id = $fields[3];
$dt = $dateParser->parse_datetime($fields[5]);
my $start_time = $dt->epoch;
$dt = $dateParser->parse_datetime($fields[6]);
my $stop_time = $dt->epoch;
my $num_nodes = $fields[11];
my $node_list = parse_nodelist($fields[13]);
my $job_state = $fields[10];
$job_state =~ s/ by [0-9]+//;
my $walltime = 0;
my $duration = $stop_time - $start_time;
# check if job already exists
my @row = $dbh->selectrow_array($sth_select_job, undef, $job_id);
if ( @row ) {
print "Job $job_id already exists!\n";
} else {
$sth_insert_job->execute(
$job_id,
$user_id,
$project_id,
$cluster_id,
$start_time,
$stop_time,
$duration,
$walltime,
$job_state,
$num_nodes,
$node_list,
0);
}
} else {
# print "$fields[1] \n";
next;
}
}
close $fh or die "can't close file $!";
print " done\n";
}
$dbh->disconnect;

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acQuery.pl Executable file
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#!/usr/bin/env perl
# =======================================================================================
#
# Author: Jan Eitzinger (je), jan.eitzinger@fau.de
# Copyright (c) 2019 RRZE, University Erlangen-Nuremberg
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
# =======================================================================================
use strict;
use warnings;
use utf8;
use Data::Dumper;
use Getopt::Long;
use Pod::Usage;
use DateTime::Format::Strptime;
use DBI;
my $database = 'jobDB';
my @conditions;
my ($add, $from, $to);
my $dateParser =
DateTime::Format::Strptime->new(
pattern => '%d.%m.%Y',
time_zone => 'Europe/Berlin',
on_error => 'undef'
);
my $help = 0;
my $man = 0;
my $mode = 'count';
my $user = '';
my $project = '';
my @numnodes;
my @starttime;
my @duration;
GetOptions (
'help' => \$help,
'man' => \$man,
'mode=s' => \$mode,
'user=s' => \$user,
'project=s' => \$project,
'numnodes=i{2}' => \@numnodes,
'starttime=s{2}' => \@starttime,
'duration=s{2}' => \@duration
) or pod2usage(2);
my %attr = (
PrintError => 1,
RaiseError => 1
);
if ( $#ARGV == 0 ) {
$database = $ARGV[0];
}
my $dbh = DBI->connect(
"DBI:SQLite:dbname=$database", "", "", \%attr)
or die("Cannot connect to database $database\n");
sub parseDate {
my $str = shift;
my $dt;
if ( $str ){
$dt = $dateParser->parse_datetime($str);
if ( $dt ) {
return $dt->epoch;
} else {
print "Cannot parse datetime string $str: Ignoring!\n";
return 0;
}
} else {
return 0;
}
}
sub parseDuration {
my $str = shift;
if ( $str =~ /([0-9]+)h/ ) {
return $1 * 3600;
} elsif ( $str =~ /([0-9]+)m/ ) {
return $1 * 60;
} elsif ( $str =~ /([0-9]+)s/ ) {
return $1;
} elsif ( $str =~ /([0-9]+)/ ) {
return $1;
} else {
print "Cannot parse duration string $str: Ignoring!\n";
return 0;
}
}
sub formatDuration {
my $ts = shift;
}
sub processRange {
my $lower = shift;
my $upper = shift;
if ( $lower && $upper ){
return (3, $lower, $upper);
} elsif ( $lower && !$upper ){
return (1, $lower, 0);
} elsif ( !$lower && $upper ){
return (2, 0, $upper);
}
}
sub buildCondition {
my $name = shift;
if ( $add ) {
if ( $add == 1 ) {
push @conditions, "$name < $from";
} elsif ( $add == 2 ) {
push @conditions, "$name > $to";
} elsif ( $add == 3 ) {
push @conditions, "$name BETWEEN $from AND $to";
}
}
}
sub printJobStat {
my $conditionstring = shift;
my $query = 'SELECT COUNT(id), SUM(duration)/3600 FROM job '.$conditionstring;
my ($count, $coreHours) = $dbh->selectrow_array($query);
print "=================================\n";
