You can test this package using the tutorial files under /usr/share/gromacs/tutor/ Methanol is yummy :)
amd64/x86 stable
On alpha, I get this: >>> Emerging (1 of 1) sci-chemistry/gromacs-4.0.3 * gromacs-4.0.3.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] * You need one of these Fortran Compilers: g77 gfortran ifc * Installed are: gfortran >>> Unpacking source... >>> Unpacking gromacs-4.0.3.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-4.0.3/work * Running eautoreconf in '/var/tmp/portage/sci-chemistry/gromacs-4.0.3/work/gromacs-4.0.3' ... * Running aclocal ... [ ok ] * Running true --copy --force --install --automake ... [ ok ] * Running aclocal ... [ ok ] * Running autoconf ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --foreign ... [ ok ] * Running elibtoolize in: gromacs-4.0.3/config * Applying install-sh-1.5.4.patch ... * Applying portage-1.5.10.patch ... * Applying sed-1.5.6.patch ... >>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-4.0.3/work >>> Compiling source in /var/tmp/portage/sci-chemistry/gromacs-4.0.3/work ... * * ERROR: sci-chemistry/gromacs-4.0.3 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 3075: Called die * The specific snippet of code: * die "If you must run gromacs without sse (not recommended) gfortran will not work."; * The die message: * If you must run gromacs without sse (not recommended) gfortran will not work. * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/log/portage/sci-chemistry:gromacs-4.0.3:20090312-223608.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-4.0.3/temp/environment'. * >>> Failed to emerge sci-chemistry/gromacs-4.0.3, Log file: >>> '/var/log/portage/sci-chemistry:gromacs-4.0.3:20090312-223608.log' Naturally, I *can't* use SSE. So where do I get g77? ifc is right out for obvious reasons.
We have the same problem on ppc64; advice?
Gromacs 4.0.4 was released and no bug fixes for 3.3.* anymore. I have worked for a while with gromacs and the ebuild seems a little obsolete: -disabling sse/sse2/mmx/3dnow just saves you some building time, the main program (mdrun) will choose its kernel automatically at the runtime. -> drop use flags or enable all assembly by default. -Fortran kernels in gromacs are more for hpc (sgi,ibm,sun,axp), with a high optimized Fortran compiler like xlf. -> disable by default, make a flags f77 with dependency g77 (but I still think g77 is slower than gcc-4.3.*, I try to find a benchmark...) -There are genieric c-kernel for all archs -> one can also build on sparc/alpha without fortran -static linking is still default, but dynamically also works -with-xml should be default, allows the use of certain file formats -do NOT use gcc 4.1.* -> wrong results Further improvements: -only build mdrun with mpi (make mdrun), analysis program do not need mpi anyway or -use --enable-mpi-environment=LAMWORLD (for lammpi), which allows to run all programs outside mpi environment. I can modify the ebuild, but comments first...
Created attachment 187861 [details] ebuild for gromacs 4.0.4 Here we go - a updated ebuild for gromacs 4.0.4: -dropped all assembly options (all-enabled by default) -added bash/zsh-completion -added env.d files -added test -renamed fortran to fkernels (disabled by default) -added some info for double-precision, fftw and fkernels Please test it on sparc and alpha....
Created attachment 187866 [details, diff] adds gfortran support to configure From gromacs developers list. Do not think about Fortran too much! I have talked to one of the gromacs developers, Fortran will be gone in gromacs 4.1.
Tha ebuild+patch (4.0.4) work fine for me (alpha).
So sparc is still missing.. But gromacs should now really run on all platforms with gcc out there.... Btw, should we add a check for gcc-4.1.* ?
How about ppc64? Make sense to patch similarily?
It should also work on ppc64! Test it.... The gfortran support (patch) is only used if you emerge with fkernels use flag. I think, the C kernels are faster as you as use gnu compilers. But with aix's xlf it could be different.
