<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Batang;
panose-1:2 3 6 0 0 1 1 1 1 1;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"\@Batang";
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
h1
{margin-top:12.0pt;
margin-right:0in;
margin-bottom:4.0pt;
margin-left:0in;
text-align:center;
text-indent:0in;
page-break-after:avoid;
mso-list:l1 level1 lfo4;
font-size:10.0pt;
font-family:"Times New Roman";
font-variant:small-caps;
font-weight:normal;}
h2
{margin-top:6.0pt;
margin-right:0in;
margin-bottom:3.0pt;
margin-left:0in;
text-indent:0in;
page-break-after:avoid;
mso-list:l1 level2 lfo4;
font-size:10.0pt;
font-family:"Times New Roman";
font-weight:normal;
font-style:italic;}
h3
{margin:0in;
margin-bottom:.0001pt;
text-indent:0in;
page-break-after:avoid;
mso-list:l1 level3 lfo4;
font-size:10.0pt;
font-family:"Times New Roman";
font-weight:normal;
font-style:italic;}
p.MsoFootnoteText, li.MsoFootnoteText, div.MsoFootnoteText
{margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Times New Roman";}
p.MsoListNumber, li.MsoListNumber, div.MsoListNumber
{margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.25in;
margin-bottom:.0001pt;
text-indent:-.25in;
mso-list:l0 level1 lfo5;
font-size:12.0pt;
font-family:"Times New Roman";}
p.MsoTitle, li.MsoTitle, div.MsoTitle
{margin:0in;
margin-bottom:.0001pt;
text-align:center;
mso-element:frame;
font-size:24.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
p
{mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman";}
p.Abstract, li.Abstract, div.Abstract
{margin-top:1.0pt;
margin-right:0in;
margin-bottom:0in;
margin-left:0in;
margin-bottom:.0001pt;
text-align:justify;
text-justify:inter-ideograph;
text-indent:10.1pt;
font-size:9.0pt;
font-family:"Times New Roman";
font-weight:bold;}
p.Authors, li.Authors, div.Authors
{margin-top:16.0pt;
margin-right:0in;
margin-bottom:16.0pt;
margin-left:0in;
text-align:center;
font-size:11.0pt;
font-family:"Times New Roman";}
p.FigureCaption, li.FigureCaption, div.FigureCaption
{margin:0in;
margin-bottom:.0001pt;
text-align:justify;
text-justify:inter-ideograph;
text-indent:28.1pt;
mso-list:l2 level1 lfo1;
font-size:8.0pt;
font-family:"Times New Roman";}
p.References, li.References, div.References
{margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.25in;
margin-bottom:.0001pt;
text-align:justify;
text-justify:inter-ideograph;
text-indent:-.25in;
mso-list:l3 level1 lfo6;
font-size:8.0pt;
font-family:"Times New Roman";}
p.TableTitle, li.TableTitle, div.TableTitle
{margin:0in;
margin-bottom:.0001pt;
text-align:center;
font-size:8.0pt;
font-family:"Times New Roman";
font-variant:small-caps;}
p.Text, li.Text, div.Text
{margin:0in;
margin-bottom:.0001pt;
text-align:justify;
text-justify:inter-ideograph;
text-indent:10.1pt;
line-height:105%;
font-size:10.0pt;
font-family:"Times New Roman";}
span.EmailStyle27
{mso-style-type:personal-reply;
font-family:Arial;
color:blue;
font-weight:normal;
font-style:normal;
text-decoration:none none;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
/* List Definitions */
@list l0
{mso-list-id:-120;
mso-list-type:simple;
mso-list-template-ids:1985357212;}
@list l0:level1
{mso-level-style-link:"List Number";
mso-level-tab-stop:.25in;
mso-level-number-position:left;
margin-left:.25in;
text-indent:-.25in;}
@list l1
{mso-list-id:-5;
mso-list-template-ids:-761218020;}
@list l1:level1
{mso-level-number-format:roman-upper;
mso-level-style-link:"Heading 1";
mso-level-tab-stop:none;
mso-level-number-position:left;
mso-level-legacy:yes;
mso-level-legacy-indent:.1in;
mso-level-legacy-space:.1in;
margin-left:0in;
text-indent:0in;
mso-ansi-font-size:10.0pt;
mso-bidi-font-size:10.0pt;}
@list l1:level2
{mso-level-number-format:alpha-upper;
mso-level-style-link:"Heading 2";
mso-level-tab-stop:none;
mso-level-number-position:left;
mso-level-legacy:yes;
mso-level-legacy-indent:.1in;
mso-level-legacy-space:.1in;
margin-left:0in;
text-indent:0in;}
@list l1:level3
{mso-level-style-link:"Heading 3";
mso-level-text:"%3\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
mso-level-legacy:yes;
mso-level-legacy-indent:.1in;
mso-level-legacy-space:.1in;
margin-left:0in;
text-indent:0in;}
@list l1:level4
{mso-level-number-format:alpha-lower;
mso-level-text:"%4\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
mso-level-legacy:yes;
mso-level-legacy-indent:.5in;
mso-level-legacy-space:0in;
margin-left:.8in;
text-indent:-.5in;}
@list l1:level5
{mso-level-text:"\(%5\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
mso-level-legacy:yes;
mso-level-legacy-indent:.5in;
mso-level-legacy-space:0in;
margin-left:1.3in;
text-indent:-.5in;}
@list l1:level6
{mso-level-number-format:alpha-lower;
mso-level-text:"\(%6\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
mso-level-legacy:yes;
mso-level-legacy-indent:.5in;
mso-level-legacy-space:0in;
margin-left:1.8in;
text-indent:-.5in;}
@list l1:level7
{mso-level-number-format:roman-lower;
mso-level-text:"\(%7\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
mso-level-legacy:yes;
mso-level-legacy-indent:.5in;
mso-level-legacy-space:0in;
margin-left:2.3in;
