It is possible to install sci-chemistry/gromacs-4.0.7 in x86-linux prefix using 'ecopy' and some manual tweaks in ebuild (add ${EPREFIX} in some places). To compile with USE=mpi, virtual/mpi had to be ecopied (blocked by missing keyword). Reproducible: Always Steps to Reproduce: 1.ecopy sci-chemistry/gromacs 2.make changes to ebuild 3.emerge gromacs Actual Results: Gromacs successfully installs in prefix and it is possible to run grompp etc. $ emerge --info Portage 2.2.00.15200-prefix (prefix/linux/x86, gcc-4.2.4, unavailable, 2.6.27.43 i686) ================================================================= System uname: Linux-2.6.27.43-i686-Intel-R-_Pentium-R-_4_CPU_3.00GHz-with-slackware-12.0.0 Timestamp of tree: Fri, 22 Jan 2010 11:19:30 +0000 distcc 2.18.3 i486-slackware-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] ccache version 2.4 [enabled] app-shells/bash: 4.0_p35 dev-lang/python: 2.6.4 dev-util/ccache: 2.4-r8 sys-devel/autoconf: 2.63-r01.1 sys-devel/automake: 1.10.2-r00.1, 1.11.1 sys-devel/binutils: 2.20.51.0.5 sys-devel/gcc-config: 1.4.1-r00.2 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="~x86-linux" ACCEPT_LICENSE="* -@EULA" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/home/user/gentoo/usr/portage/distfiles" FEATURES="assume-digests ccache collision-protect distlocks fixpackages news parallel-fetch preserve-libs protect-owned sfperms strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" MAKEOPTS="-s -j3" PKGDIR="/home/user/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/home/user/gentoo/" 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="/home/user/gentoo/var/tmp" PORTDIR="/home/user/gentoo/usr/portage" PORTDIR_OVERLAY="/home/user/gentoo/usr/local/portage/sci" SYNC="rsync://rsync.prefix.freens.org/gentoo-portage-prefix" USE="bash-completion berkdb bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 modules mudflap ncurses nls nptl nptlonly openmp pcre perl pppd prefix 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" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic nv r128 radeon savage sis tdfx trident vesa via vmware voodoo" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 217183 [details, diff] gromsca-4.0.7.ebuild prefix patch
I have an issue running gromacs in prefix using lam-mpi: $ lamboot LAM 7.1.4/MPI 2 C++ - Indiana University $ mpirun -np 2 mdrun -s mol_min.tpr -deffnm mol_min & [1] 21409 $ ----------------------------------------------------------------------------- The selected RPI failed to initialize during MPI_INIT. This is a fatal error; I must abort. This occurred on host myhost (n0). The PID of failed process was 21410 (MPI_COMM_WORLD rank: 0) ----------------------------------------------------------------------------- But the mpirun process and associated mdrun processes doesn't die, but they are not doing any work either (0% CPU usage), ang go away only if I terminate one of mdrun processes manually. In serial it runs.
Justin (jlec), Care to fix this bug?
Can do that, but I am actually not using gromacs until now.
I merged the changes into gromacs-4.0.7-r3 in science overlay. @justin: Can you take a look at it, because I am not very familiar with prefix.
Looks good so far. Do we have an open bug for the other changes you made?
I discussed them with alexxy, basically it is all trivial. I added static-libs use flag and included patches from the stable branch of the upstream repo (the name of the patch is not optimal, we can fix that). So I guess this bug can be closed.
Not until it is committed into the prefix tree.
The ebuilds in the tree are broken for prefix. As the documentation says DESTDIR for make install should not be changed: http://www.gentoo.org/proj/en/gentoo-alt/prefix/techdocs.xml
Created attachment 237999 [details, diff] Patch for the latest ebuild in the tree
Fixed in science overlay
fixed in the portage tree by alexxy, yesterday.
