OpenMPI on SL
Nils
n.bruenggel at gmail.com
Fri Sep 18 07:02:01 PDT 2009
Hi all
I just installed ports on SL so far I was able to install various
things [1] however openmpi does not seem to compile. I attached the
build log below [2], hoping that somebody can help me :)
I also have two further questions:
- Instead of building everything on your own machine, are there binary
packages available?
- When port builds the packages (eg after typing port install blah)
does it use all available cores for compiling and if not, where can I
configure that?
Nils
[1]
The following ports are currently installed:
autoconf @2.64_2 (active)
automake @1.11_0 (active)
boost @1.40.0_1 (active)
boost-jam @3.1.17_0 (active)
bzip2 @1.0.5_2+darwin (active)
cmake @2.6.4_1 (active)
curl @7.19.6_0 (active)
dbus @1.2.14_0 (active)
expat @2.0.1_0 (active)
gettext @0.17_4 (active)
git-core @1.6.4.3_0+doc (active)
gmp @4.3.1_1 (active)
gmp-cxx-wrappers @4.2.1_2+darwin_i386
gperf @3.0.4_0 (active)
help2man @1.36.4_1 (active)
jpeg @6b_3 (active)
lcms @1.18a_0 (active)
libiconv @1.13_0 (active)
libidn @1.15_0 (active)
libmng @1.0.10_0 (active)
libpng @1.2.38_0 (active)
libtool @2.2.6a_0 (active)
lzmautils @4.32.7_1 (active)
m4 @1.4.13_0 (active)
metis @4.0.1_0 (active)
mpfr @2.4.1-p4_1 (active)
ncurses @5.7_0+darwin_10 (active)
ncursesw @5.7_0+darwin_10 (active)
openssl @0.9.8k_0+darwin (active)
p5-error @0.17015_0 (active)
p5-locale-gettext @1.05_0 (active)
perl5 @5.8.9_0 (active)
perl5.8 @5.8.9_3 (active)
pkgconfig @0.23_1 (active)
popt @1.15_0 (active)
readline @6.0.000_1+darwin (active)
rsync @3.0.6_0 (active)
sqlite3 @3.6.18_0 (active)
tiff @3.9.1_0+macosx (active)
zlib @1.2.3_3 (active)
[2]
~ # port install openmpi
---> Computing dependencies for openmpi
---> Fetching gcc43
---> Attempting to fetch gcc-core-4.3.4.tar.bz2 from
ftp://ftp.lip6.fr/pub/gnu//gcc/gcc-4.3.4
---> Attempting to fetch gcc-fortran-4.3.4.tar.bz2 from
ftp://ftp.lip6.fr/pub/gnu//gcc/gcc-4.3.4
---> Attempting to fetch gcc-g++-4.3.4.tar.bz2 from
ftp://ftp.lip6.fr/pub/gnu//gcc/gcc-4.3.4
---> Attempting to fetch gcc-java-4.3.4.tar.bz2 from
ftp://ftp.lip6.fr/pub/gnu//gcc/gcc-4.3.4
---> Attempting to fetch gcc-objc-4.3.4.tar.bz2 from
ftp://ftp.lip6.fr/pub/gnu//gcc/gcc-4.3.4
---> Verifying checksum(s) for gcc43
---> Extracting gcc43
---> Configuring gcc43
---> Building gcc43
Error: Target org.macports.build returned: shell command " cd
"/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build"
&& /usr/bin/make -j2 all " returned error 2
Command output:
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/xgcc
-B/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/
-B/opt/local/x86_64-apple-darwin10/bin/ -c -g -O2 -DIN_GCC -W
-Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wold-style-definition -Wmissing-format-attribute -pedantic
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings
-DHAVE_CONFIG_H -I. -I. -I../../gcc-4.3.4/gcc -I../../gcc-4.3.4/gcc/.
-I../../gcc-4.3.4/gcc/../include
-I../../gcc-4.3.4/gcc/../libcpp/include -I/opt/local/include
-I/opt/local/include -I../../gcc-4.3.4/gcc/../libdecnumber
-I../../gcc-4.3.4/gcc/../libdecnumber/dpd -I../libdecnumber
../../gcc-4.3.4/gcc/value-prof.c -o value-prof.o
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/xgcc
-B/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/
-B/opt/local/x86_64-apple-darwin10/bin/ -c -g -O2 -DIN_GCC -W
-Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wold-style-definition -Wmissing-format-attribute -pedantic
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings
-DHAVE_CONFIG_H -I. -I. -I../../gcc-4.3.4/gcc -I../../gcc-4.3.4/gcc/.