text-indent:-.5in;}
@list l1:level8
{mso-level-number-format:alpha-lower;
mso-level-text:"\(%8\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
mso-level-legacy:yes;
mso-level-legacy-indent:.5in;
mso-level-legacy-space:0in;
margin-left:2.8in;
text-indent:-.5in;}
@list l1:level9
{mso-level-number-format:roman-lower;
mso-level-text:"\(%9\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
mso-level-legacy:yes;
mso-level-legacy-indent:.5in;
mso-level-legacy-space:0in;
margin-left:3.3in;
text-indent:-.5in;}
@list l2
{mso-list-id:29569615;
mso-list-type:hybrid;
mso-list-template-ids:1906351762 1873050708 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l2:level1
{mso-level-style-link:"Figure Caption";
mso-level-text:"Fig\. %1\.";
mso-level-tab-stop:46.1pt;
mso-level-number-position:left;
margin-left:0in;
text-indent:28.1pt;}
@list l3
{mso-list-id:981957988;
mso-list-type:simple;
mso-list-template-ids:1571224598;}
@list l3:level1
{mso-level-style-link:References;
mso-level-text:"\[%1\]";
mso-level-tab-stop:.25in;
mso-level-number-position:left;
margin-left:.25in;
text-indent:-.25in;}
ol
{margin-bottom:0in;}
ul
{margin-bottom:0in;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-US link=blue vlink=blue>
<div class=Section1>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'>Thanks, Simon.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'>When I have “/gate/output/root/setSaveRndmFlag
0” and run one of the split task (ie. Gate SPECTbench_cluster4.mac), I get the error
saying,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'>!!! From Gate v5.0 – This command is
obsolete<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'>!!! See the new Random mechanism in the
Users Guide<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'>*** G4Exception: Aborting execution ***<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'>Aborted<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'>Without this line, it looks okay.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'>Yonggang<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:blue'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Simon Stute
[mailto:gate.stute@gmail.com] <br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, September 30,
2009 6:49 AM<br>
<b><span style='font-weight:bold'>To:</span></b> Cui, Yonggang<br>
<b><span style='font-weight:bold'>Cc:</span></b>
gate-users@lists.healthgrid.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Gate-users] Random
generation mechanism in Gate 5</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Hi Yonggang,<br>
<br>
It is strange that the first line causes abortion of the simulation ... but as
it is the case, you have to delete it, manually (very annoying) or in the
source code of the gjs program. To do so, open the
Cluster_Tools/jobsplitter/src/GateMacFileParser.cc file and comment line number
289 (the line that says: 'output<<"/gate/output/root/setSaveRndmFlag
0"<<endl;'), and recompile the gjs program.<br>
<br>
The second line is necessary because it will set a different seed for each job.<br>
<br>
The third line, I think, is added when you have not clearly disabled the ascii
output in your original macro file. So add the command
/gate/output/ascii/disable.<br>
<br>
Tell us if something goes wrong again.<br>
Cheers,<br>
Simon<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Wed, Sep 30, 2009 at 5:06 AM, Cui, Yonggang <<a
href="mailto:ycui@bnl.gov">ycui@bnl.gov</a>> wrote:<o:p></o:p></span></font></p>
<div link=blue vlink=purple>
<div>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>Dear
All,</span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>I
am trying to run GATE 5 on a cluster machine. “gjs” splits the job and
always adds the following lines to each “mac” file.</span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>/gate/output/root/setSaveRndmFlag
0</span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>/gate/random/setEngineSeed
…</span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>/gate/output/ascii/setfileName
…</span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>The
first line causes abortion of the simulation. It seems that GATE 5 uses
different random generation mechanism.</span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>Can
anybody explain it in detail? How do we control “gjs” and get rid of this
line?</span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>Thanks,</span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'>Yonggang</span></font><o:p></o:p></p>
<p><font size=3 face=Arial><span style='font-size:12.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
</div>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><br>
_______________________________________________<br>
Gate-users mailing list<br>
<a href="mailto:Gate-users@lists.healthgrid.org">Gate-users@lists.healthgrid.org</a><br>
<a href="http://lists.healthgrid.org/mailman/listinfo/gate-users"
target="_blank">http://lists.healthgrid.org/mailman/listinfo/gate-users</a><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</body>
</html>