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

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tawinan
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Joined: Thu Feb 28, 2013 11:19 pm

error at the end of compiling abinit 7.0.5 in OSX 10.8.2

Post by tawinan » Thu Feb 28, 2013 11:27 pm

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
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Alain_Jacques
Posts: 279
Joined: Sat Aug 15, 2009 9:34 pm
Location: Université catholique de Louvain - Belgium

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

Post by Alain_Jacques » Fri Mar 01, 2013 11:27 am

Hi Tawinan,

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

Kind regards,

Alain
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tawinan
Posts: 2
Joined: Thu Feb 28, 2013 11:19 pm

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

Post by tawinan » Fri Mar 01, 2013 4:43 pm

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
Attachments
Makefile.log
(114.21 KiB) Downloaded 370 times
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t-nissie
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Re: error at the end of compiling abinit 7.0.5 in OSX 10.8.2  [SOLVED]

Post by t-nissie » Thu Jun 13, 2013 10:50 am

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.
Takeshi Nishimatsu
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http://loto.sourceforge.net/feram/
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