Created attachment 188799 [details] ebuild for gromacs 4.0.4 Minor changes: -added doc flags (incl. manual) -apply patch only, when fkernels enabled
(In reply to comment #11) > Created an attachment (id=188799) [edit] > ebuild for gromacs 4.0.4 > > Minor changes: > -added doc flags (incl. manual) > -apply patch only, when fkernels enabled > please post diff against currrent tree version. I'll test it and will add it to tree
Created attachment 188807 [details, diff] gromacs from 4.0.3 to 4.0.4 patch
(In reply to comment #13) > Created an attachment (id=188807) [edit] > gromacs from 4.0.3 to 4.0.4 patch > Ok added in EAPI=2 form
Perfectly reworked, thanks. Worked for me! The description of "fkernels" is maybe a little confusing, there are fortran kernels for a all archs, but in general they are not faster (at least not with gnu compilers). "Use Fortran kernels instead of c kernels" would be a better description, because the flags switches hard from c to Fortran.
(In reply to comment #15) > Perfectly reworked, thanks. Worked for me! > > The description of "fkernels" is maybe a little confusing, there are fortran > kernels for a all archs, but in general they are not faster (at least not with > gnu compilers). "Use Fortran kernels instead of c kernels" would be a better > description, because the flags switches hard from c to Fortran. > I know =) I also have gromacs ebuild with qmmm-mopac support in science overlay but its needs updateing =) PS i'm using gromacs in my work =)
@alexey: Have you tried to build gromacs with gamess or mopac support ? Both are in the tree and there is --with-XXX option. Is there a legal issue? I know there is one with gaussian, but it is anyway not free.
(In reply to comment #17) > @alexey: Have you tried to build gromacs with gamess or mopac support ? Both > are in the tree and there is --with-XXX option. > Is there a legal issue? I know there is one with gaussian, but it is anyway not > free. > First of all gromacs works with GAMESS-UK version =) Also in science overlay there are gromacs version with mopac qmmmm =) BTW i already add gamess-us with its internal qmmm to tree
On sparc, -4.0.3 will not build because it can't use gfortran. -4.0.4 will not build because of this: ======================= In file included from gmx_cyclecounter.c:33: ../../include/gmx_cyclecounter.h: In function ‘gmx_cycles_read’: ../../include/gmx_cyclecounter.h:411: error: ‘ticks’ undeclared (first use in this function) ../../include/gmx_cyclecounter.h:411: error: (Each undeclared identifier is reported only once ../../include/gmx_cyclecounter.h:411: error: for each function it appears in.) ../../include/gmx_cyclecounter.h:411: error: expected ‘;’ before ‘ret’ ../../include/gmx_cyclecounter.h:412: error: ‘ret’ undeclared (first use in this function) ../../include/gmx_cyclecounter.h:412: error: invalid lvalue in asm output 0 =================================== sparc is using sparc-unknown-linux-gnu-4.3.2 (sys-devel/gcc-4.3.2-r3) and sys-devel/binutils-2.18-r3 (both current stable). Suggestions?
Created attachment 190685 [details, diff] Patch to disable cyclecounter on sparc Try this patch and look if there are other problems on sparc. Can you provide more informations about your system, because it seems like the assembly code is broken for your system.
(In reply to comment #20) > Created an attachment (id=190685) [edit] > Patch to disable cyclecounter on sparc > > Try this patch and look if there are other problems on sparc. > > Can you provide more informations about your system, because it seems like the > assembly code is broken for your system. > With that patch, everything looks fine on sparc for -4.0.4. Tutorials seem to run. I suspect that the problem with the assembler comes in because linux/sparc is 32-bit user mode, but solaris/sparc is 64-bit user mode. Or perhaps gromacs wants a newer binutils than gentoo/stable. Several packages have to disable assembly code because of reasons like this, but if the assembler didn't work, gcc couldn't compile anything.
