Re: amber6 compilation failure (fwd)

From: David Skinner <dskinner_at_nersc.gov>
Date: Tue 20 Mar 2001 13:09:49 -0800 (PST)

On Tue, 20 Mar 2001, Jamal G. Musaev wrote:
> ld: 0711-224 WARNING: Duplicate symbol: last_key
> ld: 0711-224 WARNING: Duplicate symbol: next_key
> ld: 0711-224 WARNING: Duplicate symbol: .connect
> ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information.
> ld: 0711-317 ERROR: Undefined symbol: thread_unlock
> ld: 0711-317 ERROR: Undefined symbol: thread_waitact
> ld: 0711-317 ERROR: Undefined symbol: thread_setmystate_fast
> ld: 0711-317 ERROR: Undefined symbol: thread_tsleep
> ld: 0711-317 ERROR: Undefined symbol: thread_twakeup
> ld: 0711-317 ERROR: Undefined symbol: thread_setstate
> ld: 0711-317 ERROR: Undefined symbol: thread_terminate_ack
> ld: 0711-317 ERROR: Undefined symbol: thread_setmystate
> ld: 0711-317 ERROR: Undefined symbol: thread_tsleep_event
> ld: 0711-317 ERROR: Undefined symbol: thread_waitlock_local
> ld: 0711-317 ERROR: Undefined symbol: thread_waitlock
> ld: 0711-317 ERROR: Undefined symbol: thread_kill
> ld: 0711-317 ERROR: Undefined symbol: thread_twakeup_event
> ld: 0711-317 ERROR: Undefined symbol: thread_getregs
> ld: 0711-317 ERROR: Undefined symbol: thread_init
> ld: 0711-317 ERROR: Undefined symbol: thread_setstate_fast
> ld: 0711-317 ERROR: Undefined symbol: thread_terminate_unlock
> make: 1254-004 The error code from the last command is 8.

 There is a namespace conflict here. I have submitted patches to
amber_at_ucsf, but have yet to see them post to the patches page. They amount
to mapping *_key to amber_*key (e.g. amber_last_key) to avoid this
conflict. Also note this SP specific modification to the leap Imakefile:

from amber6.sp3/src/leap/src/leap/Imakefile

   /* Flags when you don't want to use shared libraries */

# if (CONFIG==distribution)
# skinner 9/00 breaks on sp3 need ifdef for non-AIX? SP2?
# namespace conflicts observed on SP3 are last_key, next_key, etc.
# also the threads api gets broken by -bI:/lib/syscalls.exp
# CDEBUGFLAGS = $(LEAP_FLAGS) -bnso -bI:/lib/syscalls.exp
          CDEBUGFLAGS = $(LEAP_FLAGS)
# else
          CDEBUGFLAGS = $(LEAP_FLAGS)
# endif

#endif

 Hope this helps. I am interested in what sort of performance and scaling
with node you see on your SP system.

 Regards,

 -David

-----------------------------------------------------
Dr. David Skinner User Services Group
dskinner_at_nersc.gov NERSC Division, Berkeley Lab
Received on Tue Mar 20 2001 - 13:09:49 PST
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