<div>I try to compile GROMACS with a combination of icc and ifort. Error occurs. These are the last lines of the compilation message:</div>
<div>Making install in gmx_blas<br>make[3]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas'<br>make[4]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas'<br>
make[4]: Nothing to be done for `install-exec-am'.<br>make[4]: Nothing to be done for `install-data-am'.<br>make[4]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas'<br>make[3]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas'<br>
Making install in gmx_lapack<br>make[3]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack'<br>make[4]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack'<br>
make[4]: Nothing to be done for `install-exec-am'.<br>make[4]: Nothing to be done for `install-data-am'.<br>make[4]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack'<br>make[3]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack'<br>
make[3]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib'<br>/bin/sh ../../libtool --tag=CC --mode=compile /disk2/junwang/soft/intel/cc/10.1.018/bin/icc -DHAVE_CONFIG_H -I. -I../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/disk2/junwang/soft/gromacs4/share/top\" -I/disk2/junwang/soft/fftw32_mpi/include -O3 -w -funroll-all-loops -MT libxdrf.lo -MD -MP -MF .deps/libxdrf.Tpo -c -o libxdrf.lo libxdrf.c<br>
/disk2/junwang/soft/intel/cc/10.1.018/bin/icc -DHAVE_CONFIG_H -I. -I../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/disk2/junwang/soft/gromacs4/share/top\" -I/disk2/junwang/soft/fftw32_mpi/include -O3 -w -funroll-all-loops -MT libxdrf.lo -MD -MP -MF .deps/libxdrf.Tpo -c libxdrf.c -o libxdrf.o<br>
libxdrf.c(112): error: identifier "XDR_INT_SIZE" is undefined<br> cnt += XDR_INT_SIZE;<br> ^</div>
<div>libxdrf.c(140): error: identifier "XDR_INT_SIZE" is undefined<br> cnt += XDR_INT_SIZE;<br> ^</div>
<div>compilation aborted for libxdrf.c (code 2)<br>make[3]: *** [libxdrf.lo] Error 1<br>make[3]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib'<br>make[2]: *** [install-recursive] Error 1<br>make[2]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib'<br>
make[1]: *** [install-recursive] Error 1<br>make[1]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src'<br>make: *** [install-recursive] Error 1</div>
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<div>My intel compiler versions are both <a href="http://10.1.018.">10.1.018.</a></div>
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<div class="gmail_quote">2008/10/27 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d">Carsten Kutzner wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br><br>Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Lee Soin wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">By invoking "uname -a":<br>Linux sgi4700 2.6.16.46-0.12-default #1 SMP Thu May 17 14:00:09 UTC<br>
2007 ia64 ia64 ia64 GNU/Linux<br> I don't know any other command to retrieve system information.<br></blockquote>Hmm, that looks like an SGI Altix 4700. IA64 kernels work on those<br>machines. <br></blockquote>Well, not exactly.<br>
</blockquote><br></div>Ah, oops. I was thinking of the Altix 3700 series, which predates Montecito. My bad.
<div class="Ih2E3d"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">They work in combination with Gromacs version <= 3.3.x,<br>but at least I have never managed to get them working with this year's<br>
CVS Gromacs or Gromacs 4.x - see also<br><br><a href="http://www.gromacs.org/pipermail/gmx-developers/2008-February/002405.html" target="_blank">http://www.gromacs.org/pipermail/gmx-developers/2008-February/002405.html</a><br>
<br>The strange thing is that these inner loops have not changed since 3.3.x,<br>so the problem might be somewhere else. But actually the Fortran loops<br>have a quite decent performance on that machine compared to assembly: In<br>
a single-CPU test I did with gmx 3.3 they were just about 10% slower.<br></blockquote><br></div>Good to know. Lee should definitely compare performance when using configure with and without --enable-fortran (and using --disable-cpu-optimization to avoid needing to set the environment variable).
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