<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 12/08/2011 12:38 AM, afsaneh maleki wrote:
<blockquote
cite="mid:CAOXtCiv206gV4p2A0G3OCCFVex7UB0gxtpy-SNVwbmiQzfGKgw@mail.gmail.com"
type="cite">
<div>Hi,</div>
<div><br clear="all">
<br>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">My characteristics
computer:</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">Root at
…fftw-3.2.2]# uname -a</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">Linux
localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat
Nov 7 21:25:57 EST 2009 i686 i686 i386 GNU/Linux</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">To install FFTW
version 3.2.2.</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">I used the
following commands:</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">Root at
…fftw-3.2.2]#<span style="mso-spacerun: yes"> </span>./configure
--enable-threads --enable-float --enable-shared</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font size="3"><font face="Times New Roman"><span
style="mso-spacerun: yes"> </span>Root at
…fftw-3.2.2]#<span style="mso-spacerun: yes"> </span>make</font></font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font size="3"><font face="Times New Roman"><span
style="mso-spacerun: yes"> </span>Root at
…fftw-3.2.2]#<span style="mso-spacerun: yes"> </span>make
install</font></font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">After using “make”
and “make install”, it get me the following text at end:</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">make[3]: Leaving
directory `/home/afsaneh/m/fftw-3.2.2/tools'</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">make[2]: Leaving
directory `/home/afsaneh/m/fftw-3.2.2/tools'</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">Making all in m4</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">make[2]: Entering
directory `/home/afsaneh/m/fftw-3.2.2/m4'</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">make[2]: Nothing
to be done for `all'.</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">make[2]: Leaving
directory `/home/afsaneh/m/fftw-3.2.2/m4'</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">make[1]: Leaving
directory `/home/afsaneh/m/fftw-3.2.2'</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">..........................</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">To install gromacs
version 4.5.1</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">root@localhost
gromacs-4.5.1]#./configure </font></p>
</div>
</blockquote>
<br>
You aren't configuring to use fftw3. You should probably use the
same --enable-shared setting for both FFTW and GROMACS.<br>
<br>
<blockquote
cite="mid:CAOXtCiv206gV4p2A0G3OCCFVex7UB0gxtpy-SNVwbmiQzfGKgw@mail.gmail.com"
type="cite">
<div>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font style="BACKGROUND-COLOR: #ffcccc" face="Times New
Roman" size="4">* On most platforms you can save 10X space
with dynamic libraries, although</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman"><font size="4"><font
style="BACKGROUND-COLOR: #ffcccc"><span
style="mso-spacerun: yes"> </span>the binaries might
be less portable. Why not try --enable-shared ?</font></font></font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"> </p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">[root@localhost
gromacs-4.5.1]#make</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">[root@localhost
gromacs-4.5.1]#make install</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">[root@localhost
gromacs-4.5.1]# make links</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">cd
/usr/local/gromacs/bin && programs=`ls` &&
cd /usr/local/bin && \</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font size="3"><font face="Times New Roman"><span
style="mso-tab-count: 1"> </span>for i in
$programs; do \</font></font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font size="3"><font face="Times New Roman"><span
style="mso-tab-count: 1"> </span><span
style="mso-spacerun: yes"> </span>(test ! -f $i
&& ln -s /usr/local/gromacs/bin/$i . ; exit 0); \</font></font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font size="3"><font face="Times New Roman"><span
style="mso-tab-count: 1"> </span>done</font></font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">when i used each
command with” –h” or “–help” I obtain the followinf error:</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">[afsaneh@localhost
~]$ g_analyze -h</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">g_analyze: error
while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory</font></p>
</div>
</blockquote>
<br>
Sounds like somehow the make environment could find the FFTW
libraries, but the execution environment could not. Do heed the
advice here
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation">http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation</a>
(and the rest of the instructions, too)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAOXtCiv206gV4p2A0G3OCCFVex7UB0gxtpy-SNVwbmiQzfGKgw@mail.gmail.com"
type="cite">
<div>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">[afsaneh@localhost
~]$ editconf -h</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">editconf: error
while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">How to solve this
problem?</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">Best wishes,</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT:
150%"><font face="Times New Roman" size="3">Afsaneh</font></p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>