Hi David,
Who did you get this version of AMBER from? - There are separate branches
for Xeon Phi development so I would be surprised if you have the 'correct'
development version. Can I suggest trying the original AMBER 14 release
version with the various update patches applied. There will be an
additional update for Xeon Phi coming in about a month but that is not
complete yet so a development version of that will not work right now.
Also note that this error is coming from the linker and has nothing to do
with AMBER - looks like a problem with GNU binutils to me. I would suggest
updating your system fully (yum update) and then also making sure you have
the very latest version of the Intel Composer Suite.
All the best
Ross
On 10/13/14, 2:10 AM, "Baker D.J." <D.J.Baker.soton.ac.uk> wrote:
>Hello,
>
>I've been a development version of Amber 14, amber14_071014.tar.gz, so
>that I can do some performance experiments on our PHI cards. I have no
>problems building this version of Amber for our x86_64 nodes, however the
>PHI "make install" fails with what appears to be a bug. This is what I
>see:
>
>./configure -mic_native -noX11 intel
>make install
>
>......
>x86_64-k1om-linux-ld:
>/scratch/djb1/phi/amber14_071014/lib/libnetcdf.a(libdispatch_la-dcopy.o)(.
>text+0xe9f): unresolvable R_X86_64_PLT32 relocation against symbol
>`free..GLIBC_2.14'
>x86_64-k1om-linux-ld:
>/scratch/djb1/phi/amber14_071014/lib/libnetcdf.a(libdispatch_la-derror.o)(
>.text+0x16): unresolvable R_X86_64_PLT32 relocation against symbol
>`strerror..GLIBC_2.14'
>x86_64-k1om-linux-ld: BFD (GNU Binutils) 2.22.52.20120302 internal error,
>aborting at
>/sandbox/build/tmp/tmp/work/x86_64-nativesdk-mpsssdk-linux/binutils-cross-
>canadian-k1om-2.22+mpss3.4-1/binutils-2.22+mpss3.4/bfd/elf64-x86-64.c
>line 3382 in elf_x86_64_relocate_section
>
>x86_64-k1om-linux-ld: Please report this bug.
>
>make[3]: *** [/scratch/djb1/phi/amber14_071014/bin/pmemd.mic_native]
>Error 1
>make[3]: Leaving directory
>`/scratch/djb1/phi/amber14_071014/src/pmemd/src'
>make[2]: *** [mic] Error 2
>make[2]: Leaving directory `/scratch/djb1/phi/amber14_071014/src/pmemd'
>make[1]: *** [mic] Error 2
>make[1]: Leaving directory `/scratch/djb1/phi/amber14_071014/src'
>make: *** [install] Error 2
>
>I'm working on a RHELS 6.4 cluster and using a recent version, v15, of
>the Intel compilers and MKL v11.0_4. Does anyone please have any ideas
>what might be wrong here? I understand, of course, that this is a
>development version of Amber 14 and so it may not come with the latest
>bug fixes.
>
>Best regards - David.
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Received on Mon Oct 13 2014 - 12:00:02 PDT
