[gridengine users] gridengine 2011.11 compile errors

Prentice Bisbal prentice at ias.edu
Wed Dec 7 21:09:42 UTC 2011


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 <prentice at ias.edu> 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
>>
>> _______________________________________________
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>> https://gridengine.org/mailman/listinfo/users


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