Hi all, I've been trying to install sci-chemistry/gromacs-3.2.1-r1 on my alpha server. I've modified the ebuild to add ~alpha keyword. By the way it doesn't compile due to a bad formed makefile. Although the ebuild is not originally relased for alpha platform, the following line is specified in econf: $(use_enable alpha axp-asm) || die "configure failed" this enables vectorized sqrt routines for alpha, but then you get this error: /bin/sh ../../libtool --mode=link mpicc -mcpu=ev67 -Wa,-mev6 -O3 -pipe -I/usr/include/libxml2 -o libgmx_mpi.la -rpath /usr/lib -version-info 3:0:0 3dview.lo atomprop.lo block_tx.lo bondfree.lo calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gbutil.lo fnbf.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo macros.lo orires.lo main.lo maths.lo matio.lo mshift.lo mvdata.lo mvxvf.lo names.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo readinp.lo replace.lo rmpbc.lo shift_util.lo sortwater.lo smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgms.lo wman.lo writeps.lo xdrd.lo xtcio.lo xvgr.lo detectcpu.lo libxdrf.lo vec.lo dihres.lo xmlio.lo innerf.lo f77_wrappers.lo axp_asm.lo -lnsl -lsrfftw_mpi -lsfftw_mpi -lsrfftw -lsfftw -lm -L/usr/lib -lxml2 -lz -lpthread -lm -L/usr/lib/gcc-lib/alphaev67-unknown-linux-gnu/3.3.2 -L/usr/lib/gcc-lib/alphaev67-unknown-linux-gnu/3.3.2/../../../../alphaev67-unknown-linux-gnu/lib -L/usr/lib/gcc-lib/alphaev67-unknown-linux-gnu/3.3.2/../../.. -lfrtbegin -lg2c -lm -lgcc_s libtool: link: `axp_asm.lo' is not a valid libtool object make[3]: *** [libgmx_mpi.la] Error 1 make[3]: Leaving directory `/var/tmp/portage/gromacs-3.2.1-r1/work/gromacs-3.2.1/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/var/tmp/portage/gromacs-3.2.1-r1/work/gromacs-3.2.1/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/var/tmp/portage/gromacs-3.2.1-r1/work/gromacs-3.2.1/src' make: *** [all-recursive] Error 1 I've then added a patch and therefore modified the ebuild to fix this. This is the diff file for the ebuild: # diff /tmp/gromacs-3.2.1-r1.ebuild gromacs-3.2.1-r1.ebuild 15c15 < KEYWORDS="~alpha x86 amd64 ~ppc64" --- > KEYWORDS="x86 amd64 ~ppc64" 30,32d29 < if use alpha; then < epatch ${FILESDIR}/${PN}-alpha-axp_asm.patch < fi and this is the patch: # cat files/gromacs-alpha-axp_asm.patch diff -Naur gromacs-3.2.1/src/gmxlib/Makefile.in gromacs-3.2.1-new/src/gmxlib/Makefile.in ivec.h --- gromacs-3.2.1/src/gmxlib/Makefile.in 2004-03-01 20:49:02.000000000 +0100 +++ gromacs-3.2.1-new/src/gmxlib/Makefile.in 2006-05-30 17:40:33.000000000 +0200 @@ -301,6 +301,7 @@ LTF77COMPILE = $(LIBTOOL) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS) F77LD = $(F77) CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS) +LTASCOMPILE = $(LIBTOOL) --mode=compile $(AS) $(AM_ASFLAGS) $(ASFLAGS) LTCCASCOMPILE = $(LIBTOOL) --mode=compile $(CCAS) $(AM_CCASFLAGS) \ $(CCASFLAGS) DIST_SOURCES = $(libgmx@LIBSUFFIX@_la_SOURCES) \ This is the information about my system: # emerge --info Portage 2.0.54 (default-linux/alpha/no-nptl/2.4, gcc-3.3.2, glibc-2.3.4.20041102-r1, 2.4.30 alpha) ================================================================= System uname: 2.4.30 alpha EV68CB Gentoo Base System version 1.6.13 dev-lang/python: 2.3.5, 2.4.2 sys-apps/sandbox: 1.2.12 sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.15.92.0.2-r10 sys-devel/libtool: 1.5.20 virtual/os-headers: 