print "Job count: $count\n";
print "Core hours: $coreHours \n";
$query = 'SELECT num_nodes, COUNT(*) FROM job '.$conditionstring.' GROUP BY 1';
my @histo_num_nodes = $dbh->selectall_array($query);
print "\nHistogram: Number of nodes\n";
print "nodes\tcount\n";
foreach my $bin ( @histo_num_nodes ) {
print "$bin->[0]\t$bin->[1]\n";
}
$query = 'SELECT duration/3600, COUNT(*) FROM job '.$conditionstring.' GROUP BY 1';
my @histo_runtime = $dbh->selectall_array($query);
print "\nHistogram: Runtime\n";
print "hours\tcount\n";
foreach my $bin ( @histo_runtime ) {
print "$bin->[0]\t$bin->[1]\n";
}
}
sub printJob {
my $job = shift;
my $jobString = <<"END_JOB";
=================================
JobId: $job->{job_id}
UserId: $job->{user_id}
Number of nodes: $job->{num_nodes}
From $job->{start_time} to $job->{stop_time}
Duration $job->{duration}
END_JOB
print $jobString;
}
pod2usage(1) if $help;
pod2usage(-verbose => 2) if $man;
# build query conditions
if ( $user ) {
push @conditions, "user_id=\'$user\'";
}
if ( $project ) {
push @conditions, "project_id=\'$project\'";
}
if ( @numnodes ) {
($add, $from, $to) = processRange($numnodes[0], $numnodes[1]);
buildCondition('num_nodes');
}
if ( @starttime ) {
($add, $from, $to) = processRange( parseDate($starttime[0]), parseDate($starttime[1]));
buildCondition('start_time');
}
if ( @duration ) {
($add, $from, $to) = processRange( parseDuration($duration[0]), parseDuration($duration[1]));
buildCondition('duration');
}
my $query;
my $conditionstring;
if ( @conditions ){
$conditionstring = ' WHERE ';
$conditionstring .= join(' AND ',@conditions);
}
# handle mode
if ( $mode eq 'query' ) {
$query = 'SELECT * FROM job'.$conditionstring;
print "$query\n";
exit;
}
if ( $mode eq 'count' ) {
$query = 'SELECT COUNT(*) FROM job'.$conditionstring;
my ($count) = $dbh->selectrow_array($query);
print "COUNT $count\n";
exit;
}
if ( $mode eq 'stat' ) {
printJobStat($conditionstring);
exit;
}
$query = 'SELECT * FROM job'.$conditionstring;
my $sth = $dbh->prepare($query);
$sth->execute;
my %row;
$sth->bind_columns( \( @row{ @{$sth->{NAME_lc} } } ));
if ( $mode eq 'list' ) {
while ($sth->fetch) {
printJob(\%row);
}
} elsif ( $mode eq 'ids' ) {
while ($sth->fetch) {
print "$row{job_id}\n";
}
} else {
die "ERROR Unknown mode $mode!\n";
}
__END__
=head1 NAME
acQuery.pl - Wrapper script to access sqlite job database.
=head1 SYNOPSIS
acQuery.pl [options] -- <DB file>
Help Options:
--help Show help text
--man Show man page
--mode <mode> Set the operation mode
--user <user_id> Search for jobs of specific user
--project <project_id> Search for jobs of specific project
--duration <from> <to> Specify duration range of jobs
--numnodes <from> <to> Specify range for number of nodes of job
--starttime <from> <to> Specify range for start time of jobs
=head1 OPTIONS
=over 8
=item B<--help>
Show a brief help information.
=item B<--man>
Read the manual, with examples
=item B<--mode [012]>
Specify output mode. Mode can be one of:
=over 4
=item B<ids>
Print list of job ids matching conditions. One job id per line. (default mode)
=item B<query>
Print the query string and then exit.
=item B<count>
Only output the number of jobs matching the conditions.
=item B<list>
Output a record of every job matching the conditions.
=item B<stat>
Output job statistic for all jobs matching the conditions.
=back
=item B<--user>
Search job for a specific user id.
=item B<--project>
Search job for a specific project.
