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Bug 420431 - sys-cluster/openmpi-1.6 looks for config files in /usr/etc
Summary: sys-cluster/openmpi-1.6 looks for config files in /usr/etc
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Core system (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Justin Bronder (RETIRED)
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2012-06-09 20:11 UTC by William Throwe
Modified: 2012-06-10 06:39 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build log (sys-cluster:openmpi-1.6:20120609-192327.log.gz,120.04 KB, application/gzip)
2012-06-09 20:16 UTC, William Throwe
Details

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Description William Throwe 2012-06-09 20:11:53 UTC
wthrowe@amandil ~ $ mpirun /bin/true
--------------------------------------------------------------------------
Open RTE was unable to open the hostfile:
    /usr/etc/openmpi-default-hostfile
Check to make sure the path and filename are correct.
--------------------------------------------------------------------------
[amandil:10879] [[51795,0],0] ORTE_ERROR_LOG: Not found in file base/ras_base_allocate.c at line 200
[amandil:10879] [[51795,0],0] ORTE_ERROR_LOG: Not found in file base/plm_base_launch_support.c at line 99
[amandil:10879] [[51795,0],0] ORTE_ERROR_LOG: Not found in file plm_rsh_module.c at line 1167
wthrowe@amandil ~ $ equery f openmpi | grep default-hostfile
/etc/openmpi/openmpi-default-hostfile
wthrowe@amandil ~ $
Comment 1 William Throwe 2012-06-09 20:16:16 UTC
Created attachment 314815 [details]
build log

Oops.  Accidentally submitted before I was done.

The package installs /etc/openmpi/openmpi-default-hostfile , but tries to read /usr/etc/openmpi-default-hostfile .

$ emerge --info hdf5
Portage 2.2.0_alpha110 (default/linux/amd64/10.0, gcc-4.6.3, glibc-2.15-r2, 3.3.5-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.3.5-gentoo-x86_64-Intel-R-_Core-TM-2_CPU_T5500_@_1.66GHz-with-gentoo-2.1
Timestamp of tree: Sat, 09 Jun 2012 06:45:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:          4.2_p29
dev-lang/python:          2.7.3-r2, 3.2.3-r1
dev-util/cmake:           2.8.8-r2
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.10.2
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.5, 1.12.1
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.6.3
sys-devel/gcc-config:     1.7.2
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r3
sys-kernel/linux-headers: 3.4 (virtual/os-headers)
sys-libs/glibc:           2.15-r2
Repositories: gentoo crossdev wthrowe
Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="@FREE"
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/gentoo-release /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"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--ask --quiet-build=n"
FEATURES="assume-digests binpkg-logs clean-logs compress-build-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://gentoo.netnitco.net http://mirror.mcs.anl.gov/pub/gentoo/ http://mirror.csclub.uwaterloo.ca/gentoo-distfiles/ http://mirror.datapipe.net/gentoo ftp://mirror.datapipe.net/gentoo"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/crossdev /var/lib/layman/wthrowe"
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
USE="X acl acpi alsa amd64 berkdb bindist bzip2 cairo caps cdr cli cracklib crypt cxx dbus dri dvd dvdr emacs fortran gd gdbm gimp gpm gtk iconv jpeg latex mmx modules mudflap multilib ncurses nptl opengl openmp pam pcre png pppd readline session smp sse sse2 ssl ssse3 system-sqlite tcpd truetype unicode xorg xscreensaver 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" SANE_BACKENDS="epson2" USERLAND="GNU" VIDEO_CARDS="radeon" 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, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

=================================================================
                        Package Settings
=================================================================

sci-libs/hdf5-1.8.9-r1 was built with the following:
USE="(multilib) threads zlib -cxx -debug -examples -fortran -fortran2003 -mpi -static-libs -szip"
Comment 2 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2012-06-09 20:23:21 UTC
Yup, fedora seems to have patch which deals with this issue[1], though it won't necessarily same for us. 

[1] http://pkgs.fedoraproject.org/gitweb/?p=openmpi.git;a=blob;f=openmpi-hostfile.patch;h=f6377674b3652a86112d891aef37c2d0f73cb3d3;hb=b657ab44d63c0148aa32aa4d0f275c1593202943
Comment 3 William Throwe 2012-06-10 03:06:08 UTC
Applying that patch seems to fix the problem.
Comment 4 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2012-06-10 06:39:01 UTC
+*openmpi-1.6-r1 (10 Jun 2012)
+
+  10 Jun 2012; Kacper Kowalik <xarthisius@gentoo.org>
+  +files/openmpi-1.6-hostfile.patch, +openmpi-1.6-r1.ebuild,
+  -openmpi-1.6.ebuild:
+  Add patch from upstream to fix default hostfile location wrt #420431 by
+  William Throwe <wtt6@cornell.edu>
+