Thanks for the advices!
Looks like the trick is to add "-shared-intel" to the LDFLAGS in
config.h ...
I do not have the earlier versions from intel so I don't know if this a
specific problem for the current version ..
I did however compile AMBER 10 sometime ago with intel 11.x.x and this
flag was not required ...
Vlad
On 12/01/2010 03:29 PM, Jason Swails wrote:
> In addition to what Dan said, did you source the intel environment scripts
> (ifortvars.sh, iccvars.sh, they should be in the same directory as ifort and
> icc)? They set up LD_LIBRARY_PATH and PATH for you. However, I can verify
> that the intel compilers version 11.1.069 works for installing Amber on my
> machine, so if you can roll back, I would suggest trying that to see if it
> works.
>
> Good luck!
> Jason
>
> On Wed, Dec 1, 2010 at 8:49 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>
>> Hi,
>>
>> Do you have any previous versions of the intel compiler, and if so
>> does compilation complete with them?
>>
>> Also, could you paste the last 20 or so lines leading up to the error?
>> A brief web search suggests this may be related to the '-lsvml' flag
>> during the link step (however the post refers to version 11.1 so no
>> guarantees, http://software.intel.com/en-us/forums/showthread.php?t=77211
>> ).
>> Intel is notorious for messing with the linking step (see their MKL
>> stuff for more linking headaches) so I'm not surprised something may
>> have broken in the new version of the compilers.
>>
>> Anyway, you could try manually editing your config.h file to remove
>> the '-lsvml' flag from the FLIBSF variable and see if compilation is
>> able to proceed.
>>
>> -Dan
>>
>> On Wed, Dec 1, 2010 at 6:34 AM, Vlad Cojocaru
>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>
>>> Dear Amber community,
>>>
>>> I am compiling AMBER 11 with the Intel compiler 12.0.0 (which I just
>>> purchased)
>>> The linking during the *SERIAL* compilation of Amber Tools 1.4 (patched
>>> with all bugfixes as of today) fails with error (see below, no other
>>> error in make.log):
>>>
>>> Has anybody experienced this with this version of the Intel compiler?
>>> I would appreciate any ideas on how to get rid of this problem
>>>
>>> Best
>>> Vlad
>>>
>>>
>>> Details:
>>> -------
>>> Architecture
>>> Linux name 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010
>>> x86_64 x86_64 x86_64 GNU/Linux
>>> CPU:
>>> 2xAMD 6-core opterons per node
>>> OS:
>>> CentOS 5.5 (RHL 5.5)
>>> Compiler
>>> Intel 2011-0-084 (version 12)
>>> Config.h file attached
>>>
>>>
>>> make error:
>>> ---------------------------
>>> ld: pbsa: hidden symbol `__intel_cpu_indicator_init' in
>>>
>>>
>> /usr/global/intel/composerxe-2011.0.084/compiler/lib/intel64/libirc.a(cpu_disp.o)
>>
>>> is referenced by DSO
>>> ld: final link failed: Nonrepresentable section on output
>>> make[1]: *** [pbsa] Error 1
>>> make[1]: Leaving directory
>>>
>>>
>> `/usr/global/amber/intel-2011.0.084-openmpi-1.5/amber11/AmberTools/src/pbsa'
>>
>>> make: *** [serial] Error 2
>>> --------------------------------------
>>>
>>>
>>>
>>> --
>>> Dr. Vlad Cojocaru
>>> Max Planck Institute for Molecular Biomedicine
>>> Department of Cellular and Developmental Biology
>>> Roentgenstrasse 20
>>> 48149 Muenster, Germany
>>> tel: +49-251-70365-324
>>> fax: +49-251-70365-399
>>> email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Wed Dec 01 2010 - 08:00:03 PST
