Bug 248346 – sci-chemistry/gromacs fails to build

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Diego Elio Pettenò (RETIRED) 2008-11-23 15:31:19 UTC]

Portage 2.2_rc14 (default/linux/x86/2008.0, gcc-4.1.2-asneeded, glibc-2.8_p20080602-r0, 2.6.27-gentoo-r2 i686)
=================================================================
System uname: Linux-2.6.27-gentoo-r2-i686-Quad-Core_AMD_Opteron-tm-_Processor_2350-with-glibc2.0
Timestamp of tree: Fri, 14 Nov 2008 00:37:01 +0000
distcc 3.0 i686-pc-linux-gnu [disabled]
ccache version 2.4 [disabled]
app-shells/bash:     3.2_p39
dev-java/java-config: 1.3.7, 2.1.6-r1
dev-lang/python:     2.4.4-r15, 2.5.2-r8
dev-python/pycrypto: 2.0.1-r6
dev-util/ccache:     2.4-r8
sys-apps/baselayout: 2.0.0
sys-apps/openrc:     0.3.0-r1
sys-apps/sandbox:    1.2.18.1-r3
sys-devel/autoconf:  2.13, 2.63
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1-r1
sys-devel/binutils:  2.19
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.27-r2
ACCEPT_KEYWORDS="x86 ~x86"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /opt/glftpd/etc /opt/glftpd/ftp-data /opt/openfire/resources/security/ /opt/openjms/config /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/bind /var/lib/hsqldb /var/phxd /var/qmail/alias /var/qmail/control /var/spool/torque /var/vpopmail/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/udev/rules.d"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage-distfiles"
FEATURES="distlocks parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo"
INSTALL_MASK=" 	/usr/share/doc 	/usr/share/man 	/usr/share/info"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j14"
PKGDIR="/usr/portage-packages"
PORTAGE_COMPRESS=""
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="acl berkdb bzip2 cli cracklib crypt cups dri fortran gdbm gpm iconv ipv6 isdnlog midi mudflap ncurses nls nptl nptlonly openmp pam pcre perl pppd python readline reflection session spl ssl sysfs tcpd unicode x86 xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="fbdev glint i810 intel mach64 mga neomagic nv r128 radeon savage sis tdfx trident vesa vga via vmware voodoo"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

[Comment 1 Diego Elio Pettenò (RETIRED) 2008-11-23 15:31:34 UTC]

Created attachment 172955 [details]
Build log

[Comment 2 Christoph Junghans (RETIRED) 2009-04-20 16:10:22 UTC]

-gcc 4.1.X is bad, update to gcc 4.3.* (stable now)
-try again with gromacs 4.0.4
-repost build.log

[Comment 3 Alexey Shvetsov 2009-04-20 16:34:22 UTC]

Diego try 4.0.4 =)
and gcc-4.1 is known to be broken in some way so gromacs produce incorrect numerical results

[Comment 4 Alexey Shvetsov 2009-04-20 16:36:24 UTC]

NOTICE: Invoking /opt/SunStudioExpress/bin/f90 -f77 -ftrap=%none -c nb_kernel230_f.f -o nb_kernel230_f.o
nb_kernel231_f.f:

this is at least strange =) dont sure if gromacs can be compiled with sun studio f90 =)

[Comment 5 Diego Elio Pettenò (RETIRED) 2009-08-09 17:27:13 UTC]

4.0.5 merged in tinderbox.