Here's the 'emerge --info' from my sparc system, in case it might be useful. ========================== fmccor@polylepis methanol [201]% emerge --info Portage 2.2_rc33 (default/linux/sparc/2008.0/desktop, gcc-4.3.2, glibc-2.8_p20080602-r1, 2.6.27-gentoo-SB1000 sparc64) ================================================================= System uname: Linux-2.6.27-gentoo-SB1000-sparc64-sun4u-with-glibc2.0 Timestamp of tree: Fri, 08 May 2009 12:30:01 +0000 distcc 3.0 sparc-unknown-linux-gnu [enabled] ccache version 2.4 [enabled] app-shells/bash: 3.2_p39 dev-java/java-config: 1.3.7, 2.1.6 dev-lang/python: 2.4.4-r14, 2.5.4-r2 dev-python/pycrypto: 2.0.1-r8 dev-util/ccache: 2.4-r7 dev-util/cmake: 2.6.4 dev-util/confcache: 0.4.2-r1 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.9 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, 1.10.2 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.27-r2 ABI="sparc32" ACCEPT_KEYWORDS="sparc" ALSA_CARDS="ca0106 cmipci ens1370 ens1371" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" AMANDA_CONFIG_NAME="DailySet1" AMANDA_DBGDIR="/var/tmp/amanda" AMANDA_DBMODE="text" AMANDA_GROUP_GID="87" AMANDA_GROUP_NAME="amanda" AMANDA_MAX_TAPE_BLOCK_KB="512" AMANDA_PORTS="" AMANDA_PORTS_BOTH="" AMANDA_PORTS_TCP="" AMANDA_PORTS_UDP="" AMANDA_SERVER="polylepis" AMANDA_SERVER_INDEX="polylepis" AMANDA_SERVER_TAPE="polylepis" AMANDA_TAR="/bin/tar" AMANDA_TAR_LISTDIR="/var/spool/amanda/tar-lists" AMANDA_TMPDIR="/var/tmp/amanda" AMANDA_USER_GROUPS="amanda" AMANDA_USER_HOMEDIR="/var/spool/amanda" AMANDA_USER_NAME="amanda" AMANDA_USER_SH="-1" AMANDA_USER_UID="87" 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" ARCH="sparc" AUTOCLEAN="yes" CBUILD="sparc-unknown-linux-gnu" CDEFINE_sparc32="!__arch64__" CDEFINE_sparc64="__arch64__" CFLAGS="-O2 -pipe -mcpu=ultrasparc3" CFLAGS_sparc32="" CHOST="sparc-unknown-linux-gnu" CHOST_sparc32="sparc-unknown-linux-gnu" CHOST_sparc64="sparc64-unknown-linux-gnu" CLASSPATH="." CLEAN_DELAY="5" CLHEP_BASE_DIR="/usr" COLLISION_IGNORE="/lib/modules" CONFIG_PROTECT="/etc /usr/kde/3.3/env /usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/lib/fax /usr/share/config /var/spool/fax/etc /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CPATH="/usr/include/libffi" CTARGETS_BINUTILS="sparc-unknown-linux-gnu sparc64-unknown-linux-gnu" CTARGET_sparc32="sparc-unknown-linux-gnu" CVS_RSH="ssh" CXXFLAGS="-O2 -pipe -mcpu=ultrasparc3" DCCC_PATH="/usr/lib/distcc/bin" DD="/jaz/portage/distfiles" DEBUG_CFLAGS="-O2 -mcpu=ultrasparc3 -pipe -g -D__GLX_ALIGN64" DEBUG_CXXFLAGS="-O1 -mcpu=ultrasparc3 -pipe -g -fno-inline-functions -D__GLX_ALIGN64" DEBUG_FFLAGS="-O2 -pipe -mcpu=ultrasparc3 -g" DEFAULT_ABI="sparc32" DISPLAY="liasis:0.0" DISTCC_DIR="/home0/ferris/.distcc" DISTCC_HOSTS="localhost/2 antaresia/2" DISTCC_LOG="" DISTCC_PATH="/usr/lib/distcc/bin" DISTCC_VERBOSE="0" DISTDIR="/usr/portage/distfiles" ECHANGELOG_EDITOR="/usr/bin/vim" EDITOR="/usr/bin/vim" ELIBC="glibc" EMERGE_DEFAULT_OPTS="--verbose" EMERGE_WARNING_DELAY="10" FEATURES="ccache cvs distcc distlocks fixpackages