Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Fri Sep 02 2005 - 00:34:03 CDT

Jason Lee wrote:

> Dear Gengbin:
>
> I am very sorry to bother you again. I didn't test charm++ for my
> careless yesterday. It comes out the following error when I checked
> the compilation output today. I didn't attach the whlole output.
>
> cp: QuickThreads/libqt.dylib: No such file or directory
> make[2]: [QuickThreads/libqt.a] Error 1 (ignored)

don't worry about this error. This happens because charm++ couldnot
build shared library with mpich which is fine for NAMD.

>
> Fatal Error by charmc in directory
> /Users/j0l6571/namd/namd2.6b1/NAMD_2.6b1_Source/charm/mpi-ppc-darwin-gm-xlc/tmp
>
> Command xlc_r -qnocommon -qpic -I /opt/gm/include -I../bin/../include
> -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -DCMK_MEMORY_BUILD_VERBOSE -O3
> -qstrict -Q -I/Users/j0l6571/bin/mpich-gm-underscore/include -c
> memory.c -o ../lib/libmemory-verbose.o returned error code 1
> charmc exiting...
> ../bin/charmc -O -DCMK_OPTIMIZE=1 -nobs -o ../lib/libmemory-paranoid.o
> -DCMK_MEMORY_BUILD_PARANOID memory.c || touch ../lib/libmemory-paranoid.o
> "memory-gnu.c", line 535.9: 1506-236 (W) Macro name __builtin_expect
> has been redefined.
> "memory-paranoid.c", line 294.14: 1506-343 (S) Redeclaration of
> meta_malloc differs from previous declaration on line 92 of "memory.c".
> "memory-paranoid.c", line 294.14: 1506-050 (I) Return type "void*" in
> redeclaration is not compatible with the previous return type "int".
> Fatal Error by charmc in directory
> /Users/j0l6571/namd/namd2.6b1/NAMD_2.6b1_Source/charm/mpi-ppc-darwin-gm-xlc/tmp
>
> Command xlc_r -qnocommon -qpic -I /opt/gm/include -I../bin/../include
> -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -DCMK_MEMORY_BUILD_PARANOID -O3
> -qstrict -Q -I/Users/j0l6571/bin/mpich-gm-underscore/include -c
> memory.c -o ../lib/libmemory-paranoid.o returned error code 1
> charmc exiting...
> ../bin/charmc -O -DCMK_OPTIMIZE=1 -nobs -o ../lib/libmemory-leak.o
> -DCMK_MEMORY_BUILD_LEAK memory.c || touch ../lib/libmemory-leak.o
> "memory-leak.c", line 175.14: 1506-343 (S) Redeclaration of
> meta_malloc differs from previous declaration on line 92 of "memory.c".
> "memory-leak.c", line 175.14: 1506-050 (I) Return type "void*" in
> redeclaration is not compatible with the previous return type "int".
> Fatal Error by charmc in directory
> /Users/j0l6571/namd/namd2.6b1/NAMD_2.6b1_Source/charm/mpi-ppc-darwin-gm-xlc/tmp
>
> Command xlc_r -qnocommon -qpic -I /opt/gm/include -I../bin/../include
> -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -DCMK_MEMORY_BUILD_LEAK -O3 -qstrict
> -Q -I/Users/j0l6571/bin/mpich-gm-underscore/include -c memory.c -o
> ../lib/libmemory-leak.o returned error code 1
> charmc exiting...
> ../bin/charmc -O -DCMK_OPTIMIZE=1 -nobs -o
> ../lib/libmemory-isomalloc.o -DCMK_MEMORY_BUILD_ISOMALLOC memory.c ||
> touch ../lib/libmemory-isomalloc.o
> "memory-gnu.c", line 535.9: 1506-236 (W) Macro name __builtin_expect
> has been redefined.
> "memory-isomalloc.c", line 33.14: 1506-343 (S) Redeclaration of
> meta_malloc differs from previous declaration on line 92 of "memory.c".
> "memory-isomalloc.c", line 33.14: 1506-050 (I) Return type "void*" in
> redeclaration is not compatible with the previous return type "int".
> Fatal Error by charmc in directory
> /Users/j0l6571/namd/namd2.6b1/NAMD_2.6b1_Source/charm/mpi-ppc-darwin-gm-xlc/tmp
>
> Command xlc_r -qnocommon -qpic -I /opt/gm/include -I../bin/../include
> -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -DCMK_MEMORY_BUILD_ISOMALLOC -O3
> -qstrict -Q -I/Users/j0l6571/bin/mpich-gm-underscore/include -c
> memory.c -o ../lib/libmemory-isomalloc.o returned error code 1
> charmc exiting...
>
>
> Then I went to ./mpi-ppc-darwin-gm-xlc/tests/charm++/simplearrayhello
> to make hello. It gives me the following ouput .
>
> ../../../bin/charmc hello.ci
> ../../../bin/charmc -c hello.C
> ../../../bin/charmc -language charm++ -o hello hello.o
> ld: warning table of contents of library: ../../../bin/../lib/libck.a
> not sorted slower link editing will result (use the ranlib(1) -s option)
> ld: warning table of contents of library:
> ../../../bin/../lib/libconv-util.a not sorted slower link editing will
> result (use the ranlib(1) -s option)
> ld: warning multiple definitions of symbol _scalable_zone_info
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _scalable_zone_info
> /usr/lib/libm.dylib(scalable_malloc.So) definition of _scalable_zone_info
> ld: warning multiple definitions of symbol _malloc_freezedry
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _malloc_freezedry
> /usr/lib/libm.dylib(scalable_malloc.So) definition of _malloc_freezedry
