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 - 05:00:02 PDT
