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error at the end of compiling abinit 7.0.5 in OSX 10.8.2

https://forum.abinit.org/viewtopic.php?f=3&t=2022

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error at the end of compiling abinit 7.0.5 in OSX 10.8.2

Posted: Thu Feb 28, 2013 11:27 pm
by tawinan
Hi All,

I'm trying to compile abinit 7.0.5 in my mac which is 10.8.2. I'm able to get around the problem of compiling libxc, but after waiting for an hour I got the following error

Code: Select all

duplicate symbol ___m_profiling_MOD_mo_c1 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_l7 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_l6 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_l5 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_l4 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_l3 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_l2 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_l1 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_i7 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_i6 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_i5 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_i4 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_i3 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_i2 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_i1 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_sp7 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_sp6 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_sp5 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_sp4 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_sp3 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_sp2 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_sp1 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_dp7 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_dp6 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_dp5 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_dp4 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_dp3 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_dp2 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_mo_dp1 in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_memocc_internal in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_r_nan in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_d_nan in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_memocc_report in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_memocc_set_memory_limit in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
duplicate symbol ___m_profiling_MOD_memocc_set_state in:
    ../../src/11_memory_mpi/lib11_memory_mpi.a(m_profiling.o)
    /Users/tawinancheiwchanchamnangij/Desktop/abinit-7.0.5/fallbacks/exports/lib/libabinit.a(m_profiling.o)
ld: 35 duplicate symbols for architecture x86_64
collect2: error: ld returned 1 exit status
make[3]: *** [abinit] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2


I still have this exactly same problem when I follow the step in this topic viewtopic.php?f=2&t=1067 by mlazar (thank you)

Could you guys please suggest the way to fix this problem? Thank you.

Tawinan

Re: error at the end of compiling abinit 7.0.5 in OSX 10.8.2

Posted: Fri Mar 01, 2013 11:27 am
by Alain_Jacques
Hi Tawinan,

Could you please show your configuration options. Did you ask to enable bindings?

Kind regards,

Alain

Re: error at the end of compiling abinit 7.0.5 in OSX 10.8.2

Posted: Fri Mar 01, 2013 4:43 pm
by tawinan
Hi Alain,

Thank you very much for replying. According to my Makefile, I didn't enable the binding.
I've also attached the config.log and Makefile with this reply. I have exactly the same error with or w/o --enable-64bit-flags options.

Best,
Tawinan

config.log
(202.1 KiB) Downloaded 369 times

Re: error at the end of compiling abinit 7.0.5 in OSX 10.8.2  [SOLVED]

Posted: Thu Jun 13, 2013 10:50 am
by t-nissie
Hi,

This error happens because there are two similar files:
fallbacks/sources/bigdft-abi-1.0.4/libABINIT/src/18_memory/m_profiling.F90
src/11_memory_mpi/m_profiling.F90

configure without bigdft, i.e. --with-dft-flavor=atompaw+libxc+wannier90
can avoid this error.
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