<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>You should never install software in the same directory as where you are building in, in particular when it is configured with GNU tools.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Apr 26, 2006, at 9:27 AM, Akshay Patny wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><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="place"> <O:SMARTTAGTYPE namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PlaceName"> <O:SMARTTAGTYPE namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PlaceType"> <DIV class="Section1"><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Hi <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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">I am trying to install Gromacs-3.3.1 The machine is SGI Altix and the output of the uname –a for machine is:<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Linux redwood 2.6.5-7.244-sn2 #1 SMP Mon Dec 12 18:32:25 UTC 2005 ia64 ia64 ia64 GNU/Linux<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">I do not have root privileges and I am trying to install it in the local directory I have permissions for which is:<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">I unpacked gromacs-3.3.1.tar in the /work1/r0914<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">It made a directory /work1/r0914/gromacs-3.3.1/<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">I first installed fftw-3.1.1 (both single precision and double precision using) in a separate directory which is:<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">ums/ro914/fftw-3.1.1<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Then, I cd to /work1/r0914/gromacs-3.3.1/<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"># setenv CPPFLAGS –I/ ums/ro914/fftw-3.1.1/include<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"># setenv LDFLAGS –L/ ums/ro914/fftw-3.1.1/lib<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"># ./configure –prefix=/work1/r0914/gromacs-3.3.1/<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"># make<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"><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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">I got the error in the make install which is:<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">/usr/bin/install: `./g_sham.1' and `/work1/r0914/gromacs-3.3.1/man/man1/g_sham.1' are the same file<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"> /usr/bin/install -c -m 644 './make_edi.1' '/work1/r0914/gromacs-3.3.1/man/man1/make_edi.1'<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">/usr/bin/install: `./make_edi.1' and `/work1/r0914/gromacs-3.3.1/man/man1/make_edi.1' are the same file<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">make[3]: *** [install-man1] Error 1<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">make[3]: Leaving directory `/work1/r0914/gromacs-3.3.1/man/man1'<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">make[2]: *** [install-am] Error 2<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">make[2]: Leaving directory `/work1/r0914/gromacs-3.3.1/man/man1'<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">make[1]: *** [install-recursive] Error 1<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">make[1]: Leaving directory `/work1/r0914/gromacs-3.3.1/man'<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">make: *** [install-recursive] Error 1<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Let me know if you need other details<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"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Regards<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><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"><STRONG><B><FONT size="3" face="Times New Roman"><SPAN style="font-size:12.0pt">Akshay Patny</SPAN></FONT></B></STRONG><B><SPAN style="font-weight:bold"><BR> <BR> <STRONG><B><FONT face="Times New Roman"><O:P></O:P></FONT></B></STRONG></SPAN></B></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)</SPAN></FONT><FONT size="1" face="Book Antiqua"><SPAN style="font-size:9.0pt;font-family:" book="" antiqua""="">; Web</SPAN></FONT><FONT size="1" face="Book Antiqua"><SPAN style="font-size:9.0pt; font-family:" book="" antiqua""="">: <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> </O:SMARTTAGTYPE></O:SMARTTAGTYPE></O:SMARTTAGTYPE></O:SMARTTAGTYPE></O:SMARTTAGTYPE></O:SMARTTAGTYPE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. 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