2.4.23 ACCEPT_KEYWORDS="alpha" AUTOCLEAN="yes" CBUILD="alphaev67-unknown-linux-gnu" CFLAGS="-mcpu=ev67 -Wa,-mev6 -O3 -pipe " CHOST="alphaev67-unknown-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/ /var/qmail/control" CONFIG_PROTECT_MASK="/etc/eselect/compiler /etc/gconf /etc/terminfo /etc/env.d" CXXFLAGS="-mcpu=ev67 -Wa,-mev6 -O3 -pipe " DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks sandbox sfperms strict" GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="alpha apache2 arts berkdb bitmap-fonts bzip2 cli crypt ctype cups curl dba dri eds encode esd expat fastbuild foomaticdb force-cgi-redirect fortran ftp gd gdbm gif gmp gnome gpm gstreamer gtk gtk2 imlib ipv6 jpeg kde ldap libg++ libwww mad memlimit mhash mikmod motif mp3 mpeg mysql ncurses nls ogg opengl oss pam pcre pdflib perl png posix python qt quicktime readline recode ruby sdl session simplexml soap sockets spell spl ssl tcpd tetex threads tokenizer truetype truetype-fonts type1-fonts vorbis xml xml2 xmms xsl xv zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTDIR_OVERLAY
Created attachment 88087 [details, diff] this is the patch for alpha
Created attachment 88088 [details] the ebuild
I've confirmed that this patch allows sci-chemistry/gromacs-3.2.3 to compile using gcc-3.4.6. However, the patch seems to have a spare "ivec.h" on line 2 of the patch. After removing this, it applies cleanly. However, when emerging this program, it by default emerged sci-libs/fftw-2.1.5-r1 as a dependency. I then tried to compile gromacs-3.2.3 but it failed with this error: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. Use CPPFLAGS and LDFLAGS if the library is installed in a non-standard location. (see FAQ at http://www.gromacs.org) If you dont care about performance you can also specify 'fftpack' to use a slower set of FFTs built into Gromacs. (Just install FFTW3 unless you really know what you are doing). Emerging the latest fftw was able to resolve this and allow me to continue, as suggested by the error. Emerge --info: Portage 2.1-r1 (default-linux/alpha/no-nptl/2.4, gcc-3.4.6, glibc-2.3.4.20041102-r1, 2.4.30 alpha) ================================================================= System uname: 2.4.30 alpha EV45 Gentoo Base System version 1.6.15 ccache version 2.3 [enabled] app-admin/eselect-compiler: [Not Present] dev-lang/python: 2.3.5, 2.4.2 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: 2.3 dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.16.1-r2 sys-devel/gcc-config: 1.3.13-r2 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.4.23 ACCEPT_KEYWORDS="alpha" AUTOCLEAN="yes" CBUILD="alpha-unknown-linux-gnu" CFLAGS="-mieee -O2 -mcpu=ev45 -pipe" CHOST="alpha-unknown-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/terminfo" CXXFLAGS="-mieee -O2 -mcpu=ev45 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig ccache metadata-transfer sandbox sfperms strict test" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="alpha alsa berkdb bitmap-fonts bzip2 cli crypt dlloader eds encode fortran gdbm gif gpm imlib jpeg libg++ libwww motif mp3 mpeg ncurses ogg pam pcre pdflib perl png python qt3 readline reflection session spl ssl tcpd userlocales vorbis xml zlib elibc_glibc input_devices_keyboard input_devices_mouse kernel_linux userland_GNU" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
added gromacs-3.3.1-r1.ebuild
