# Error when trying to install CNS make install compiler=gfortran **URL:** \ **Category:** HADDOCK\ **Tags:** haddock\ **Created:** [July 14, 2025, 6:38am UTC](https://ask.bioexcel.eu/t/error-when-trying-to-install-cns-make-install-compiler-gfortran/5806 "2025-07-14T06:38:04Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![shinyi](https://avatars.discourse-cdn.com/v4/letter/s/6bbea6/32.png) [@shinyi](https://ask.bioexcel.eu/u/shinyi)\ **Post date:** [July 14, 2025, 6:38am UTC](https://ask.bioexcel.eu/t/error-when-trying-to-install-cns-make-install-compiler-gfortran/5806/1 "2025-07-14T06:38:04Z")
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](https://github.com/haddocking/haddock3/blob/main/docs/CNS.md). 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](http://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 ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 14, 2025, 1:34pm UTC](https://ask.bioexcel.eu/t/error-when-trying-to-install-cns-make-install-compiler-gfortran/5806/2 "2025-07-14T13:34:36Z")
Did you try to match the Makefile’s header to the one under section 3 (Makefile) of the online CNS instructions? Also on WSL a `pip install` (or `pip install .`) might work directly, installing the proper CNS executable. Check: [https://www.bonvinlab.org/haddock3-user-manual/install.html](https://www.bonvinlab.org/haddock3-user-manual/install.html) ---
**Author:** ![shinyi](https://avatars.discourse-cdn.com/v4/letter/s/6bbea6/32.png) [@shinyi](https://ask.bioexcel.eu/u/shinyi)\ **Post date:** [July 15, 2025, 12:27pm UTC](https://ask.bioexcel.eu/t/error-when-trying-to-install-cns-make-install-compiler-gfortran/5806/3 "2025-07-15T12:27:50Z")
Hi Prof, Thank you so much for the reply. I retry the full steps from the link i still get the same error when running until step ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/5/575a62615f98217a275b7fbd994901f064c73e1a.png) I also tried just build a new environment with just pip install . and run the haddock3 config.toml this is my toml file looks like: # === General parameters === run\_dir = “run1-docking” ncores = 4 molecules = [ “data/xxx.pdb”, “data/xxx.pdb” ] [topoaa] [rigidbody] [seletop] select = 10 [clustfcc] strictness = 0.75 [clustrmsd] The error i got from running haddock3 config.toml is below Traceback (most recent call last): File “/home/shinyi/haddock3/.haddock3-env/lib/python3.12/site-packages/haddock/libs/libutil.py”, line 378, in log\_error\_and\_exit yield File “/home/shinyi/haddock3/.haddock3-env/lib/python3.12/site-packages/haddock/clis/cli.py”, line 193, in main workflow.run() File “/home/shinyi/haddock3/.haddock3-env/lib/python3.12/site-packages/haddock/libs/libworkflow.py”, line 43, in run step.execute() File “/home/shinyi/haddock3/.haddock3-env/lib/python3.12/site-packages/haddock/libs/libworkflow.py”, line 173, in execute self.module.run() # type: ignore ^^^^^^^^^^^^^^^^^ File “/home/shinyi/haddock3/.haddock3-env/lib/python3.12/site-packages/haddock/modules/base\_cns\_module.py”, line 61, in run self.\_run() File “/home/shinyi/haddock3/.haddock3-env/lib/python3.12/site-packages/haddock/modules/sampling/rigidbody/ **init**.py”, line 250, in \_run self.export\_io\_models(faulty\_tolerance=self.params[“tolerance”]) File “/home/shinyi/haddock3/.haddock3-env/lib/python3.12/site-packages/haddock/modules/ **init**.py”, line 309, in export\_io\_models self.finish\_with\_error(\_msg) File “/home/shinyi/haddock3/.haddock3-env/lib/python3.12/site-packages/haddock/modules/ **init**.py”, line 317, in finish\_with\_error raise RuntimeError(reason) RuntimeError: 100.00% of output was not generated for this module and tolerance was set to 5.00%. Just some extra information the both pdb file i am able to run it on the website Haddock server, so the pdb file should have no issues. Really need some guidance on this. And again thank you so much for the help. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 15, 2025, 12:48pm UTC](https://ask.bioexcel.eu/t/error-when-trying-to-install-cns-make-install-compiler-gfortran/5806/4 "2025-07-15T12:48:53Z")
Try to go into the `unknown…/source` directory in your CNS installation directory (or whatever directory was created when giving the make install command) Edit the Makefile in that directory to match the header described in the CNS installation instructions. Then in the same directory type: `make cns_solve` And see if it compiles… If successful there should be a cns… .exe file created. If present call it from the command line to see if you get the CNS prompt. ---
**Author:** ![shinyi](https://avatars.discourse-cdn.com/v4/letter/s/6bbea6/32.png) [@shinyi](https://ask.bioexcel.eu/u/shinyi)\ **Post date:** [August 23, 2025, 6:40am UTC](https://ask.bioexcel.eu/t/error-when-trying-to-install-cns-make-install-compiler-gfortran/5806/5 "2025-08-23T06:40:37Z")
Hi Prof, Hope it is finding you well, I’m sorry that I’m being busy lately. I retry again with the changes on the makefile header in the source file just like this. ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/8/8102ed14e0cfe9577ddd16eb190042d079229b81.png) But i still fail in running make cns\_solve The error logs is below: make[1]: Entering directory ‘/mnt/c/WSL/cns\_solve\_1.3/intel-x86\_64bit-linux/source’ flags: fortran → [gfortran] -fdefault-integer-8 -w -fallow-argument-mismatch -O3 -funroll-loops -ffast-math -march=native -mtune=native c → [gcc] -O -DINTEGER=‘long int’ -DCNS\_ARCH\_TYPE\_ link → [gfortran] -w -static-libgfortran make[1]: Leaving directory ