Hi,
I have been keep trying to run the compiler makefile but fail to do so. Anybody can help me on this? I’m not sure where do i get wrong steps, but i just do as follow on the guid on this link haddock3/docs/CNS.md at main · haddocking/haddock3 · GitHub.
By the way i’m using WSL for this installation. Any help will be gratefully appreciated. Thank you
Error list is:
(base) xxxx:/mnt/c/wsl/cns_solve_1.3$ make install compiler=gfortran
Installation directory: /mnt/c/wsl/cns_solve_1.3/intel-x86_64bit-linux
copying files in instlib directory intel-x86_64bit-linux to intel-x86_64bit-linux
0read.me
Makefile.header.1.ifort
Makefile.header.2.gfortran
Makefile.header.3.ifort_mp
Makefile.header.4.pgf95
Makefile.header.5.ifort_mp_profile
Makefile.header.6.ifort_mp_tcheck
Makefile.header.7.gfortran_mp
arch_env
machine_c.c
machine_f.f
Using Makefile template for compiler: gfortran
Segmentation fault (core dumped)
linking source files to intel-x86_64bit-linux/source
Segmentation fault (core dumped)
removing old object files
linking machine_f.f to source directory
linking machine_c.c to source directory
linking generic fft file to source directory
making Makefile in source directory
testing Fortran and C compilers
compiling: gcc -O -DINTEGER=‘long int’ -DCNS_ARCH_TYPE_LINUX
C compiler passes test
compiling: gfortran -fdefault-integer-8 -w -fallow-argument-mismatch -O3 -funroll-loops -ffast-math -static
linking: gfortran -w -static-libgfortran
Fortran compiler passes test
making utility programs
make relink
make default
gfortran -o PSmapx -w -O PSmapx.f
gfortran -o PSmapy -w -O PSmapy.f
gfortran -o PSmapz -w -O PSmapz.f
gcc -o to_cns -O to_cns.c -lm
to_cns.c:65:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
65 | main(int argc, char argv[]) {
| ^~~~
to_cns.c: In function ‘read_header’:
to_cns.c:231:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-resul]
231 | fscanf(stream,“%d”,&nindex);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
to_cns.c:232:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-resul]
232 | fscanf(stream,“%d”,&ndata);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
to_cns.c:233:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
233 | fgets(line,MAXLINE,stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
to_cns.c:234:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
234 | fgets(line,MAXLINE,stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
to_cns.c:242:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-resul]
242 | fscanf(stream,“%d %d %d %d\n”,&nindex,&ndata,&nextra,&ninfo);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
to_cns.c:249:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
249 | fgets(info,MAXLINE,stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
to_cns.c:252:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-resul]
252 | fscanf(stream,“%s”,index);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
to_cns.c:256:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-resul]
256 | fscanf(stream,“%s”,data);
| ^~~~~~~~~~~~~~~~~~~~~~~~
to_cns.c:265:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-resul]
265 | fscanf(stream,“%s”,extra);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
to_cns.c: In function ‘read_reflections’:
to_cns.c:282:16: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
282 | if ( ! fscanf(stream,“%d %d %d %lf %lf %lf %lf %lf %lf”,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
283 | &h, &k, &l,
| ~~~~~~~~~~~
284 | &mean_i, &mean_s,
| ~~~~~~~~~~~~~~~~~
285 | &plus_i, &plus_s,
| ~~~~~~~~~~~~~~~~~
286 | &minus_i, &minus_s) == 9 ) {
| ~~~~~~~~~~~~~~~~~~~
to_cns.c:335:16: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
335 | if ( ! fscanf(stream,“%d %d %d %lf %lf”,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
336 | &h, &k, &l,
| ~~~~~~~~~~~
337 | &mean_i, &mean_s) == 5 ) {
| ~~~~~~~~~~~~~~~~~
to_cns.c: In function ‘get_hkl_refs’:
to_cns.c:431:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
431 | fgets(line,MAXLINE,stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o cluster_struc -O cluster_struc.cpp -lm
cluster_struc.cpp: In function ‘int main(int, char*)’:
cluster_struc.cpp:122:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
122 | fgets(buf, 1000, f);
| ~^
lex refloat.l
gcc -O -o refloat lex.yy.c -lm -lfl
make clean
flags:
fortran → [gfortran] -fdefault-integer-8 -w -fallow-argument-mismatch -O3 -funroll-loops -ffast-math -static
c → [gcc] -O -DINTEGER=‘long int’ -DCNS_ARCH_TYPE_LINUX
link → [gfortran] -w -static-libgfortran
compiling: Segmentation
gfortran: warning: Segmentation: linker input file unused because linking not done
gfortran: error: Segmentation: linker input file not found: No such file or directory
make[3]: *** [Makefile:64: Segmentation] Error 1
compiling: fault
gfortran: warning: fault: linker input file unused because linking not done
gfortran: error: fault: linker input file not found: No such file or directory
make[3]: *** [Makefile:64: fault] Error 1
/bin/sh: 2: Syntax error: “(” unexpected
make[3]: *** [Makefile:64: (core] Error 2
/bin/sh: 2: Syntax error: “)” unexpected
make[3]: *** [Makefile:64: dumped)] Error 2
compiling: dmemory.c
compiling: machine_c.c
make[3]: Target ‘../bin/cns_solve’ not remade because of errors.
make[2]: *** [Makefile:59: cns_solve] Error 2
make[1]: *** [Makefile:64: cns_solve] Error 2
