Hi Shan-ho,
First, you should add the "-lpthread" option for AIX.
Second, try to remove the "-static-libgcc" option see if this
helps.
Sincerely,
Wei
On Jan 9, 2009, at 10:27 AM, Shan-ho Tsai wrote:
>
> Hello all,
> I am trying to build AmberTools 1.2 on an IBM power4+
> node running AIX 5.2, using gcc/g++ 3.3.2 and gnu make. I
> am having trouble getting sleap to compile (gcc/g++ 4.1.2
> gave the same error). The error message is
>
> g++ -static-libgcc -o sleap strmain.o strbuff.o plugins.o ../
> freelib/readline/libreadline.a -lm ../plugins/libplugins.a ../
> mortsrc/libmort.a
> ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_lock
> ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_unlock
> ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_init
> ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_destroy
> ld: 0711-317 ERROR: Undefined symbol: .rt_errormsg_s(int, char*,
> char*)
> ld: 0711-317 ERROR: Undefined symbol: .imatrix(int, int, int, int)
> ld: 0711-317 ERROR: Undefined symbol: .matrix(int, int, int, int)
>
> There was no error reported when compiling the programs
> that make libreadline.a, libplugins.a and libmort.a.
> Also, strmain.cpp, strbuff.cpp and plugins.cpp compiled fine.
>
> I see that rt_errormsg_s is defined in traceback.c
> in src/gleap/mortsrc/nablib and imatrix and matrix are
> defined in memutil.c in the same directory. These codes
> compiled fine (no error messages), so I am not sure why
> I am getting these undefined symbol errors.
>
> Using nm on libmort.a I get
>
> nm libmort.a | grep rt_errormsg_s
>
> .rt_errormsg_s U -
> .rt_errormsg_s U -
> .rt_errormsg_s T 112
> rt_errormsg_s D 460
> rt_errormsg_s d 460 12
> ._Z13rt_errormsg_siPcS_ U -
>
> nm libmort.a | grep matrix
>
> .....
> .imatrix T 864
> .matrix T 544
> imatrix D 1888
> imatrix d 1888 12
> matrix D 1876
> matrix d 1876 12
> .matrix U -
>
> I can get rid of the pthread undefined symbols by adding
> -lpthread in the sleap compilation line, but I am not sure
> if I am supposed to add this option. Earlier I had built
> AmberTools 1.2 on a Linux cluster (RHEL4) using gcc 3.4.6
> and all went well (I didn't have to add -lpthread and I
> didn't have any of the undefined symbol errors above).
>
> Should I add the -lpthread option?
>
> Any ideas why I am getting the other undefined symbols
> and how to get this problem resolved?
>
> Thank you very much for any help! I really appreciate it!
> Best regards,
> Shan-Ho
>
> -----------------------------------------------------------
> Shan-Ho Tsai
> University of Georgia, Athens, GA (USA)
>
>
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Received on Sun Jan 11 2009 - 01:11:58 PST
