<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:st1="urn:schemas-microsoft-com:office:smarttags" 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)">
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PostalCode"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="State"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceName"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceType"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="City"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Book Antiqua";
panose-1:2 4 6 2 5 3 5 3 3 4;}
@font-face
{font-family:"Arial Narrow";
panose-1:2 11 5 6 2 2 2 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:Arial;
color:windowtext;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
-->
</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=purple>
<div class=Section1>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear Sir<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I am trying to install GROMACS. I have tried to install
program and it goes through okay. However, when I try to compile the program in
parallel using the –enable-mpi option, it gives me an error:
“Cannot compile and link MPI code with cc”<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>See below for the command and the error.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Can you suggest what I can do to fix the same?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>_____________________________________________________________________________________________________<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>redwood r0914/gromacs-3.3.1> ./configure
--prefix=/ptmp/r0914/gromacsp --enable-mpi<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking build system type... ia64-unknown-linux-gnu<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking host system type... ia64-unknown-linux-gnu<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for a BSD-compatible install... /usr/bin/install -c<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking whether build environment is sane... yes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for gawk... gawk<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking whether make sets $(MAKE)... yes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking how to create a ustar tar archive... cpio<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for cc... cc<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for C compiler default output file name... a.out<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking whether the C compiler works... yes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking whether we are cross compiling... no<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for suffix of executables... <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for suffix of object files... o<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking whether we are using the GNU C compiler... yes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking whether cc accepts -g... yes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for cc option to accept ANSI C... none needed<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for style of include used by make... GNU<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking dependency style of cc... gcc3<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for mpxlc... no<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for mpicc... no<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for mpcc... no<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking for hcc... no<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>checking whether the MPI cc command works... configure:
error: Cannot compile and link MPI code with cc<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>_____________________________________________________________________________________________________<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Regards<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Akshay<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><strong><b><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Akshay Patny<o:p></o:p></span></font></b></strong></p>
<p class=MsoNormal><strong><b><font size=3 color=red face="Times New Roman"><span
style='font-size:12.0pt;color:red'>Graduate Research Assistant</span></font></b></strong><font
size=2 face="Arial Narrow"><span style='font-size:11.0pt;font-family:"Arial Narrow"'><br>
Faser Hall 417, Department of Medicinal Chemistry</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 face="Arial Narrow"><span style='font-size:
11.0pt;font-family:"Arial Narrow"'>Research Institute of Pharmaceutical
Sciences</span></font><font color=red><span style='color:red'><br>
</span></font><st1:place w:st="on"><st1:PlaceType w:st="on"><font size=2
face="Arial Narrow"><span style='font-size:11.0pt;font-family:"Arial Narrow"'>University</span></font></st1:PlaceType><font
size=2 face="Arial Narrow"><span style='font-size:11.0pt;font-family:"Arial Narrow"'>
of <st1:PlaceName w:st="on">Mississippi</st1:PlaceName></span></font></st1:place><font
color=red><span style='color:red'><br>
</span></font><st1:place w:st="on"><st1:City w:st="on"><font size=2
face="Arial Narrow"><span style='font-size:11.0pt;font-family:"Arial Narrow"'>University</span></font></st1:City><font
size=2 face="Arial Narrow"><span style='font-size:11.0pt;font-family:"Arial Narrow"'>,
<st1:State w:st="on">MS</st1:State> <st1:PostalCode w:st="on">38677</st1:PostalCode></span></font></st1:place><font
color=red><span style='color:red'><br>
</span></font><font size=1 face="Book Antiqua"><span style='font-size:9.0pt;
font-family:"Book Antiqua"'>E-mail: <a href="mailto:akshay17@olemiss.edu">akshay17@olemiss.edu</a></span></font><font
color=red><span style='color:red'><br>
</span></font><font size=1 face="Book Antiqua"><span style='font-size:9.0pt;
font-family:"Book Antiqua"'>Tel: 662-915-1286 (office); Web: <a
href="http://www.olemiss.edu">www.olemiss.edu</a> </span></font><font size=2
face="Arial Narrow"><span style='font-size:11.0pt;font-family:"Arial Narrow"'><o:p></o:p></span></font></p>
<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>