Intel compile seems to work for me now. Thanks.
-Dan
On Thu, Mar 26, 2015 at 1:09 PM, Hai Nguyen <nmhai24021984.gmail.com> wrote:
> Hi,
>
> Jason is right that I missed pushing cythonized_shared_methods.cpp
> file (from _shared_methods.pyx) to Amber master. I always use cython
> so have never met this problem (so now I should start create new env
> with no cython to test and remove *.cpp files from .gitignore). Can
> you guys try again? thanks.
>
> Hai
>
>
> On Thu, Mar 26, 2015 at 2:16 PM, Jason Swails <jason.swails.gmail.com> wrote:
>>
>>
>> On Thu, Mar 26, 2015 at 2:13 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> I see the same problem/behavior with intel compilers:
>>>
>>> building 'pytraj._shared_methods' extension
>>> gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
>>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>>> --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
>>> -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
>>> -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC
>>>
>>> -I/uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-intel/AmberTools/src/cpptraj//src/
>>>
>>> -I/uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-intel/AmberTools/src/pytraj/pytraj/
>>> -I/usr/include/python2.6 -c
>>>
>>> /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-intel/AmberTools/src/pytraj/pytraj/_shared_methods.cpp
>>> -o
>>> build/temp.linux-x86_64-2.6/uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-intel/AmberTools/src/pytraj/pytraj/_shared_methods.o
>>> -O0 -ggdb
>>> gcc:
>>> /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-intel/AmberTools/src/pytraj/pytraj/_shared_methods.cpp:
>>> No such file or directory
>>> gcc: no input files
>>>
>>> Again, gcc being used instead of icc (also seems awkward that it's
>>> even calling gcc for a .cpp file). Haven't been able to pin down
>>> what's happening yet.
>>
>>
>> This is a Python thing. Not much you can do about it (nor is there much you
>> *should* do about it). Basically, Python calls the compilers that was used
>> to build Python itself when building extensions.
>>
>> But I think there might be an accidental omission of a Cythonized C++ file
>> here...
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 26 2015 - 13:30:02 PDT
