GROMACS version: 5.1.3
GROMACS modification: Yes/No
Here post your question
I am encountering these errors during my Gromacs 5.1.3 installation. I’m not sure what to do.
First error:
[ 3%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/lib/tng_io.c.o
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:47: note: length computed here
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c: In function ‘tng_file_headers_write’:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:11701:17: warning: ‘len’ may be used uninitialized [-Wmaybe-uninitialized]
11701 | tot_len += len;
| ^~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:11671:13: note: ‘len’ declared here
11671 | int64_t len, orig_len, tot_len = 0, data_start_pos, temp_pos = -1;
| ^~~
In function ‘tng_gen_data_block_add’,
inlined from ‘tng_data_block_add’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12801:12:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c: In function ‘tng_data_block_add’:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:47: note: length computed here
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~
In function ‘tng_gen_data_block_add’,
inlined from ‘tng_particle_data_block_add’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12826:12:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c: In function ‘tng_particle_data_block_add’:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:47: note: length computed here
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c: In function ‘tng_time_get_str’:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:15205:24: warning: ‘%02d’ directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=]
15205 | “%4d-%02d-%02d %02d:%02d:%02d”,
| ^~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:376:22: note: ‘snprintf’ output between 20 and 72 bytes into a destination of size 24
376 | #define TNG_SNPRINTF snprintf
| ^
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:15204:5: note: in expansion of macro ‘TNG_SNPRINTF’
15204 | TNG_SNPRINTF(time, TNG_MAX_DATE_STR_LEN,
| ^~~~~~~~~~~~
In function ‘tng_gen_data_block_add’,
inlined from ‘tng_data_block_add’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12801:12,
inlined from ‘tng_util_generic_write_interval_set’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:16177:20:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c: In function ‘tng_util_generic_write_interval_set’:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:47: note: length computed here
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~
In function ‘tng_gen_data_block_add’,
inlined from ‘tng_data_block_add’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12801:12,
inlined from ‘tng_util_generic_write_interval_double_set’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:16307:20:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c: In function ‘tng_util_generic_write_interval_double_set’:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:47: note: length computed here
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~
In function ‘tng_gen_data_block_add’,
inlined from ‘tng_data_block_add’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12801:12,
inlined from ‘tng_util_generic_write’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:16669:20:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c: In function ‘tng_util_generic_write’:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:47: note: length computed here
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~
In function ‘tng_gen_data_block_add’,
inlined from ‘tng_data_block_add’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12801:12,
inlined from ‘tng_util_generic_double_write’ at /cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:16907:20:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation]
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c: In function ‘tng_util_generic_double_write’:
/cygdrive/c/cygwin64/gromacs-5.1.3/src/external/tng_io/src/lib/tng_io.c:12613:47: note: length computed here
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~
[ 3%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/lib/md5.c.o
Then it compounded to several errors until it the compilation was terminated.
[ 50%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/copyrite.cpp.o
[ 50%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/disre.c.o
[ 51%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gmx_cpuid.c.o
[ 51%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gmx_detect_hardware.cpp.o
[ 51%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gmx_omp_nthreads.c.o
[ 51%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gmx_thread_affinity.c.o
/cygdrive/c/cygwin64/gromacs-5.1.3/src/gromacs/gmxlib/gmx_thread_affinity.c:48:12: fatal error: sys/syscall.h: No such file or directory
48 | # include <sys/syscall.h>
| ^~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/build.make:8413: src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gmx_thread_affinity.c.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:2611: src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [Makefile:166: all] Error 2
Can you assist me? I’m installing it in my windows laptop using Cygwin. Thank you.