> ld: warning multiple definitions of symbol _szone_batch_free
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _szone_batch_free
> /usr/lib/libm.dylib(scalable_malloc.So) definition of _szone_batch_free
> ld: warning multiple definitions of symbol _szone_check_modulo
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _szone_check_modulo
> /usr/lib/libm.dylib(scalable_malloc.So) definition of _szone_check_modulo
> ld: warning multiple definitions of symbol _szone_batch_malloc
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _szone_batch_malloc
> /usr/lib/libm.dylib(scalable_malloc.So) definition of _szone_batch_malloc
> ld: warning multiple definitions of symbol _create_scalable_zone
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _create_scalable_zone
> /usr/lib/libm.dylib(scalable_malloc.So) definition of
> _create_scalable_zone
> ld: warning multiple definitions of symbol _szone_check_counter
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _szone_check_counter
> /usr/lib/libm.dylib(scalable_malloc.So) definition of
> _szone_check_counter
> ld: warning multiple definitions of symbol _scalable_zone_statistics
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _scalable_zone_statistics
> /usr/lib/libm.dylib(scalable_malloc.So) definition of
> _scalable_zone_statistics
> ld: warning multiple definitions of symbol _szone_check_start
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _szone_check_start
> /usr/lib/libm.dylib(scalable_malloc.So) definition of _szone_check_start
> ld: warning multiple definitions of symbol _malloc_jumpstart
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> definition of _malloc_jumpstart
> /usr/lib/libm.dylib(scalable_malloc.So) definition of _malloc_jumpstart
> ld: warning suggest use of -bind_at_load, as lazy binding may result
> in errors or different symbols being used
> symbol _malloc_freezedry used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library
> /usr/lib/libSystem.B.dylib(scalable_malloc.So)
> symbol _szone_check_counter used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library
> /usr/lib/libSystem.B.dylib(scalable_malloc.S
> o)
> symbol _szone_check_start used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library
> /usr/lib/libSystem.B.dylib(scalable_malloc.So)
> symbol _szone_check_modulo used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library
> /usr/lib/libSystem.B.dylib(scalable_malloc.So
> )
> symbol _create_scalable_zone used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library
> /usr/lib/libSystem.B.dylib(scalable_malloc.
> So)
> symbol _szone_batch_malloc used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library
> /usr/lib/libSystem.B.dylib(scalable_malloc.So
> )
> symbol _szone_batch_free used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library
> /usr/lib/libSystem.B.dylib(scalable_malloc.So)
> symbol _scalable_zone_statistics used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library /usr/lib/libSystem.B.dylib(scalable_mal
> loc.So)
> symbol _scalable_zone_info used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library
> /usr/lib/libSystem.B.dylib(scalable_malloc.So
> )
> symbol _malloc_jumpstart used from dynamic library
> /Users/j0l6571/bin/mpich-gm-underscore/lib/shared/libmpich.dylib(gmpi_malloc.o)
> not from earlier dynamic library
> /usr/lib/libSystem.B.dylib(scalable_malloc.So)
> ld: Undefined symbols:
> _CmiFreeListSendFn
> _meta_malloc
> Fatal Error by charmc in directory
> /Users/j0l6571/namd/namd2.6b1/NAMD_2.6b1_Source/charm/mpi-ppc-darwin-gm-xlc/tests/charm++/simplearrayhello
>
> Command xlc++_r -qstaticinline -qnocommon -qpic -qnofullpath -L
> /opt/gm/lib -L/Users/j0l6571/bin/mpich-gm-underscore/lib/shared
> -L/Users/j0l6571/bin/mpich-gm-underscore/lib/shared -o hello
> -L../../../bin/../l
> ib -I../../../bin/../include ../../../bin/../lib/libldb-rand.o hello.o
> moduleinit22834.o ../../../bin/../lib/libmemory-default.o
> ../../../bin/../lib/libthreads-default.o -lck -lconv-cplus-y
> -lconv-core -lconv-ut
> il -lm -Wl,-u,_gmpi_macosx_malloc_hack -lckqt -lmpich -L/opt/gm/lib
> -lgm -lpthread -lpmpich -lgm -ldl -lz returned error code 1
> charmc exiting...
> make: *** [hello] Error 1
>
>

Those warnings about symbols are fine.
The missing _CmiFreeListSendFn seems to be due to that you replaced the
conv-mach-gm.h and sh files from net-ppc-darwin.
undef'ed meta_malloc is a bug introduced by a former group member
yesterday and should be fixed now in the cvs of the development branch.
You can always download stable version charm-5.9 which has the fixes I
backported yesterday.

Gengbin

> Could you give me any hints?
> Appreciate it.
> Jason
>
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