Dear Dave, Dear all,
Editing the Makefile in FEW worked for that particular program but
unfortunately, there are other pieces of code with amber tools that are
trying to use gcc when intel is chosen as compiler. Now, this is the
error I get from parmed code ....
This looks like it has something to do with a conflict between the
default python installed and the one built together with Amber .... But
this is just guessing ... I will try to run the "amber.sh" script before
installation and see if that fixes the issue ...
Best
Vlad
------------------Error
--------------------------------------------------------------------
creating build/temp.linux-x86_64-2.7/src
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong
--param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong
--param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fwrapv -fPIC
-I/home/mpg05/vcojoca/apps/gwdu102/amber/16_tools-16_intel/AmberTools/src/parmed/src
-I/usr/include/python2.7 -c src/_rdparm.cpp -o
build/temp.linux-x86_64-2.7/src/_rdparm.o
In file included from /usr/include/python2.7/Python.h:19:0,
from src/_rdparm.cpp:4:
.........................................................................
In file included from /usr/include/python2.7/pyport.h:325:0,
from /usr/include/python2.7/Python.h:58,
from src/_rdparm.cpp:4:
/cm/shared/apps/intel/compilers_and_libraries/2016.3.210/compiler/include/math.h:29:3:
error: #error "This Intel <math.h> is for use with only the Intel
compilers!"
# error "This Intel <math.h> is for use with only the Intel compilers!"
^
In file included from /usr/include/inttypes.h:27:0,
from /usr/include/python2.7/pyport.h:9,
from /usr/include/python2.7/Python.h:58,
from src/_rdparm.cpp:4:
/cm/shared/apps/intel/compilers_and_libraries/2016.3.210/compiler/include/stdint.h:292:9:
error: ‘uint__INTPTR_WIDTH___t’ does not name a type
typedef __uintn_t(__INTPTR_WIDTH__) uintptr_t;
^
In file included from /usr/include/python2.7/Python.h:58:0,
from src/_rdparm.cpp:4:
/usr/include/python2.7/pyport.h:159:9: error: ‘uintptr_t’ does not name
a type
typedef uintptr_t Py_uintptr_t;
^
error: command 'gcc' failed with exit status 1
make[2]: *** [parmed] Error 1
make[2]: Leaving directory
`/home/mpg05/vcojoca/apps/gwdu102/amber/16_tools-16_intel/AmberTools/src'
make[1]: *** [serial] Error 2
make[1]: Leaving directory
`/home/mpg05/vcojoca/apps/gwdu102/amber/16_tools-16_intel/AmberTools/src'
make: *** [install] Error 2
On 10/17/2016 01:56 PM, Vlad Cojocaru wrote:
> Dear all,
>
> I am trying to compile Amber16 on a cluster with Intel compiler
> (16.0.3). However, I get the error below. The error tells that even if I
> specify the -intel option to configure, there is some stuff that
> automatically compiles with gcc. And then I get the incompatibility
> between the math.h file from intel and gnu.
>
> Is there anything that can be done to fix this problem ?
>
> Thanks
>
> Best wishes
> Vlad
>
> ----error message-----
>
> ifort -fPIC -I/usr/users/vcojoca/apps/gwdu102/amber/16_tools-16/include
> -I/usr/users/vcojoca/apps/gwdu102/amber/16_tools-16/include
> -I/cm/shared/apps/intel/compilers_and_libraries/2016.3.210/mkl/include
> -c -o make_crd_hg.o make_crd_hg.F
> ifort -DMKL -DBINTRAJ -DEMIL -fPIC
> -I/usr/users/vcojoca/apps/gwdu102/amber/16_tools-16/include
> -I/usr/users/vcojoca/apps/gwdu102/amber/16_tools-16/include
> -I/cm/shared/apps/intel/compilers_and_libraries/2016.3.210/mkl/include
> -o /usr/users/vcojoca/apps/gwdu102/amber/16_tools-16/bin/make_crd_hg
> make_crd_hg.o \
> ../lib/amopen.o ../lib/mexit.o -shared-intel
> /usr/users/vcojoca/apps/gwdu102/amber/16_tools-16/bin/nab -o
> /usr/users/vcojoca/apps/gwdu102/amber/16_tools-16/bin/mm_pbsa_nabnmode
> mm_pbsa_nabnmode.nab
> cp mm_pbsa.pl mm_pbsa_statistics.pl
> /usr/users/vcojoca/apps/gwdu102/amber/16_tools-16/bin
> make[2]: Leaving directory
> `/home/mpg05/vcojoca/apps/gwdu102/amber/16_tools-16/AmberTools/src/mm_pbsa'
> (cd FEW && make install)
> make[2]: Entering directory
> `/home/mpg05/vcojoca/apps/gwdu102/amber/16_tools-16/AmberTools/src/FEW'
> gcc miscellaneous/draw_membrane2.c -lm -o miscellaneous/draw_membrane2
> In file included from miscellaneous/draw_membrane2.c:58:0:
> /cm/shared/apps/intel/compilers_and_libraries/2016.3.210/compiler/include/math.h:29:3:
> error: #error "This Intel <math.h> is for use with only the Intel
> compilers!"
> # error "This Intel <math.h> is for use with only the Intel compilers!"
> ^
> make[2]: *** [install] Error 1
> make[2]: Leaving directory
> `/home/mpg05/vcojoca/apps/gwdu102/amber/16_tools-16/AmberTools/src/FEW'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory
> `/home/mpg05/vcojoca/apps/gwdu102/amber/16_tools-16/AmberTools/src'
> make: *** [install] Error 2
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Tue Oct 18 2016 - 06:00:03 PDT
