Re: parallel/sge 6.x

["George Georgalis" <george%galis.org@localhost>]

On Wed, Aug 09, 2006 at 11:56:31AM +1200, Mark Davies wrote:
>On Wednesday 09 August 2006 04:10, George Georgalis wrote:
>> I'm discussing adopting parallel/sge for $WORK and
>> was wondering if anyone else is in need of a 6.x
>> version or using a non-committed pkgsrc method?
>
>http://www.mcs.vuw.ac.nz/~mark/sge6.tgz is a package for sge6 that 
>successfully builds but apparently doesn't work - from memory it was  
>problems with initialising some databases that it uses.
>
>Hasn't been looked at for some months but it would be a good starting point 
>for you.  I'm happy to help.

Hey! Thanks! There is a lot of work in there :)

I made some progress, but don't know much about the last error...

First in the Makefile, I added -no-jni to to the lines that have
it below, so JAVA_HOME doesn't need define (sigh).

do-build:
        cd ${WRKSRC}/source && ${AIMK} -no-jni -only-depend
        cd ${WRKSRC}/source && ${SETENV} ${MAKE_ENV} ./scripts/zerodepend
        cd ${WRKSRC}/source && ${AIMK} -no-jni -no-qmake -no-qtcsh depend
        cd ${WRKSRC}/source && ${AIMK} -no-jni
        cd ${WRKSRC}/source && ${AIMK} -no-jni -man


The MESSAGE file could include

sge_qmaster     8701/tcp        # grid engine 6 qmaster
sge_execd       8702/tcp        # grid engine 6 execd

(thoes ports are from another install, may (or not) be a good port
choice.)

doesn't seem to depend on database/db4, I guess it should by default

Then, the DB errors...
        cd /usr/pkg/sge && ./install_qmaster -csp
invokes

./utilbin/nbsd-x86_64/spoolinit berkeleydb libspoolb 
/usr/pkg/sge/grid/spool/spooldb init

which looks at /usr/pkg/lib/libspoolb.so and /usr/lib/libspoolb.so
but fails to check where it was actually installed, to quick fix:
ln -s /usr/pkg/sge/lib/nbsd-x86_64/libspoolb.so /usr/pkg/lib/libspoolb.so

Similar problem, libdb4-4.4.so.4 is only looked for in one
location, quick fix:
ln -s /usr/pkg/lib/libdb4-4.4.so.4 /usr/lib/libdb4-4.4.so.4

Then I get:

Berkeley Database spooling parameters
-------------------------------------

Please enter the Database Directory now, even if you want to spool locally,
it is necessary to enter this Database Directory.

Default: [/usr/pkg/sge/grid/spool/spooldb] >>

creating directory: /usr/pkg/sge/grid/spool/spooldb
Dumping bootstrapping information
Initializing spooling database
critical error: Profiling array is not initialized!

[1]   Abort trap              ${SGE_UTILBIN}/a...

Command failed: ./utilbin/nbsd-x86_64/spoolinit berkeleydb libspoolb 
/usr/pkg/sge/grid/spool/spooldb init


the ktrace, for what it's worth...

 14536 spoolinit CALL  open(0x2005af280,0,0x64)
 14536 spoolinit NAMI  "/usr/lib/libdb4-4.4.so.4"
 14536 spoolinit RET   open 3
 14536 spoolinit CALL  __fstat13(3,0x7f7fffffd5d0)
 14536 spoolinit RET   __fstat13 0
 14536 spoolinit CALL  mmap(0,0x1000,1,1,3,0x7f7f00000000,0)
 14536 spoolinit RET   mmap 8595918848/0x2005b5000
 14536 spoolinit CALL  munmap(0x2005b5000,0x1000)
 14536 spoolinit RET   munmap 0
 14536 spoolinit CALL  mmap(0,0x1fd000,5,0x14000002,3,0x7f7f00000000,0)
 14536 spoolinit RET   mmap 8608808960/0x201200000
 14536 spoolinit CALL  mmap(0x2013e7000,0x16000,3,0x12,3,0x7f7f00000000,0xe7000)
 14536 spoolinit RET   mmap 8610803712/0x2013e7000
 14536 spoolinit CALL  mmap(0x2013fd000,0,3,0x1012,0xffffffff,0x7f7f00000000,0)
 14536 spoolinit RET   mmap 8610893824/0x2013fd000
 14536 spoolinit CALL  mprotect(0x2012e7000,0x100000,0)
 14536 spoolinit RET   mprotect 0
 14536 spoolinit CALL  close(3)
 14536 spoolinit RET   close 0
 14536 spoolinit CALL  write(2,0x7f7fffffcb80,0x35)
 14536 spoolinit GIO   fd 2 wrote 53 bytes
       "critical error: Profiling array is not initialized!

       "


Looks like a sge software problem. Maybe ./install_qmaster is not
properly setting env? The other stuff is cleanup, but this one
looks like some effort is needed, any idea what's wrong?

// George


-- 
George Georgalis, systems architect, administrator <IXOYE><