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On 10/01/2012 5:45 PM, Dialing Pretty wrote:
<blockquote
cite="mid:1326177951.1925.YahooMailNeo@web121701.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div style="RIGHT: auto"><span style="RIGHT: auto">Dear Mark,</span></div>
<div style="RIGHT: auto"><span style="RIGHT: auto"></span> </div>
<div style="RIGHT: auto"><span style="RIGHT: auto">If "<span
style="FONT-FAMILY: courier new, courier, monospace">--<font
style="BACKGROUND-COLOR: yellow">disable</font>-threads</span>
", how it will influence the function of GROMACS?</span></div>
</div>
</blockquote>
<br>
By preventing you from running mdrun with a separate execution
thread in parallel on each physical processor that your machine has.
If you need parallel functionality, compile with MPI enabled.<br>
<br>
<blockquote
cite="mid:1326177951.1925.YahooMailNeo@web121701.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div style="RIGHT: auto"><span style="RIGHT: auto"></span> </div>
<div style="RIGHT: auto"><span style="RIGHT: auto">Secondly, for
the webpage you introduced to me "<a moz-do-not-send="true"
style="RIGHT: auto"
href="http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO"
rel="nofollow" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO</a>",
"Edit your login files to source
/usr/local/gromacs/bin/GMXRC (or manually add
/usr/local/gromacs/man to the MANPATH and check that
/usr/local/bin is in the PATH)" is a little difficult to me.
What is "GMXRC"? What is the login files? How to find the
MANPATH? How do I know whther /usr/local/bin is in the PATH
is in the path? How can source /usr/local/gromacs/bin/GMXRC?</span></div>
</div>
</blockquote>
<br>
That page contains the strongly-worded advice to check the normal
GROMACS installation instructions, which has a fuller discussion of
this "getting access to GROMACS" issue. Please search the web for
tutorials and discussion of how UNIX PATH environment variables
function.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1326177951.1925.YahooMailNeo@web121701.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:12pt">
<div style="RIGHT: auto"><span style="RIGHT: auto"></span> </div>
<div style="RIGHT: auto"><span style="RIGHT: auto">I am looking
forward to getting a reply from you.</span></div>
<div style="RIGHT: auto"><span style="RIGHT: auto"></span> </div>
<div style="RIGHT: auto"><span style="RIGHT: auto">Dialing</span></div>
<div><br>
</div>
<div style="FONT-FAMILY: times new roman, new york, times,
serif; FONT-SIZE: 12pt">
<div style="FONT-FAMILY: times new roman, new york, times,
serif; FONT-SIZE: 12pt"><font face="Arial" size="2">
<b><span style="FONT-WEIGHT: bold">From:</span></b> Mark
Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="FONT-WEIGHT: bold">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="FONT-WEIGHT: bold">Sent:</span></b>
Tuesday, 10 January 2012 12:29 PM<br>
<b><span style="FONT-WEIGHT: bold">Subject:</span></b> Re:
[gmx-users] q question related to gromacsinstallation by
cygwin<br>
</font><br>
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<div style="RIGHT: auto" id="yiv1678134569">
<div style="RIGHT: auto">On 10/01/2012 12:24 PM, Dialing
Pretty wrote:
<blockquote style="RIGHT: auto" type="cite">
<div style="BACKGROUND-COLOR: rgb(255,255,255);
FONT-FAMILY: times new roman, new york, times,
serif; COLOR: rgb(0,0,0); FONT-SIZE: 12pt">
<div style="RIGHT: auto">Dear All,<br>
<br>
I have tried to install gromacs-4.5.5 by cygwin
but I meet the following problems.<br>
<br>
I am looking forward to getting your suggestions
on how to solve the problem.<br>
<br>
Dialing<br>
<br>
<br>
<br>
$ make</div>
<div>Making all in include</div>
<div>make[1]: Entering directory
`/cygdrive/d/GROMACS2/gromacs-4.5.5/include'</div>
<div>Making all in .</div>
<div>make[2]: Entering directory
`/cygdrive/d/GROMACS2/gromacs-4.5.5/include'</div>
<div>make[2]: Nothing to be done for `all-am'.</div>
<div>make[2]: Leaving directory
`/cygdrive/d/GROMACS2/gromacs-4.5.5/include'</div>
<div>Making all in types</div>
<div>make[2]: Entering directory
`/cygdrive/d/GROMACS2/gromacs-4.5.5/include/types'</div>
<div>make[2]: *** No rule to make target `all'.
Stop.</div>
<div>make[2]: Leaving directory
`/cygdrive/d/GROMACS2/gromacs-4.5.5/include/types'</div>
<div>Makefile:479: recipe for target `all-recursive'
failed</div>
<div>make[1]: *** [all-recursive] Error 1</div>
<div>make[1]: Leaving directory
`/cygdrive/d/GROMACS2/gromacs-4.5.5/include'</div>
<div>Makefile:347: recipe for target `all-recursive'
failed</div>
<div>make: *** [all-recursive] Error 1</div>
</div>
</blockquote>
<br>
The actual error occurred further up, so we cannot give
specific help. Be sure you are following the
instructions here <a moz-do-not-send="true"
style="RIGHT: auto"
href="http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO"
rel="nofollow" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO</a>,
in particular --disable-threads.<br>
<br>
Mark<br>
</div>
</div>
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<br>
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