=item B<--duration>
Specify condition for job duration. This option takes two arguments: If both
arguments are positive integers the condition is duration between first
argument and second argument. If the second argument is zero condition is duration
smaller than first argument. If first argument is zero condition is duration
larger than second argument. Duration can be in seconds, minutes (append m) or
hours (append h).
=item B<--numnodes>
Specify condition for number of node range of job. This option takes two
arguments: If both arguments are positive integers the condition is number of
nodes between first argument and second argument. If the second argument is
zero condition is number of nodes smaller than first argument. If first
argument is zero condition is number of nodes larger than second argument.
=item B<--starttime>
Specify condition for the starttime of job. This option takes two
arguments: If both arguments are positive integers the condition is start time
between first argument and second argument. If the second argument is
zero condition is start time smaller than first argument. If first
argument is zero condition is start time larger than second argument.
Start time must be given as date in the following format: %d.%m.%Y
=back
=head1 DESCRIPTION
=head1 EXAMPLES
=head1 AUTHOR
Jan Eitzinger - L<https://hpc.fau.de/person/jan-eitzinger/>
=cut

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acSync.pl Executable file
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#!/usr/bin/env perl
# =======================================================================================
#
# Author: Jan Eitzinger (je), jan.eitzinger@fau.de
# Copyright (c) 2019 RRZE, University Erlangen-Nuremberg
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
# =======================================================================================
use strict;
use warnings;
use utf8;
use File::Slurp;
use Data::Dumper;
use JSON::MaybeXS qw(encode_json decode_json);
use DBI;
my $database = 'jobDB';
my $basedir = './data';
my %attr = (
PrintError => 1,
RaiseError => 1
);
my $dbh = DBI->connect(
"DBI:SQLite:dbname=$database", "", "", \%attr);
my $sth_select_job = $dbh->prepare(qq{
SELECT id, user_id, job_id, cluster_id,
start_time, stop_time, duration, num_nodes
FROM job
WHERE job_id=?
});
my $jobcount = 0;
my $wrongjobcount = 0;
opendir my $dh, $basedir or die "can't open directory: $!";
while ( readdir $dh ) {
chomp;
next if $_ eq '.' or $_ eq '..';
my $jobID = $_;
my $needsUpdate = 0;
my $jobmeta_json = read_file("$basedir/$jobID/meta.json");
my $job = decode_json $jobmeta_json;
my @row = $dbh->selectrow_array($sth_select_job, undef, $jobID);
if ( @row ) {
$jobcount++;
# print Dumper(@row);
my $duration_diff = abs($job->{duration} - $row[6]);
if ( $duration_diff > 120 ) {
$needsUpdate = 1;
# print "$jobID DIFF DURATION $duration_diff\n";
# print "CC $row[4] - $row[5]\n";
# print "DB $job->{start_time} - $job->{stop_time}\n"
}
if ( $row[7] != $job->{num_nodes} ){
$needsUpdate = 1;
# print "$jobID DIFF NODES $row[7] $job->{num_nodes}\n";
}
} else {
print "$jobID NOT in DB!\n";
}
if ( $needsUpdate ){
$wrongjobcount++;
print "$jobID\n";
}
}
closedir $dh or die "can't close directory: $!";
$dbh->disconnect;
print "$wrongjobcount of $jobcount need update\n";

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initDB.sql Normal file
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CREATE TABLE job ( id INTEGER PRIMARY KEY,
job_id TEXT, user_id TEXT, project_id TEXT, cluster_id TEXT,
start_time INTEGER, stop_time INTEGER, duration INTEGER,
walltime INTEGER, job_state TEXT,
num_nodes INTEGER, node_list TEXT, has_profile INTEGER,
mem_used REAL, flops_any REAL, mem_bw REAL, ib_bw REAL, file_bw REAL);
CREATE TABLE tag ( id INTEGER PRIMARY KEY, tag_type TEXT, tag_name TEXT);
CREATE TABLE jobtag ( job_id INTEGER, tag_id INTEGER, PRIMARY KEY (job_id, tag_id),
FOREIGN KEY (job_id) REFERENCES job (id) ON DELETE CASCADE ON UPDATE NO ACTION,
FOREIGN KEY (tag_id) REFERENCES tag (id) ON DELETE CASCADE ON UPDATE NO ACTION );