<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:x="urn:schemas-microsoft-com:office:excel" xmlns:p="urn:schemas-microsoft-com:office:powerpoint" xmlns:a="urn:schemas-microsoft-com:office:access" xmlns:dt="uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:s="uuid:BDC6E3F0-6DA3-11d1-A2A3-00AA00C14882" xmlns:rs="urn:schemas-microsoft-com:rowset" xmlns:z="#RowsetSchema" xmlns:b="urn:schemas-microsoft-com:office:publisher" xmlns:ss="urn:schemas-microsoft-com:office:spreadsheet" xmlns:c="urn:schemas-microsoft-com:office:component:spreadsheet" xmlns:odc="urn:schemas-microsoft-com:office:odc" xmlns:oa="urn:schemas-microsoft-com:office:activation" xmlns:html="http://www.w3.org/TR/REC-html40" xmlns:q="http://schemas.xmlsoap.org/soap/envelope/" xmlns:rtc="http://microsoft.com/officenet/conferencing" xmlns:D="DAV:" xmlns:Repl="http://schemas.microsoft.com/repl/" xmlns:mt="http://schemas.microsoft.com/sharepoint/soap/meetings/" xmlns:x2="http://schemas.microsoft.com/office/excel/2003/xml" xmlns:ppda="http://www.passport.com/NameSpace.xsd" xmlns:ois="http://schemas.microsoft.com/sharepoint/soap/ois/" xmlns:dir="http://schemas.microsoft.com/sharepoint/soap/directory/" xmlns:ds="http://www.w3.org/2000/09/xmldsig#" xmlns:dsp="http://schemas.microsoft.com/sharepoint/dsp" xmlns:udc="http://schemas.microsoft.com/data/udc" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:sub="http://schemas.microsoft.com/sharepoint/soap/2002/1/alerts/" xmlns:ec="http://www.w3.org/2001/04/xmlenc#" xmlns:sp="http://schemas.microsoft.com/sharepoint/" xmlns:sps="http://schemas.microsoft.com/sharepoint/soap/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:udcs="http://schemas.microsoft.com/data/udc/soap" xmlns:udcxf="http://schemas.microsoft.com/data/udc/xmlfile" xmlns:udcp2p="http://schemas.microsoft.com/data/udc/parttopart" xmlns:wf="http://schemas.microsoft.com/sharepoint/soap/workflow/" xmlns:dsss="http://schemas.microsoft.com/office/2006/digsig-setup" xmlns:dssi="http://schemas.microsoft.com/office/2006/digsig" xmlns:mdssi="http://schemas.openxmlformats.org/package/2006/digital-signature" xmlns:mver="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:mrels="http://schemas.openxmlformats.org/package/2006/relationships" xmlns:spwp="http://microsoft.com/sharepoint/webpartpages" xmlns:ex12t="http://schemas.microsoft.com/exchange/services/2006/types" xmlns:ex12m="http://schemas.microsoft.com/exchange/services/2006/messages" xmlns:pptsl="http://schemas.microsoft.com/sharepoint/soap/SlideLibrary/" xmlns:spsl="http://microsoft.com/webservices/SharePointPortalServer/PublishedLinksService" xmlns:Z="urn:schemas-microsoft-com:" xmlns:st="" 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 12 (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:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"Futura Bk";
panose-1:2 11 5 2 2 2 4 2 3 3;}
@font-face
{font-family:"Arial Rounded MT Bold";
panose-1:2 15 7 4 3 5 4 3 2 4;}
@font-face
{font-family:"Britannic Bold";
panose-1:2 11 9 3 6 7 3 2 2 4;}
@font-face
{font-family:Aharoni;
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:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0in;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Arial","sans-serif";
color:windowtext;
font-weight:normal;
font-style:normal;
text-decoration:none none;}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="2050" />
</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=purple>
<div class=WordSection1>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Hello,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I
am new to CitcomS. I just built the code and started a run on a single
node (12 cores) as:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>mpirun
-np 4 CitcomSFull cookbook3.cfg >& cbook3.4.out<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>However,
I get an error such as:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>node
0: error: error: either use z_layer for non dim layer depths, or set num_mat to
