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
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
|
#!/bin/sh
#
# *********
# ATTENTION
# *********
# This file has been replaced by sge_mpirun. This file applies only to
# MPICH-GM versions prior to the 1.2.4..8a release.
#
#___INFO__MARK_BEGIN__
##########################################################################
#
# The Contents of this file are made available subject to the terms of
# the Sun Industry Standards Source License Version 1.2
#
# Sun Microsystems Inc., March, 2001
#
#
# Sun Industry Standards Source License Version 1.2
# =================================================
# The contents of this file are subject to the Sun Industry Standards
# Source License Version 1.2 (the "License"); You may not use this file
# except in compliance with the License. You may obtain a copy of the
# License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
#
# Software provided under this License is provided on an "AS IS" basis,
# WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
# WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
# MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
# See the License for the specific provisions governing your rights and
# obligations concerning the Software.
#
# The Initial Developer of the Original Code is: Sun Microsystems, Inc.
#
# Copyright: 2001 by Sun Microsystems, Inc.
#
# All Rights Reserved.
#
##########################################################################
#___INFO__MARK_END__
#
# preparation of the mpi machine file
#
# usage: startmpi.sh [options] <pe_hostfile> <path_of_mpirun_command>
#
# options are:
# -catch_hostname
# force use of hostname wrapper in $TMPDIR when
# starting mpirun
# -catch_rsh
# force use of rsh wrapper in $TMPDIR when starting mpirun
# -unique
# generate a machinefile where each hostname appears
# only once. This is needed to setup a multithreaded
# mpi application
#
PeHostfile2MachineFile()
{
make_unique=0
if [ "$1" = "-unique" ]; then
shift 1
make_unique=1
fi
host_list=
prev_host=
mpi_tasks=0
while read line; do
host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`
nslots=`echo $line|cut -f2 -d" "`
port=`echo $line|cut -f4 -d" "`
if [ $make_unique = 0 ] || [ "$host" != "$prev_host" ]; then
if [ $make_unique = 1 ]; then
nslots=1
fi
i=1
while [ $i -le $nslots ]; do
# add code here to map regular hostnames into ATM hostnames
host_list="${host_list}$host $port
"
i=`expr $i + 1`
mpi_tasks=`expr $mpi_tasks + 1`
done
fi
prev_host=$host
done <$1
echo $mpi_tasks
echo "$host_list"
}
#
# startup of MPI conforming with the Grid Engine
# Parallel Environment interface
#
# on success the job will find a machine-file in $TMPDIR/machines
#
# useful to control parameters passed to us
echo $*
# parse options
catch_rsh=0
catch_hostname=0
unique=0
while [ "$1" != "" ]; do
case "$1" in
-catch_rsh)
catch_rsh=1
;;
-catch_hostname)
catch_hostname=1
;;
-unique)
unique=1
;;
-param)
shift
eval $2
;;
*)
break;
;;
esac
shift
done
me=`basename $0`
# test number of args
if [ $# -ne 2 ]; then
echo "$me: got wrong number of arguments" >&2
echo "$me: usage $0 pe_hostfile mpirun_command" >&2
exit 1
fi
# get arguments
pe_hostfile=$1
mpirun=$2
export mpirun
# ensure job will be able to exec mpirun
if [ ! -x $mpirun ]; then
echo "$me: can't execute $mpirun" >&2
echo "$me: PE $PE does not specify a valid mpirun_command" >&2
exit 1
fi
# link the mpirun command to TMPDIR, so sge_mpirun can call it
ln -s $mpirun $TMPDIR/mpirun.sge
# ensure pe_hostfile is readable
if [ ! -r $pe_hostfile ]; then
echo "$me: can't read $pe_hostfile" >&2
exit 1
fi
# create machine-file
# remove column with number of slots per queue
# mpi does not support them in this form
machines="$TMPDIR/machines"
if [ $unique = 1 ]; then
PeHostfile2MachineFile -unique $pe_hostfile >> $machines
else
PeHostfile2MachineFile $pe_hostfile >> $machines
fi
# trace machines file
echo Machine file is $machines
cat $machines
#
# Make script wrapper for 'rsh' available in jobs tmp dir
#
if [ $catch_rsh = 1 ]; then
rsh_wrapper=$SGE_ROOT/mpi/rsh
if [ ! -x $rsh_wrapper ]; then
echo "$me: can't execute $rsh_wrapper" >&2
echo " maybe it resides at a file system not available at this machine" >&2
exit 1
fi
rshcmd=rsh
case "$ARC" in
hp|hp10|hp11) rshcmd=remsh ;;
*) ;;
esac
# note: This could also be done using rcp, ftp or s.th.
# else. We use a symbolic link since it is the
# cheapest in case of a shared filesystem
#
ln -s $rsh_wrapper $TMPDIR/$rshcmd
fi
#
# Make script wrapper for 'hostname' available in jobs tmp dir
#
if [ $catch_hostname = 1 ]; then
hostname_wrapper=$SGE_ROOT/mpi/hostname
if [ ! -x $hostname_wrapper ]; then
echo "$me: can't execute $hostname_wrapper" >&2
echo " maybe it resides at a file system not available at this machine" >&2
exit 1
fi
# note: This could also be done using rcp, ftp or s.th.
# else. We use a symbolic link since it is the
# cheapest in case of a shared filesystem
#
ln -s $hostname_wrapper $TMPDIR/hostname
fi
# signal success to caller
exit 0
|