metadata-transfer parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch" FETCHCOMMAND="/usr/bin/wget -t 5 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}"" FFLAGS="-O2 -pipe -mcpu=ultrasparc3" FLTK_DOCDIR="/usr/share/doc/fltk-2.0_pre6525/html" FREECIV_DATADIR="/home0/freeciv/share/freeciv" FREECIV_DIR="/home0/freeciv/share/freeciv" G4ABLADATA="/usr/share/geant4/data/G4ABLA3.0" G4DATA="/usr/share/geant4/data" G4INCLUDE="/usr/include/geant" G4INSTALL="/usr/share/geant4" G4LEDATA="/usr/share/geant4/data/G4EMLOW6.2" G4LEVELGAMMADATA="/usr/share/geant4/data/PhotonEvaporation2.0" G4LIB="/usr/lib/geant4" G4LIB_BUILD_SHARED="y" G4LIB_USE_GRANULAR="y" G4LIB_USE_ZLIB="y" G4NEUTRONHPCROSSSECTIONS="/usr/share/geant4/data/G4NDL3.13" G4OPTIMIZE="y" G4RADIOACTIVEDATA="/usr/share/geant4/data/RadioactiveDecay3.2" G4SYSTEM="Linux-g++" G4UI_BUILD_QT_SESSION="y" G4UI_BUILD_XM_SESSION="y" G4VIS_BUILD_DAWN_DRIVER="y" G4VIS_BUILD_OI_DRIVER="y" G4VIS_BUILD_OPENGLXM_DRIVER="y" G4VIS_BUILD_OPENGLX_DRIVER="y" G4VIS_BUILD_RAYTRACERX_DRIVER="y" G4VIS_BUILD_VRMLFILE_DRIVER="y" G4VIS_BUILD_VRML_DRIVER="y" G4VIS_USE_DAWN="y" G4VIS_USE_OI="y" G4VIS_USE_OPENGLX="y" G4VIS_USE_OPENGLXM="y" G4VIS_USE_RAYTRACERX="y" G4VIS_USE_VRML="y" G4VIS_USE_VRMLFILE="y" G4WORKDIR="${HOME}/geant4" GCC_SPECS="" GDK_USE_XFT="1" GENTOO_MIRRORS="ftp://gentoo.imj.fr/pub/gentoo/ http://mirror.uni-c.dk/pub/gentoo/ ftp://212.219.56.139/sites/www.ibiblio.org/gentoo/ ftp://ftp.snt.utwente.nl/pub/os/linux/gentoo ftp://212.219.56.132/sites/www.ibiblio.org/gentoo/" GMXBIN="/usr/bin" GMXDATA="/usr/share" GMXLDLIB="/usr/lib" GMXMAN="/usr/share/man" GUILE_LOAD_PATH="/usr/share/guile/1.8" HG="/usr/bin/hg" HOME="/homes/home0/ferris" ICEPY_HOME="/cache/IcePy-3.0.0/python" ICE_HOME="/cache/Ice-3.0.0" ICE_VERSION="3.0.0" INFOPATH="/usr/share/info:/usr/share/binutils-data/sparc-unknown-linux-gnu/2.18/info:/usr/share/gcc-data/sparc-unknown-linux-gnu/4.3.2/info:/opt/xmingw/info:/usr/share/info/emacs-22:/homes/cache/info" INPUT_DEVICES="evdev keyboard mouse" JAVAC="/usr/bin/jikes" JAVA_HOME="/etc/java-config-2/current-system-vm" JDK_HOME="/etc/java-config-2/current-system-vm" KDEDIRS="/usr:/usr/local:/usr/kde/3.5" KERNEL="linux" KERNEL_ABI="sparc64" LADSPA_PATH="/usr/lib/ladspa" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LC_ALL="en_US.utf8" LDFLAGS="-Wl,-O1" LDFLAGS_sparc32="" LDFLAGS_sparc64="-m elf64_sparc" LESS="-R -M --shift 5" LESSCHARSET="utf-8" LESSOPEN="|lesspipe.sh %s" LIBDIR_amd64="lib64" LIBDIR_amd64_fbsd="lib64" LIBDIR_ppc="lib" LIBDIR_ppc64="lib64" LIBDIR_sparc32="lib" LIBDIR_sparc64="lib64" LIBDIR_x86="lib" LIBDIR_x86_fbsd="lib32" LINGUAS="de en en_US fr" LOGNAME="fmccor" LS_COLORS="no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.svgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:" MAIL="/var/mail/fmccor" MAKEOPTS="-j6" MANPATH="/etc/java-config-2/current-system-vm/man:/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/sparc-unknown-linux-gnu/2.18/man:/usr/share/gcc-data/sparc-unknown-linux-gnu/4.3.2/man:/opt/xmingw/man:/etc/java-config/system-vm/man/:/usr/lib/php5/man/:/usr/kde/3.5/share/man:/usr/qt/3/doc/man:/opt/opera/share/man:/homes/cache/man" MULTILIB_ABIS="sparc32" MULTILIB_STRICT_DENY="64-bit.