-I../../gcc-4.3.4/gcc/../include
-I../../gcc-4.3.4/gcc/../libcpp/include -I/opt/local/include
-I/opt/local/include -I../../gcc-4.3.4/gcc/../libdecnumber
-I../../gcc-4.3.4/gcc/../libdecnumber/dpd -I../libdecnumber
../../gcc-4.3.4/gcc/ipa-inline.c -o ipa-inline.o
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/xgcc
-B/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/
-B/opt/local/x86_64-apple-darwin10/bin/ -c -g -O2 -DIN_GCC -W
-Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wold-style-definition -Wmissing-format-attribute -pedantic
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings
-DHAVE_CONFIG_H -I. -I. -I../../gcc-4.3.4/gcc -I../../gcc-4.3.4/gcc/.
-I../../gcc-4.3.4/gcc/../include
-I../../gcc-4.3.4/gcc/../libcpp/include -I/opt/local/include
-I/opt/local/include -I../../gcc-4.3.4/gcc/../libdecnumber
-I../../gcc-4.3.4/gcc/../libdecnumber/dpd -I../libdecnumber
../../gcc-4.3.4/gcc/ipa-struct-reorg.c -o ipa-struct-reorg.o
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/xgcc
-B/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/
-B/opt/local/x86_64-apple-darwin10/bin/ -c -g -O2 -DIN_GCC -W
-Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wold-style-definition -Wmissing-format-attribute -pedantic
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings
-DHAVE_CONFIG_H -I. -I. -I../../gcc-4.3.4/gcc -I../../gcc-4.3.4/gcc/.
-I../../gcc-4.3.4/gcc/../include
-I../../gcc-4.3.4/gcc/../libcpp/include -I/opt/local/include
-I/opt/local/include -I../../gcc-4.3.4/gcc/../libdecnumber
-I../../gcc-4.3.4/gcc/../libdecnumber/dpd -I../libdecnumber
../../gcc-4.3.4/gcc/gcov.c -o gcov.o
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/xgcc
-B/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/
-B/opt/local/x86_64-apple-darwin10/bin/ -c -g -O2 -DIN_GCC -W
-Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wold-style-definition -Wmissing-format-attribute -pedantic
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings
-DHAVE_CONFIG_H -I. -I. -I../../gcc-4.3.4/gcc -I../../gcc-4.3.4/gcc/.
-I../../gcc-4.3.4/gcc/../include
-I../../gcc-4.3.4/gcc/../libcpp/include -I/opt/local/include
-I/opt/local/include -I../../gcc-4.3.4/gcc/../libdecnumber
-I../../gcc-4.3.4/gcc/../libdecnumber/dpd -I../libdecnumber
../../gcc-4.3.4/gcc/gcov-dump.c -o gcov-dump.o
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/xgcc
-B/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/
-B/opt/local/x86_64-apple-darwin10/bin/ -g -O2 -DIN_GCC -W -Wall
-Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wold-style-definition -Wmissing-format-attribute -pedantic
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings
-DHAVE_CONFIG_H gcov.o intl.o version.o errors.o ../libcpp/libcpp.a
../libiberty/libiberty.a ../libdecnumber/libdecnumber.a -o gcov
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/xgcc
-B/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/
-B/opt/local/x86_64-apple-darwin10/bin/ -g -O2 -DIN_GCC -W -Wall
-Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wold-style-definition -Wmissing-format-attribute -pedantic
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings
-DHAVE_CONFIG_H gcov-dump.o version.o errors.o ../libcpp/libcpp.a
