Maybe it is useful to add that if I ignore the errors on configure
(those from my previous email), I get the following error upon "make"
(which is very similar though)
Best, Vlad
make[2]: Entering directory
'/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/AmberTools/src/nfe-umbrella-slice'
[NFE] CXX utils.cc
[NFE] CXX umbrella.cc
[NFE] CXX dimension.cc
[NFE] CXX main.cc
[NFE] CXX nfe-umbrella-slice
make[2]: Leaving directory
'/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/AmberTools/src/nfe-umbrella-slice'
(if [ "no" = "no" ]; then \
make python_serial ;\
fi;\
)
make[2]: Entering directory
'/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/AmberTools/src'
(cd parmed &&
PYTHONPATH=/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/lib/python2.7/site-packages
/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/bin/amber.python
setup.py install -f
--prefix=/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1 > build.log)
warning: no files found matching 'versioneer.py'
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
C/ObjC but not for C++
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
C/ObjC but not for C++
/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/compiler_compat/ld:
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to
initialize decompress status for section .debug_aranges
/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/compiler_compat/ld:
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to
initialize decompress status for section .debug_aranges
/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/compiler_compat/ld:
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to
initialize decompress status for section .debug_aranges
/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/compiler_compat/ld:
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to
initialize decompress status for section .debug_aranges
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: file not
recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: command 'g++' failed with exit status 1
make[2]: *** [Makefile:525: parmed] Error 1
make[2]: Leaving directory
'/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/AmberTools/src'
make[1]: *** [Makefile:56: serial] Error 2
make[1]: Leaving directory
'/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/AmberTools/src'
make: *** [Makefile:7: install] Error 2
On 5/27/19 1:42 PM, Vlad Cojocaru wrote:
> Dear all,
>
> I am trying to compile Amber Tools 19 on a computer with openSUSE
> Tumbleweed (x86_64). Both when using gcc 7.4.1 and gcc 8.3.1 I get
> errors like the one below (crti.o: file not recognized: file format not
> recognized). This one I attach below appeared on the first run of
> configure but the same error also happen upon make (after configure).
>
> I have previously compiled and used successfully Amber Tools 18 on the
> same machine (both compile gcc 8 and gcc 7)
>
> Thanks a lot for any idea how to solve this
>
> Best wishes
> Vlad
>
>
> In file included from
> /apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/include/python2.7/Python.h:8:0,
> from _posixsubprocess.c:16:
> /apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/include/python2.7/pyconfig.h:1223:0:
> warning: "_POSIX_C_SOURCE" redefined
> #define _POSIX_C_SOURCE 200112L
>
> In file included from /usr/include/sys/cdefs.h:23:0,
> from _posixsubprocess.c:12:
> /usr/include/features.h:266:0: note: this is the location of the
> previous definition
> # define _POSIX_C_SOURCE 200809L
>
> In file included from
> /apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/include/python2.7/Python.h:8:0,
> from _posixsubprocess.c:16:
> /apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/include/python2.7/pyconfig.h:1245:0:
> warning: "_XOPEN_SOURCE" redefined
> #define _XOPEN_SOURCE 600
>
> In file included from /usr/include/sys/cdefs.h:23:0,
> from _posixsubprocess.c:12:
> /usr/include/features.h:203:0: note: this is the location of the
> previous definition
> # define _XOPEN_SOURCE 700
>
> gcc -pthread -shared -B
> /apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/compiler_compat
> -L/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/lib
> -Wl,-rpath=/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/lib
> -Wl,--no-as-needed -Wl,--sysroot=/
> build/temp.linux-x86_64-2.7/_posixsubprocess.o
> -L/apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/lib
> -lpython2.7 -o build/lib.linux-x86_64-2.7/_posixsubprocess32.so
> /apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/compiler_compat/ld:
> /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to
> initialize decompress status for section .debug_aranges
> /apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/compiler_compat/ld:
> /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to
> initialize decompress status for section .debug_aranges
> /apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/compiler_compat/ld:
> /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to
> initialize decompress status for section .debug_aranges
> /apps/amber/18_tools-19_openmpi-4.0.1_gnu-7.4.1/miniconda/compiler_compat/ld:
> /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to
> initialize decompress status for section .debug_aranges
> /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: file not
> recognized: file format not recognized
> collect2: error: ld returned 1 exit status
> error: command 'gcc' failed with exit status 1
> ----------------------------------------
> ERROR: Failed building wheel for subprocess32
>
--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
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 Mon May 27 2019 - 05:30:02 PDT