*shared object" MULTILIB_STRICT_DIRS="/lib32 /lib /usr/lib32 /usr/lib /usr/kde/*/lib32 /usr/kde/*/lib /usr/qt/*/lib32 /usr/qt/*/lib /usr/X11R6/lib32 /usr/X11R6/lib" MULTILIB_STRICT_EXEMPT="(perl5|gcc|gcc-lib|binutils|eclipse-3|debug|portage)" NETBEANS="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" NIGHTLY="http://www.open-mpi.org/nightly/v0.9/" NS="/home1/PROJECTS/SIMULATION/ALL-IN-ONE/NS28/bin/ns" NSDIR="/home1/PROJECTS/SIMULATION/ALL-IN-ONE/NS28/ns-2.28" OLDPWD="/homes/home0/ferris/Packages/GROMACS/tutor" OMNIORB_CONFIG="/etc/omniorb/omniORB.cfg" OMPI="/home1/PROJECTS/OPEN-MPI" OPENGL_PROFILE="xorg-x11" PAGER="/usr/bin/less" PATH=".:/usr/local/lib/sablevm/bin:/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/sparc-unknown-linux-gnu/gcc-bin/4.3.2:/usr/sparc-unknown-linux-gnu/sparc64-unknown-linux-gnu/gcc-bin/4.1.2:/opt/xmingw/bin:/usr/kde/3.5/bin:/usr/qt/3/bin:/usr/kde/3.3/bin:/opt/firebird/bin:/usr/games/bin:/usr/share/omniORB/bin/scripts:/var/spool/fax/bin:/usr/sbin:/sbin" PBS_SERVER_HOME="/var/spool/torque" PD="/jaz/portage/packages" PKGDIR="/usr/portage/packages" PKG_CONFIG_PATH="/usr/qt/3/lib/pkgconfig" PORTAGE_ARCHLIST="ppc s390 amd64 x86 ppc64 x86-fbsd m68k arm sparc sh mips ia64 alpha hppa amd64-fbsd sparc-fbsd" PORTAGE_BINHOST_CHUNKSIZE="3000" PORTAGE_BIN_PATH="/usr/lib/portage/bin" PORTAGE_COMPRESS_EXCLUDE_SUFFIXES="css gif htm[l]? jp[e]?g js pdf png" PORTAGE_CONFIGROOT="/" PORTAGE_DEBUG="0" PORTAGE_DEPCACHEDIR="/var/cache/edb/dep" PORTAGE_ECLASS_WARNING_ENABLE="0" PORTAGE_ELOG_CLASSES="warn error log" PORTAGE_ELOG_MAILFROM="portage@localhost" PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}" PORTAGE_ELOG_MAILURI="root" PORTAGE_ELOG_SYSTEM="save" PORTAGE_FETCH_CHECKSUM_TRY_MIRRORS="5" PORTAGE_FETCH_RESUME_MIN_SIZE="350K" PORTAGE_GID="250" PORTAGE_INST_GID="0" PORTAGE_INST_UID="0" PORTAGE_PYM_PATH="/usr/lib/portage/pym" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_RSYNC_RETRIES="3" PORTAGE_TMPDIR="/var/tmp" PORTAGE_VERBOSE="1" PORTAGE_WORKDIR_MODE="0700" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" PROFILE_ARCH="sparc64" PROFILE_ONLY_VARIABLES="ARCH ELIBC KERNEL USERLAND" PS1="\[\033[01;32m\]\u@\h \[\033[01;31m\]\W [\#]% \[\033[00m\]" PS2="> " PWD="/homes/home0/ferris/Packages/GROMACS/tutor/methanol" PYTHIA8="/usr" PYTHIA8DATA="/usr/share/pythia/xmldoc" PYTHONPATH="/usr/lib/root:/cache/IcePy-3.0.0/python" QMAKESPEC="linux-g++" QTDIR="/usr/qt/3" REMOTEHOST="liasis.inforead.com" RESUMECOMMAND="/usr/bin/wget -c -t 5 