1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
|
#! /usr/bin/perl
use strict;
#######################
#Default parameters
#parameters for submiiting processes through SGE
#NOTE: group name is ws06ossmt (with 2 's') and not ws06osmt (with 1 's')
my $queueparameters="-l ws06ossmt=true -l mem_free=0.5G";
my $workingdir=$ENV{PWD};
my $tmpdir="$workingdir/tmp$$";
my $jobscript="$workingdir/job$$";
my $qsubout="$workingdir/out.job$$";
my $qsuberr="$workingdir/err.job$$";
$SIG{INT} = \&kill_all_and_quit; # catch exception for CTRL-C
my $help="";
my $dbg="";
my $version="";
my $qsubname="WR$$";
my $cmd="";
my $cmdout="";
my $cmderr="";
my $parameters="";
sub init(){
use Getopt::Long qw(:config pass_through);
GetOptions('version'=>\$version,
'help'=>\$help,
'debug'=>\$dbg,
'qsub-prefix=s'=> \$qsubname,
'command=s'=> \$cmd,
'stdout=s'=> \$cmdout,
'stderr=s'=> \$cmderr,
'queue-parameter=s'=> \$queueparameters
) or exit(1);
$parameters="@ARGV";
version() if $version;
usage() if $help;
print_parameters() if $dbg;
}
#######################
##print version
sub version(){
# print STDERR "version 1.0 (29-07-2006)\n";
print STDERR "version 1.1 (31-07-2006)\n";
exit(1);
}
#usage
sub usage(){
print STDERR "qsub-wrapper.pl [options]\n";
print STDERR "Options:\n";
print STDERR "-command <file> command to run\n";
print STDERR "-stdout <file> file to save stdout of cmd (optional)\n";
print STDERR "-stderr <file> file to save stderr of cmd (optional)\n";
print STDERR "-qsub-prefix <string> name for sumbitted jobs (optional)\n";
print STDERR "-queue-parameters <string> parameter for the queue (optional)\n";
print STDERR "-debug debug\n";
print STDERR "-version print version of the script\n";
print STDERR "-help this help\n";
exit(1);
}
#printparameters
sub print_parameters(){
print STDERR "command: $cmd\n";
print STDERR "file for stdout: $cmdout\n";
print STDERR "file for stderr: $cmderr\n";
print STDERR "Qsub name: $qsubname\n";
print STDERR "Queue parameters: $queueparameters\n";
print STDERR "parameters directly passed to cmd: $parameters\n";
exit(1);
}
#script creation
sub preparing_script(){
my $scriptheader="\#\! /bin/bash\n\n";
$scriptheader.="uname -a\n\n";
$scriptheader.="cd $workingdir\n\n";
open (OUT, "> ${jobscript}.bash");
print OUT $scriptheader;
print OUT "($cmd $parameters > $tmpdir/cmdout$$) 2> $tmpdir/cmderr$$\n\n";
print OUT "echo exit status \$\?\n\n";
if ($cmdout){
print OUT "mv $tmpdir/cmdout$$ $cmdout\n\n";
print OUT "echo exit status \$\?\n\n";
}
else{
print OUT "rm $tmpdir/cmdout$$\n\n";
print OUT "echo exit status \$\?\n\n";
}
if ($cmderr){
print OUT "mv $tmpdir/cmderr$$ $cmderr\n\n";
print OUT "echo exit status \$\?\n\n";
}
else{
print OUT "rm $tmpdir/cmderr$$\n\n";
print OUT "echo exit status \$\?\n\n";
}
close(OUT);
}
#######################
#Script starts here
init();
usage() if $cmd eq "";
safesystem("mkdir -p $tmpdir") or die;
preparing_script();
my $qsubcmd="qsub $queueparameters -sync yes -o $qsubout -e $qsuberr -N $qsubname ${jobscript}.bash >& ${jobscript}.log";
print STDERR "$qsubcmd\n";
safesystem($qsubcmd) or die;
#getting id of submitted job
my $res;
open (IN,"${jobscript}.log");
chomp($res=<IN>);
split(/\s+/,$res);
my $id=$_[2];
close(IN);
print SDTERR " res:$res\n";
print SDTERR " id:$id\n";
my $failure=&check_exit_status();
&kill_all_and_quit() if $failure;
&remove_temporary_files();
sub check_exit_status(){
my $failure=0;
print STDERR "check_exit_status of submitted job $id\n";
open(IN,"$qsubout");
while (<IN>){
$failure=1 if (/exit status 1/);
}
close(IN);
return $failure;
}
sub kill_all_and_quit(){
print STDERR "kill_all_and_quit\n";
print STDERR "qdel $id\n";
safesystem("qdel $id");
print STDERR "The submitted jobs died not correctly\n";
print STDERR "Send qdel signal to the submitted jobs\n";
exit(1);
}
sub remove_temporary_files(){
#removing temporary files
unlink("${jobscript}.bash");
unlink("${jobscript}.log");
unlink("$qsubout");
unlink("$qsuberr");
rmdir("$tmpdir");
}
sub safesystem {
print STDERR "Executing: @_\n";
system(@_);
if ($? == -1) {
print STDERR "Failed to execute: @_\n $!\n";
exit(1);
}
elsif ($? & 127) {
printf STDERR "Execution of: @_\n died with signal %d, %s coredump\n",
($? & 127), ($? & 128) ? 'with' : 'without';
exit(1);
}
else {
my $exitcode = $? >> 8;
print STDERR "Exit code: $exitcode\n" if $exitcode;
return ! $exitcode;
}
}
|
