<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="City"/>
<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="place"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Arial Narrow";
panose-1:2 11 5 6 2 2 2 3 2 4;}
@font-face
{font-family:"Book Antiqua";
panose-1:2 4 6 2 5 3 5 3 3 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;
font-family:Arial;
color:windowtext;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@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>
<div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt'>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Dear All<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>This is Akshay Patny from The
University of Mississippi.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>I am trying to install GROMACS 3.3.1
on SGI ORIGIN 350 with 8 parallel 700 MHz MIPS R16000 (IP35) processors.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>As I do not have access to root, I
am trying to install everything including the FFTW and GROMACS in my home
directory which is:<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>/mnt1/usr/akshayp/<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>I used the following source code
from the website <o:p></o:p></span></font></p>
<table class=MsoNormalTable border=1 cellspacing=0 cellpadding=0 width="100%"
style='width:100.0%'>
<tr>
<td valign=top style='padding:3.75pt 3.75pt 3.75pt 3.75pt'>
<p class=MsoNormal style='text-align:justify'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><a
href="ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.1.tar.gz">gromacs-3.3.1.tar.gz</a><font
color=black><span style='color:black'><o:p></o:p></span></font></span></font></p>
</td>
<td valign=top style='padding:3.75pt 3.75pt 3.75pt 3.75pt'>
<p class=MsoNormal style='text-align:justify'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>2006-04-06<font
color=black><span style='color:black'><o:p></o:p></span></font></span></font></p>
</td>
<td style='padding:3.75pt 3.75pt 3.75pt 3.75pt'>
<p class=MsoNormal style='text-align:justify'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>1af34a99950813ca7cf893253c447cd1
<font color=black><span style='color:black'><o:p></o:p></span></font></span></font></p>
</td>
</tr>
</table>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>I think I already have ANSI C compiler
so I installed FFTW 3.1 before installing GROMACS as mentioned. I installed
FFTW in both single as well as double precision mode as advised and it went
through.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>I installed FFTW in
/mnt1/usr/akshayp/fftw-3.1.1<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>After that, I tried installing the GROMACS
as given<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>In installed it in
/mnt1/usr/akshayp/gromacs-3.3.1 which was the directory created after I untared
the source code file.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>First step:<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>./configure<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>The output of this command is given
in Output_Gromacs_Configure.txt file.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Second step:<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>make >&l og<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>The output of this command is given
in Output_Gromacs_make_log.txt file.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Third step:<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>make install<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>The output of this command is given
in Output_Gromacs_make_install.txt file.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>The second and third steps gave some
errors. The last few lines including error for are as follows:<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>cc-3316 cc: ERROR File =
gmx_fft_fftw3.c, Line = 186<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>The expression must be a pointer to
a complete object type.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> pc +=
8; <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>cc-3316 cc: ERROR File =
gmx_fft_fftw3.c, Line = 190<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> The expression must be a
pointer to a complete object type.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> pc +=
8; <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>2 errors detected in the compilation
of "gmx_fft_fftw3.c".<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>*** Error code 1 (bu21)<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>*** Error code 1 (bu21)<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>*** Error code 1 (bu21)<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Can somebody guide me how can I fix
this error? Also, please tell me as I have installed GROMACS in a local
directory, what else I need to change (such as in the cshrc) and how? A little
detailed answer will be of great help, as I am new to the UNIX installation
area.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Please let me know in case you need
any additional information from my side.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Looking forward to hear from you<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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='text-align:justify'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Kind Regards<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-align:justify'><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 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>
</div>
</body>
</html>