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}"" ROOT="/" ROOTPATH="/opt/bin:/usr/sparc-unknown-linux-gnu/gcc-bin/4.3.2:/usr/sparc-unknown-linux-gnu/sparc64-unknown-linux-gnu/gcc-bin/4.1.2:/opt/xmingw/bin:/usr/kde/3.5/sbin:/usr/kde/3.5/bin:/usr/qt/3/bin:/usr/kde/3.3/sbin:/usr/kde/3.3/bin:/opt/firebird/bin:/homes/cache/bin" RPMDIR="/usr/portage/rpm" RUBYLIB="/usr/lib/root" RUBYOPT="-rubygems" R_HOME="/usr/lib/R" SBCL_HOME="/usr/lib/sbcl" SBCL_SOURCE_ROOT="/usr/lib/sbcl/src" SCHEME_LIBRARY_PATH="/usr/share/slib/" SGML_CATALOG_FILES="/etc/sgml/sgml-ent.cat:/etc/sgml/sgml-docbook.cat:/etc/sgml/openjade-1.3.2.cat:/etc/sgml/sgml-docbook-4.1.cat:/etc/sgml/sgml-docbook-4.0.cat:/etc/sgml/dsssl-docbook-stylesheets.cat:/etc/sgml/sgml-docbook-3.0.cat:/etc/sgml/sgml-docbook-3.1.cat:/etc/sgml/xml-simple-docbook-4.1.2.4.cat:/etc/sgml/xml-simple-docbook-1.0.cat:/etc/sgml/xml-docbook-4.4.cat:/etc/sgml/xml-docbook-4.1.2.cat:/etc/sgml/sgml-docbook-4.2.cat:/etc/sgml/sgml-lite.cat:/etc/sgml/sgml-docbook-4.4.cat" SHELL="/bin/bash" SHLVL="2" SSH_AGENT_PID="6003" SSH_AUTH_SOCK="/tmp/ssh-kXUbkm6002/agent.6002" SSH_CLIENT="192.168.1.213 37321 22" SSH_CONNECTION="192.168.1.213 37321 192.168.1.212 22" STAGE1_USE="nptl nptlonly unicode gcc64" SYMLINK_LIB="no" SYNC="rsync://rsync.gentoo.org/gentoo-portage" TERM="xterm" TEXINPUTS="/usr/lib/ocaml/ocamldoc:" TMP="/tmp/.private/fmccor" TMPDIR="/tmp/.private/fmccor" USE="X Xaw3d acl alsa berkdb bluetooth branding bzip2 cairo cdr cli cracklib crypt cscope cups dbus dri dvd dvdr dvdread eds emboss encode esd evo examples fam firefox fortran gcc64 gdbm gif glx gpm graphviz gstreamer gtk hal iconv idea isdnlog jpeg kerberos kpathsea latex ldap libnotify lzo lzw-tiff mad midi mikmod mp3 mpeg mudflap mysql ncurses nls nptl nptlonly ogg opengl openmp pam pcre pdf perl png ppds pppd python qt3 qt3support qt4 quicktime readline reflection ruby ruby18 sdl session sparc speex spell spl sqlite sqlite3 ssl startup-notification stroke svg sysfs tcl tcltk tcpd tex tiff tk truetype unicode usb vim-syntax vorbis xcb xetex xml xorg xulrunner xv zlib" ALSA_CARDS="ca0106 cmipci ens1370 ens1371" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter 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="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de en en_US fr" USERLAND="GNU" VIDEO_CARDS="dummy fbdev sunffb" USER="fmccor" USERLAND="GNU" USE_EXPAND="ALSA_CARDS ALSA_PCM_PLUGINS APACHE2_MODULES APACHE2_MPMS CAMERAS CROSSCOMPILE_OPTS DVB_CARDS ELIBC FCDSL_CARDS FOO2ZJS_DEVICES FRITZCAPI_CARDS INPUT_DEVICES KERNEL LCD_DEVICES LINGUAS LIRC_DEVICES MISDN_CARDS NETBEANS_MODULES USERLAND VIDEO_CARDS" USE_EXPAND_HIDDEN="CROSSCOMPILE_OPTS ELIBC KERNEL USERLAND" USE_ORDER="env:pkg:conf:defaults:pkginternal:env.d" VIDEO_CARDS="dummy fbdev sunffb" WANT_AUTOCONF="2.5" WANT_MP="true" WINDOWID="44040216" WINDOWMANAGER="/usr/bin/fvwm" XDG_DATA_DIRS="/usr/share:/usr/kde/3.5/share:/usr/local/share" XERCESC_NLS_HOME="/usr/share/xerces-c/msg" XGUILOADPATH="/home1/ferris/Packages/SNNS/SNNSv4.2" XTERM_LOCALE="C" XTERM_SHELL="/bin/bash" XTERM_VERSION="XTerm(239)" _="/usr/bin/emerge"
So far, so good. Now let us look for real solution.... Nothing sparc specific has been changed in the CVS head of gromacs in the gmx_cyclecounter.h till this morning. Filled a upstream bug: http://bugzilla.gromacs.org/show_bug.cgi?id=323
Created attachment 190780 [details, diff] Patch for Cyclecounter on sparc A suggestion from Erik Lindahl (gromacs core team) Please test.