../libiberty/libiberty.a ../libdecnumber/libdecnumber.a -o gcov-dump
rm -rf libbackend.a
ar rc libbackend.a insn-attrtab.o insn-automata.o insn-emit.o
insn-extract.o insn-modes.o insn-opinit.o insn-output.o insn-peep.o
insn-preds.o insn-recog.o ggc-page.o alias.o alloc-pool.o
auto-inc-dec.o bb-reorder.o bitmap.o bt-load.o builtins.o
caller-save.o calls.o cfg.o cfganal.o cfgbuild.o cfgcleanup.o
cfgexpand.o cfghooks.o cfglayout.o cfgloop.o cfgloopanal.o
cfgloopmanip.o cfgrtl.o combine.o combine-stack-adj.o convert.o
coverage.o cse.o cselib.o dbxout.o dbgcnt.o dce.o ddg.o debug.o
df-core.o df-problems.o df-scan.o dfp.o diagnostic.o dojump.o
dominance.o domwalk.o double-int.o dse.o dwarf2asm.o dwarf2out.o
ebitmap.o emit-rtl.o et-forest.o except.o explow.o expmed.o expr.o
final.o fixed-value.o fold-const.o function.o fwprop.o gcse.o genrtl.o
ggc-common.o gimple-low.o gimplify.o global.o graph.o graphds.o
gtype-desc.o haifa-sched.o hooks.o ifcvt.o init-regs.o integrate.o
intl.o jump.o lambda-code.o lambda-mat.o lambda-trans.o langhooks.o
lcm.o lists.o local-alloc.o loop-doloop.o loop-init.o loop-invariant.o
loop-iv.o loop-unroll.o loop-unswitch.o lower-subreg.o
mode-switching.o modulo-sched.o omega.o omp-low.o optabs.o options.o
opts-common.o opts.o params.o passes.o pointer-set.o postreload-gcse.o
postreload.o predict.o pretty-print.o print-rtl.o print-tree.o
profile.o ra-conflict.o real.o recog.o reg-stack.o regclass.o
regmove.o regrename.o regstat.o reload.o reload1.o reorg.o resource.o
rtl-error.o rtl-factoring.o rtl.o rtlanal.o rtlhooks.o sbitmap.o
sched-deps.o sched-ebb.o sched-rgn.o sched-vis.o sdbout.o see.o
simplify-rtx.o sparseset.o sreal.o stack-ptr-mod.o stmt.o
stor-layout.o stringpool.o struct-equiv.o targhooks.o timevar.o
toplev.o tracer.o tree-affine.o tree-cfg.o tree-cfgcleanup.o
tree-chrec.o tree-complex.o tree-data-ref.o tree-dfa.o tree-dump.o
tree-eh.o tree-gimple.o tree-if-conv.o tree-into-ssa.o tree-iterator.o
tree-loop-linear.o tree-nested.o tree-nrv.o tree-object-size.o
tree-optimize.o tree-outof-ssa.o tree-parloops.o tree-phinodes.o
tree-predcom.o tree-pretty-print.o tree-profile.o
tree-scalar-evolution.o tree-sra.o tree-ssa-address.o tree-ssa-alias.o
tree-ssa-alias-warnings.o tree-ssa-ccp.o tree-ssa-coalesce.o
tree-ssa-copy.o tree-ssa-copyrename.o tree-ssa-dce.o tree-ssa-dom.o
tree-ssa-dse.o tree-ssa-forwprop.o tree-ssa-ifcombine.o
tree-ssa-live.o tree-ssa-loop-ch.o tree-ssa-loop-im.o
tree-ssa-loop-ivcanon.o tree-ssa-loop-ivopts.o tree-ssa-loop-manip.o
tree-ssa-loop-niter.o tree-ssa-loop-prefetch.o
tree-ssa-loop-unswitch.o tree-ssa-loop.o tree-ssa-math-opts.o
tree-ssa-operands.o tree-ssa-phiopt.o tree-ssa-pre.o
tree-ssa-propagate.o tree-ssa-reassoc.o tree-ssa-sccvn.o
tree-ssa-sink.o tree-ssa-structalias.o tree-ssa-ter.o
tree-ssa-threadedge.o tree-ssa-threadupdate.o tree-ssa-uncprop.o
tree-ssa.o tree-ssanames.o tree-stdarg.o tree-tailcall.o
tree-vect-analyze.o tree-vect-generic.o tree-vect-patterns.o
tree-vect-transform.o tree-vectorizer.o tree-vn.o tree-vrp.o tree.o
value-prof.o var-tracking.o varasm.o varray.o vec.o version.o
vmsdbgout.o web.o xcoffout.o i386.o darwin.o host-darwin.o
host-i386-darwin.o cgraph.o cgraphbuild.o cgraphunit.o ipa-cp.o
ipa-inline.o ipa-prop.o ipa-pure-const.o ipa-reference.o
