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On 10/03/2012 5:52 PM, Dialing Pretty wrote:
<blockquote
cite="mid:1331362346.78961.YahooMailNeo@web121706.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><span>Dear All,</span></div>
<div><span></span> </div>
<div><span>My command is ./configure --disable-threads</span></div>
</div>
</blockquote>
<br>
Thanks. You do need --disable-threads, as noted by the Cygwin
installation guide. Your earlier errors looked consistent with not
having used it.<br>
<blockquote
cite="mid:1331362346.78961.YahooMailNeo@web121706.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><span></span> </div>
<div><span>The error message are as following. I am looking
forward to getting a message from you on how to avoid the
error message.</span></div>
</div>
</blockquote>
<br>
I do observe intermittent issues with builds on Cygwin that look
somewhat similar to the ones you suggest. Re-running make eventually
succeeds. I expect this is some upstream issue that has nothing to
do with GROMACS.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1331362346.78961.YahooMailNeo@web121706.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><span></span> </div>
<div><span>Cheers,</span></div>
<div><span></span> </div>
<div><span>Dialing</span></div>
<div><span> </span></div>
<div><span>
</span></div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">/bin/sh
../../../libtool
--tag=CC<span style="mso-spacerun: yes;"> </span>--mode=compile
cc
-DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2<span
style="mso-spacerun: yes;"> </span>-I../../../include<span
style="mso-spacerun: yes;"> </span>-O3
-fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
-fexcess-precision=fast
-MT sdot.lo -MD -MP -MF .deps/sdot.Tpo -c -o sdot.lo
sdot.c<!--?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /--><o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make[4]:
execvp: /bin/sh: Bad
address<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">../../../libtool:
fork:
retry: Resource temporarily unavailable<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">../../../libtool:
fork: retry:
Resource temporarily unavailable<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">../../../libtool:
fork:
retry: Resource temporarily unavailable<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">../../../libtool:
fork:
retry: Resource temporarily unavailable<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">../../../libtool:
fork:
Resource temporarily unavailable<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">Makefile:338:
recipe for
target `sdot.lo' failed<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make[4]: ***
[sdot.lo] Error
254<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make[4]:
Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib/gmx_blas'<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">Makefile:599:
recipe for
target `all-recursive' failed<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make[3]: ***
[all-recursive]
Error 1<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make[3]:
Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib'<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">Makefile:302:
recipe for
target `all-recursive' failed<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make[2]: ***
[all-recursive]
Error 1<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make[2]:
Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">Makefile:238:
recipe for
target `all' failed<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make[1]: ***
[all] Error 2<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make[1]:
Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">Makefile:347:
recipe for
target `all-recursive' failed<o:p></o:p></font></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="font-size: 12pt;"><font face="Calibri">make: ***
[all-recursive]
Error 1<o:p></o:p></font></span></div>
<div>
</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;">
<div dir="ltr"> <font size="2" face="Arial"> <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>
Saturday, 10 March 2012 2:07 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] error message during make after gtomacs
configuration<br>
</font> </div>
<br>
<meta content="off" http-equiv="x-dns-prefetch-control">
<div id="yiv1605284085">
<div> On 10/03/2012 2:50 PM, Dialing Pretty wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times
new roman, new york, times, serif; font-size: 12pt;
background-color: rgb(255, 255, 255);">
<div> </div>
<div><span style="color: black;" lang="EN-US">Dear
All,</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">After
I run the Gromacs 4.5.5 configuration (in this
step there is no error), I run make, but I meet
the following error messages.</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">Will
you please give me some suggestions on how to
avoid these error messages?</span></div>
</div>
</blockquote>
<br>
No. You haven't told us your configure command, so we're
not going to guess what you're doing wrong.<br>
<br>
Mark<br>
<br>
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times
new roman, new york, times, serif; font-size: 12pt;
background-color: rgb(255, 255, 255);">
<div><span style="color: black;" lang="EN-US"></span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">Cheers,</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">Dialing</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:151:5:
error: ‘smalloc_GetCurrentProcessorNumberEx’
undeclared (first use in this function)</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:151:5:
note: each undeclared identifier is reported
only once for each function it appears in</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:151:44:
error: ‘func_GetCurrentProcessorNumberEx_t’
undeclared (first use in this function)</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:151:79:
error: expected ‘;’ before ‘GetProcAddress’</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:152:5:
error: ‘smalloc_GetNumaProcessorNodeEx’
undeclared (first use in this function)</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:152:39:
error: ‘func_GetNumaProcessorNodeEx_t’
undeclared (first use in this function)</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:152:69:
error: expected ‘;’ before ‘GetProcAddress’</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:
In function ‘ReturnHeapHandle’:</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:246:5:
error: ‘PROCESSOR_NUMBER’ undeclared (first use
in this function)</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:246:22:
error: expected ‘;’ before
‘CurrentProcessorNumber’</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:285:5:
warning: implicit declaration of function
‘smalloc_GetCurrentProcessorNumberEx’</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:285:42:
error: ‘CurrentProcessorNumber’ undeclared
(first use in this function)</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:287:5:
warning: implicit declaration of function
‘smalloc_GetNumaProcessorNodeEx’</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">numa_malloc.c:324:9:
warning: implicit declaration of function
‘HeapSetInformation’</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">Makefile:332:
recipe for target `numa_malloc.lo' failed</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">make[4]:
*** [numa_malloc.lo] Error 1</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">make[4]:
Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib/thread_mpi'</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">Makefile:599:
recipe for target `all-recursive' failed</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">make[3]:
*** [all-recursive] Error 1</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">make[3]:
Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib'</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">Makefile:302:
recipe for target `all-recursive' failed</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">make[2]:
*** [all-recursive] Error 1</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">make[2]:
Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">Makefile:238:
recipe for target `all' failed</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">make[1]:
*** [all] Error 2</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">make[1]:
Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">Makefile:347:
recipe for target `all-recursive' failed</span></div>
<div> </div>
<div><span style="color: black;" lang="EN-US">make:
*** [all-recursive] Error 1</span></div>
<div> </div>
</div>
<br>
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