(In reply to comment #24) > Created an attachment (id=190780) [edit] > Patch for Cyclecounter on sparc > > A suggestion from Erik Lindahl (gromacs core team) > > Please test. > That fixes it. Thanks. I see one test failure out of 16, but it's apparently not fatal (install contilues). It's certainly not related to the patch, and I'll look at it later.
(In reply to comment #25) > (In reply to comment #24) > > Created an attachment (id=190780) [edit] > > Patch for Cyclecounter on sparc > > > > A suggestion from Erik Lindahl (gromacs core team) > > > > Please test. > > > > That fixes it. Thanks. I see one test failure out of 16, but it's apparently > not fatal (install contilues). It's certainly not related to the patch, and > I'll look at it later. > The test failure seems to come from differences in precision between sparc and apple, and differences between gromacs-3.3.2 and gromacs-4.0.4. I guess there's a reason that the bug suggests testing with the tutorial files. They still seem fine. So I'll mark sparc stable once this patch is added to the package in the tree.
(In reply to comment #26) > The test failure seems to come from differences in precision between sparc and > apple, and differences between gromacs-3.3.2 and gromacs-4.0.4. I guess > there's a reason that the bug suggests testing with the tutorial files. They > still seem fine. They already know about the problems with the test suite: http://bugzilla.gromacs.org/show_bug.cgi?id=313 If you run "gmxtest.pl all" instead "gmxtest.pl simple", you will see even more tests fail. Let's hope that with gromacs-4.0.5 this problem will be solved!
(In reply to comment #24) > Created an attachment (id=190780) [edit] > Patch for Cyclecounter on sparc > > A suggestion from Erik Lindahl (gromacs core team) > > Please test. > The patch was added to the source: http://bugzilla.gromacs.org/show_bug.cgi?id=323 So it seems safe to add it to the ebuild.
(In reply to comment #28) > (In reply to comment #24) > > Created an attachment (id=190780) [edit] > > Patch for Cyclecounter on sparc > > > > A suggestion from Erik Lindahl (gromacs core team) > > > > Please test. > > > > The patch was added to the source: > http://bugzilla.gromacs.org/show_bug.cgi?id=323 > > So it seems safe to add it to the ebuild. > Ok patch added. BTW seems gromacs going to change license to LGPL
sparc stable for -4.0.4. See comment 19 for why -4.0.3 is impossible (gfortran).
Ok. GROMACS 4.0.4 is fine enough so let it be stabilazed =)
Stable on alpha.
x86 stable
There are also ia64 and ppc assembly loops, has somebody ever tested them?
amd64 stable
Any news from ppc64 team?
ppc64 done
its over 3 mouth since gromacs 4.0.5 in tree Please stabilize it!
sparc stable
Created attachment 217095 [details] ppc64 failure
I am seeing compile errors on ppc64 now. I have attached a build log.
for ppc64, 4.0.7 builds and appears to pass tests ... Any objections moving forward to that version and forget about 4.0.5 ?
I would go for 4.0.7-r1 due the fact that it works around Bug #302048 in addition to 4.0.7. But it is important to note that the way how gromacs libraries are build has changed since 4.0.5. If mpi is enabled gromacs is now compiled twice to get mpi and non-mpi version of libmd and libgmx.
*** This bug has been marked as a duplicate of bug 326151 ***
