Rayson, Thanks for the information. I can use the pre-compiled binaries for now. Not as much fun, but they'll do. :)
Prentice On 12/07/2011 04:35 PM, Rayson Ho wrote: > Prentice, > > The problem similar to this one encountered by the Open MPI build (Re: > [OMPI users] EXTERNAL: Re: Unresolved reference 'mbind' and > 'get_mempolicy'): > > http://www.open-mpi.org/community/lists/users/2011/09/17479.php > > In Grid Engine 2011.11, we don't use the NUMA functions (as users can > do it easily in the job scripts by using the numactl (8) command). So > we don't need the NUMA library. In Open MPI, there is the > "--without-libnuma" option, which is actually not available in hwloc's > configure script. > > So there are 3 options: > > 1) Use the precompiled binary: > http://dl.dropbox.com/u/47200624/ge2011.11-x64.tar.gz > > 2) Modify configure in hwloc-1.2.2 to force linking against "-lnuma" to fail. > > 3) Or wait 1-2 days and I will check in a fix that disables using the > NUMA library in hwloc. > > I will check with the hwloc guys and see if they will add a configure > switch for hwloc in their future releases. > > Rayson > > > > On Wed, Dec 7, 2011 at 4:09 PM, Prentice Bisbal <[email protected]> wrote: >> Rayson, >> >> Thanks. That was the problem. Now I'm getting another problem. It looks >> like it can't find libnuma, even though I have the numactl and >> numactl-devel packages installed. See error messages at bottom. >> >> I've verified that I have the numa RPMs installed >> >> $ rpm -qa | grep numa >> numactl-devel-0.9.8-12.el5_6 >> numactl-0.9.8-12.el5_6 >> numactl-0.9.8-12.el5_6 >> numactl-devel-0.9.8-12.el5_6 >> >> They're listed twice because I have both the i386 and x86_64 versions >> installed. In the past, I've had problems with the linker can't find the >> correct version (32-bit vs. 64-bit version) of the library. I noticed >> that there's a "-lhwloc" in the command, but no "-lnuma". Is that correct? >> >> >> gcc -o sge_execd -L/build/berkeleydb/lib/ -L. -rdynamic >> -Wl,-rpath,\$ORIGIN/../../lib/linux-x64 -L/build/openssl-install/lib >> execd.o sge_load_sensor.o dispatcher.o exec_job.o execd_ck_to_do.o >> execd_get_new_conf.o execd_job_exec.o execd_kill_execd.o >> execd_signal_queue.o execd_ticket.o get_path.o job_report_execd.o >> load_avg.o pdc.o procfs.o ptf.o reaper_execd.o sge_report_execd.o >> setup_execd.o tmpdir.o usage.o sge_options.o admin_mail.o config_file.o >> mail.o read_write_job.o sge_dirent.o execution_states.o sig_handlers.o >> startprog.o shutdown.o sge_mt_init.o -lgdi -lsgeobj -lsgeobjd -lcull >> -lcomm -lcommlists -luti -llck -lrmon -ldl >> -L/work/prentice/GE2011.11/source/3rdparty/hwloc/hwloc-1.2.2/LINUXX64/src/.libs/ >> -lhwloc -ljemalloc -lm -lpthread >> /work/prentice/GE2011.11/source/3rdparty/hwloc/hwloc-1.2.2/LINUXX64/src/.libs//libhwloc.a(topology-linux.o): >> In function `hwloc_linux_set_area_membind': >> topology-linux.c:(.text+0x331): undefined reference to `mbind' >> topology-linux.c:(.text+0x3ac): undefined reference to `mbind' >> /work/prentice/GE2011.11/source/3rdparty/hwloc/hwloc-1.2.2/LINUXX64/src/.libs//libhwloc.a(topology-linux.o): >> In function `hwloc_linux_get_thisthread_membind': >> topology-linux.c:(.text+0x4d5): undefined reference to `get_mempolicy' >> topology-linux.c:(.text+0x5eb): undefined reference to `get_mempolicy' >> /work/prentice/GE2011.11/source/3rdparty/hwloc/hwloc-1.2.2/LINUXX64/src/.libs//libhwloc.a(topology-linux.o): >> In function `hwloc_linux_set_thisthread_membind': >> topology-linux.c:(.text+0x68e): undefined reference to `set_mempolicy' >> topology-linux.c:(.text+0x711): undefined reference to `migrate_pages' >> topology-linux.c:(.text+0x734): undefined reference to `set_mempolicy' >> >> -- >> Prentice >> >> >> On 12/07/2011 03:29 PM, Rayson Ho wrote: >>> Likely due to your $JAVA_HOME. >>> >>> If you don't have Java installed, then compile with aimk flags: -no-java >>> -no-jni >>> >>> Otherwise, make sure it is set correctly: >>> >>> 1) Find the java real directory: >>> $ readlink -f `which java` >>> /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/bin/java >>> >>> 2) set the JAVA_HOME env. var: >>> $ setenv JAVA_HOME /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/ >>> >>> ("export" instead of "setenv" for bash/sh/ksh) >>> >>> The $JAVA_HOME/include has to contain "jni.h" or else you won't be >>> able to compile the JNI related code in Grid Engine. >>> >>> Rayson >>> >>> >>> >>> On Wed, Dec 7, 2011 at 3:12 PM, Prentice Bisbal <[email protected]> wrote: >>>> I'm trying to compile GE2011.11. I downloaded the tarball from >>>> sourceforge. And I'm getting this error: >>>> >>>> In file included from /usr/include/_G_config.h:44, >>>> from /usr/include/libio.h:32, >>>> from /usr/include/stdio.h:72, >>>> from ../libs/sgeobj/config.c:33: >>>> /usr/include/gconv.h:72: error: expected declaration specifiers or ‘...’ >>>> before ‘size_t’ >>>> /usr/include/gconv.h:88: error: expected declaration specifiers or ‘...’ >>>> before ‘size_t’ >>>> /usr/include/gconv.h:97: error: expected declaration specifiers or ‘...’ >>>> before ‘size_t’ >>>> /usr/include/gconv.h:174: error: expected specifier-qualifier-list >>>> before ‘size_t’ >>>> In file included from /usr/include/stdio.h:72, >>>> >>>> I'm sure I'm missing some include file(s) somewhere, but I can't figure >>>> out which one. Of, course when I google for these errors, I get >>>> a bazillion hits for other errors include the string "size_t", so it >>>> hasn't been very fruitful. >>>> >>>> Any assistance will be greatly appreciated. I'm sure it's something >>>> minor. I'm building on a RHEL 5.7 system, using gcc >>>> >>>> -- >>>> Prentice >>>> >>>> _______________________________________________ >>>> users mailing list >>>> [email protected] >>>> https://gridengine.org/mailman/listinfo/users >> _______________________________________________ >> users mailing list >> [email protected] >> https://gridengine.org/mailman/listinfo/users _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