ipa-struct-reorg.o ipa-type-escape.o ipa-utils.o ipa.o matrix-reorg.o
tree-inline.o tree-nomudflap.o varpool.o
ranlib: file: libbackend.a(insn-peep.o) has no symbols
ranlib: file: libbackend.a(loop-doloop.o) has no symbols
ranlib: file: libbackend.a(vmsdbgout.o) has no symbols
ranlib: file: libbackend.a(xcoffout.o) has no symbols
ranlib -c libbackend.a
ranlib: file: libbackend.a(insn-peep.o) has no symbols
ranlib: file: libbackend.a(loop-doloop.o) has no symbols
ranlib: file: libbackend.a(vmsdbgout.o) has no symbols
ranlib: file: libbackend.a(xcoffout.o) has no symbols
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/xgcc
-B/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/
-B/opt/local/x86_64-apple-darwin10/bin/ -g -O2 -DIN_GCC -W -Wall
-Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wold-style-definition -Wmissing-format-attribute -pedantic
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings
-DHAVE_CONFIG_H -o cc1-dummy c-lang.o stub-objc.o attribs.o
c-errors.o c-lex.o c-pragma.o c-decl.o c-typeck.o c-convert.o
c-aux-info.o c-common.o c-opts.o c-format.o c-semantics.o c-incpath.o
cppdefault.o c-ppoutput.o c-cppbuiltin.o prefix.o c-objc-common.o
c-dump.o c-pch.o c-parser.o darwin-c.o c-gimplify.o tree-mudflap.o
c-pretty-print.o c-omp.o dummy-checksum.o \
main.o libbackend.a ../libcpp/libcpp.a
../libdecnumber/libdecnumber.a ../libcpp/libcpp.a
../libiberty/libiberty.a ../libdecnumber/libdecnumber.a
-L/opt/local/lib -L/opt/local/lib -lmpfr -lgmp
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/xgcc
-B/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_lang_gcc43/work/build/./prev-gcc/
-B/opt/local/x86_64-apple-darwin10/bin/ -g -O2 -DIN_GCC -W -Wall
-Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wold-style-definition -Wmissing-format-attribute -pedantic
-Wno-long-long -Wno-variadic-macros -Wno-overlength-strings
-DHAVE_CONFIG_H -o cc1plus-dummy \
cp/cp-lang.o stub-objc.o cp/call.o cp/decl.o cp/expr.o cp/pt.o
cp/typeck2.o cp/class.o cp/decl2.o cp/error.o cp/lex.o cp/parser.o
cp/ptree.o cp/rtti.o cp/typeck.o cp/cvt.o cp/except.o cp/friend.o
cp/init.o cp/method.o cp/search.o cp/semantics.o cp/tree.o cp/repo.o
cp/dump.o cp/optimize.o cp/mangle.o cp/cp-objcp-common.o
cp/name-lookup.o cp/cxx-pretty-print.o cp/cp-gimplify.o tree-mudflap.o
attribs.o c-common.o c-format.o c-pragma.o c-semantics.o c-lex.o
c-dump.o darwin-c.o c-pretty-print.o c-opts.o c-pch.o c-incpath.o
cppdefault.o c-ppoutput.o c-cppbuiltin.o prefix.o c-gimplify.o c-omp.o
tree-inline.o dummy-checksum.o main.o libbackend.a ../libcpp/libcpp.a
../libdecnumber/libdecnumber.a ../libcpp/libcpp.a
../libiberty/libiberty.a ../libdecnumber/libdecnumber.a
-L/opt/local/lib -L/opt/local/lib -lmpfr -lgmp
ld: duplicate symbol _init_inline_once in libbackend.a(tree-inline.o)
and tree-inline.o
collect2: ld returned 1 exit status
make[3]: *** [cc1plus-dummy] Error 1
make[3]: *** Waiting for unfinished jobs....
rm gfortran.pod
make[2]: *** [all-stage2-gcc] Error 2
make[1]: *** [stage2-bubble] Error 2
make: *** [all] Error 2
Error: The following dependencies failed to build: gcc43
Error: Status 1 encountered during processing.
~ #
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