On Mar 14, 2013, at 10:51 AM, javacfish <javacfish.yahoo.com.cn> wrote:
> Hi Jason and everyone,
>
> Thanks for your suggestion. But the problem seem still to happen again. When I enter the command:"./patch_amber.py --update"
> -----------------------------------------------------------------------------------------------------------------------------
> javacfish.linux-th8x:~/soft/amber12> ./patch_amber.py --update
> Determining patches to download for AmberTools12
> AmberTools12 is up to date. Nothing to download
>
> Determining patches to download for Amber12
> Amber12 is up to date. Nothing to download
> -----------------------------------------------------------------------------------------------------------------------------
>
> I make sure all update completely. However, I run ./configure gnu, and then knock the command:"make install", the err happens as below:
>
> ********************************************************************************************
> vrank3-transpose.c:(.text+0x1246): undefined reference to `__intel_ssse3_memcpy'
> /home/bai/soft/amber12/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x1261): more undefined references to `__intel_ssse3_memcpy' follow
> /home/bai/soft/amber12/lib/libfftw3.a(trig.o): In function `cexpl_sincos':
> trig.c:(.text+0x189): undefined reference to `__libm_sse2_sincos'
These errors suggest that you have not sourced the appropriate intel compiler environment.
Intel provides csh and bash scripts that you can source to properly load your environment so these symbols can be found by the linker.
If you still have a hard time figuring this out and there is no local Linux expert to help get this sorted out, then you can always try using the GNU compilers instead.
But since this is a compiler issue whose solution depends on your system setup, there is a limit to how much we can help remotely.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 14 2013 - 10:00:05 PDT
