This issue is not solved by executing amber.sh prior to installation. If
needed, I can attach the log file of the make command through private
email (too large for the list).
For the record, I should add that amber compiles fine with gcc 4.8.5 on
this cluster ... So, I'll stick to that for now, I guess there shouldn't
be much difference in performance ....
Vlad
On 10/18/2016 02:31 PM, Vlad Cojocaru wrote:
> 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 - 08:00:03 PDT
