<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:m="http://schemas.microsoft.com/office/2004/12/omml" 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)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 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;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","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;}
span.apple-style-span
{mso-style-name:apple-style-span;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page Section1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
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 style='word-wrap: break-word;
-webkit-nbsp-mode: space;-webkit-line-break: after-white-space'>
<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks Diego,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>But, the latest I found on downloads of gromcs webpage was
4.0.3! Is 4.0.4 somewhere else?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Payman <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>Diego Enry Gomes<br>
<b>Sent:</b> May 8, 2009 11:27 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] make install-mdrun<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal>get gromacs 4.04<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Confirm if you changed the permissions correctly and can
write anywhere in /usr/local/ <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<p class=MsoNormal>Are you doing this as 'root' or super user (sudo) ?
Because if you are just a regular user, will won't be able to change the
permissions in /usr/local/. So, configure gmx to be installed in your local
dir.<o:p></o:p></p>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>./configure --prefix=/global/home/pirzadeh/gmx404 <o:p></o:p></p>
</div>
<div>
<div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p class=MsoNormal>On May 8, 2009, at 10:10 AM, Payman Pirzadeh wrote:<o:p></o:p></p>
</div>
<p class=MsoNormal><br>
<br>
<o:p></o:p></p>
<div>
<div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Hi All,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>I realized that I am missing (Lib and bin folders) analysis tools
and mdrun MPI. I re-installed the GROMACS 4.0.3, and I found that when I get to
‘make install-mdrun’ the following messages show up ( I am just copying last
lines):<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>make[2]: *** [install-libLTLIBRARIES] Error 1<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>make[2]: Leaving directory
`/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/mdlib'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>make[1]: *** [install-am] Error 2<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>make[1]: Leaving directory
`/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/mdlib'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>(cd ./src/kernel && make install-mdrun ; exit 0)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>make[1]: Entering directory
`/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/kernel'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>/bin/sh ../../config/mkinstalldirs /usr/local/gromacs/bin<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>mkdir -p -- /usr/local/gromacs/bin<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>mkdir: cannot create directory `/usr/local/gromacs': Permission
denied<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>make[1]: *** [install-mdrun] Error 1<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>make[1]: Leaving directory
`/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/kernel'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>I changed the permissions and I am still receiving the same
message. I will e appreciated if someone tell me what is going wrong?!<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Payman<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<span class=apple-converted-space> </span><a
href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span
class=apple-converted-space> </span>before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<span
class=apple-converted-space> </span><br>
www interface or send it to<span class=apple-converted-space> </span><a
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read<span class=apple-converted-space> </span><a
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
</div>
</div>
</div>
</body>
</html>