Currently it is possible to compile VMD on Gentoo Prefix with some modifications to the ebuild and providing an ebuild for fltk:1.1, but it still doesn't run. Reproducible: Always Steps to Reproduce: 1. Set up fltk ebuild 2. Modify vmd ebuild 3. emerge vmd 4. vmd launch fails Actual Results: Successful compilation after some modifications to the ebuild, but VMD really dosn't work. Expected Results: It compiles and also works correctly. Portage 2.2.01.15352-prefix (prefix/linux/amd64, gcc-4.4.3, unavailable, 2.6.34 x86_64) ================================================================= System uname: Linux-2.6.34-x86_64-Intel-R-_Pentium-R-_4_CPU_3.00GHz-with-slackware-13.1.0 Timestamp of tree: Wed, 07 Jul 2010 07:39:08 +0000 distcc 2.18.3 x86_64-slackware-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] ccache version 2.4 [enabled] app-shells/bash: 4.0_p38 dev-lang/python: 2.6.5-r2 dev-util/ccache: 2.4-r8 sys-devel/autoconf: 2.65-r1 sys-devel/automake: 1.11.1 sys-devel/binutils: 2.20.51.0.8 sys-devel/gcc: 4.4.3-r2 sys-devel/gcc-config: 1.4.1-r00.2 sys-devel/libtool: 2.2.10 virtual/os-headers: 2.6.34 ACCEPT_KEYWORDS="~amd64-linux" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/home/danne/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" LANG="en_US" LDFLAGS="-Wl,-O1" MAKEOPTS="-s -j3" PKGDIR="/home/danne/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/home/danne/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/danne/gentoo/var/tmp" PORTDIR="/home/danne/gentoo/usr/portage" SYNC="rsync://rsync.prefix.freens.org/gentoo-portage-prefix" USE="amd64 bash-completion berkdb bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx modules mudflap ncurses nls nptl nptlonly openmp pcre perl pppd prefix python readline reflection session spl sse sse2 ssl sysfs tcpd unicode xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci 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" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Created attachment 238045 [details, diff] Patch for the latest ebuild in the tree With this patch VMD compiles, given that fltk:1.1 is installed (I'll make a separate bug for that one). The issue is that: - it tries to find headers and libraries in system's Python installation not in the prefix and - the plugins should be installed appropriately
The next issue is that 'defaultvmddir' variable at the beginning of usr/bin/vmd has to be set to "${EPREFIX}/usr/lib/vmd". Then the next issue is that it can't find fltk library, so the LD_LIBRARY_PATH has to be set to include "${EPREFIX}/usr/lib/fltk-1.1": ~ $ LD_LIBRARY_PATH="${EPREFIX}/usr/lib/fltk-1.1" vmd Info) VMD for LINUX, version 1.8.7 (July 8, 2010) Info) http://www.ks.uiuc.edu/Research/vmd/ Info) Email questions and bug reports to vmd@ks.uiuc.edu Info) Please include this reference in published work using VMD: Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38. Info) ------------------------------------------------------------- Info) Multithreading available, 2 CPUs detected. Info) Free system memory: 950MB (47%) Warning) Detected X11 'Composite' extension: if incorrect display occurs Warning) try disabling this optional X server feature. ERROR) A TrueColor visual is required, but not available. ERROR) The X server is not capable of displaying double-buffered, ERROR) RGB images with a Z buffer. Exiting ... Info) VMD for LINUX, version 1.8.7 (July 8, 2010) Info) Unable to create OpenGL window. xdpyinfo says that 24 and 32bit TrueColor is there. At this point I have no idea what is going on. Is it another problem with finding some libraries? Any ideas?
Justin, can you please pursue this? :)
@Jeremy Yes I will do that. I am interested in that myself. Should I also do fltk? @rei4dan python_get_*() are prefix aware, so you don't need to add EPREFIX in front
@jlec, no they are not. I installed it in my prefix and it gives locations for system python, not the python in prefix and consequently doesn't find numpy which is only in the prefix. And Arfrever also said that they return paths relative to the prefix.
(In reply to comment #5) > @jlec, no they are not. I installed it in my prefix and it gives locations for > system python, not the python in prefix and consequently doesn't find numpy > which is only in the prefix. And Arfrever also said that they return paths > relative to the prefix. > Ah you are are tight, my mistake.
(In reply to comment #4) > @Jeremy > Yes I will do that. I am interested in that myself. Should I also do fltk? Yea, probably run it by Samuli real quick, should be no issue. I just whitelisted fltk so it will be in when you make your changes.
+ 24 Jul 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r1.ebuild: + Added prefix changes, thanks rei4dan #327517; keyworded for ~-linux prefix +
Missing -R or rpath when linking against libfltk.
fixed now
