[gmx-users] compilation terminated with error

Alex alexanderwien2k at gmail.com
Wed Sep 5 20:08:18 CEST 2018


Dear all,
The compilation of the Gromacs.2018.2 on a cluster terminated with error in
below step, would you please let me know how I can overcome the issue? I
use gcc/7.3.0.


[  0%] Building C object
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o

cd /p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build/src/gromacs &&
/opt/cray/pe/craype/2.5.13/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -isystem
/p/home/alex/.local/gromacs/2018.2/gromac
s-2018.2/src/external/lmfit
-I/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build/src -isystem
/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/src/external/thread_mpi/include
-I/p/hom
e/alex/.local/gromacs/2018.2/gromacs-2018.2/src -isystem /usr/include
-isystem /opt/cray/pe/fftw/3.3.4.11/broadwell/include
-I/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/src/external/
tng_io/external/zlib  -msse2   -dynamic  -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast   -fPIC   -o
CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o   -c
/p/h
ome/alex/.local/gromacs/2018.2/gromacs-2018.2/src/external/tng_io/external/zlib/crc32.c

make[2]: Leaving directory
'/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build'
make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make
src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[2]: Entering directory
'/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build'
make[2]: Entering directory
'/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build'
make[2]: Entering directory
'/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build'
In file included from
/opt/gcc/7.3.0/snos/include/g++/ext/string_conversions.h:41:0,
                from
/opt/gcc/7.3.0/snos/include/g++/bits/basic_string.h:6349,
                from /opt/gcc/7.3.0/snos/include/g++/string:52,
                from
/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/src/programs/view/view.cpp:45:

/opt/gcc/7.3.0/snos/include/g++/cstdlib:75:15: fatal error: stdlib.h: No
such file or directory
#include_next <stdlib.h>
               ^~~~~~~~~~
compilation terminated.

Thank you.
Regards,
Alex


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