four<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>node
1: error: error: either use z_layer for non dim layer depths, or set num_mat to
four<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>The
num_mat is already set to 4 in the cfg file. How do I make this work ?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I
tried the cookbook1 and is asking me to set nodex, nodey which are not set in
the cfg file.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>What
are the recommended values to these and nodez, if needed ?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Thanks.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Logan<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Britannic Bold","sans-serif";
color:#7030A0'>Logan Sankaran Ph.D.<b><o:p></o:p></b></span></p>
<p class=MsoNormal><span style='color:#7030A0'>Sr. Performance Specialist, HPC
Benchmarking<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#7030A0'>Solution Technology Services
(STS) <o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#7030A0'>Americas Shared Solutions
Architecture (SSA)<i><o:p></o:p></i></span></p>
<p class=MsoNormal><b><span style='color:#7030A0'>Hewlett-Packard Company <o:p></o:p></span></b></p>
<p class=MsoNormal><b><span style='color:#7030A0'>PLANO, Texas, USA<o:p></o:p></span></b></p>
<p class=MsoNormal><b><span style='color:#7030A0'><o:p> </o:p></span></b></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Futura Bk","sans-serif";
color:#C00000'> 972 - 727 - 9561</span><span style='font-size:10.0pt;
font-family:"Futura Bk","sans-serif";color:#221E1F'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;color:#003300'> <a
href="mailto:logan.sankaran@hp.com"><span style='color:blue'>logan.sankaran@hp.com</span></a></span><span
style='color:#7030A0'><o:p></o:p></span></p>
<p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:14.0pt;
font-family:"Arial Rounded MT Bold","sans-serif";color:#C00000'>Passion for
Performance<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><b><i><span style='font-size:
8.0pt;font-family:"Futura Bk","sans-serif";color:#1F497D'><o:p> </o:p></span></i></b></p>
<p class=MsoNormal style='text-autospace:none'><i><span style='font-size:12.0pt;
font-family:"Futura Bk","sans-serif";color:#1F497D'>Visit our website: </span></i><span
style='font-size:12.0pt'><a
href="http://enhanced2.sharepoint.hp.com/teams/presales/ama/ssa/default.aspx"><i><span
style='font-family:"Futura Bk","sans-serif";color:blue'>http://enhanced2.sharepoint.hp.com/teams/presales/ama/ssa/default.aspx</span></i></a></span><i><span
style='font-size:12.0pt;font-family:"Futura Bk","sans-serif";color:#1F497D'><o:p></o:p></span></i></p>
<p class=MsoNormal style='text-autospace:none'><i><span style='font-size:12.0pt;
font-family:"Futura Bk","sans-serif";color:#1F497D'>Engage our services: Web
- </span></i><span style='font-size:12.0pt'><a
href="http://engage.presales.hp.com/"><i><span style='font-family:"Futura Bk","sans-serif";
color:blue'>http://engage.presales.hp.com</span></i></a></span><i><span
style='font-size:12.0pt;font-family:"Futura Bk","sans-serif";color:#1F497D'><o:p></o:p></span></i></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><a
href="http://h18004.www1.hp.com/products/solutions/converged/main.html"
title="http://h18004.www1.hp.com/products/solutions/converged/main.html"><span
style='color:windowtext;text-decoration:none'><img border=0 width=92 height=75
id="Picture_x0020_1" src="cid:image001.png@01CB226E.31ADECE0"
alt="cid:image001.gif@01CAA598.B0CCBC20"></span></a><span style='font-size:
10.0pt;font-family:"Futura Bk","sans-serif";color:#00B050'> </span><span
style='color:#1F497D'><img border=0 width=475 height=30 id="Picture_x0020_2"
src="cid:image002.gif@01CB226E.31ADECE0" alt="email_footer_tree_text"></span><span
style='font-size:12.0pt;font-family:"Futura Bk","sans-serif";color:#221E1F'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
</div>
</body>
</html>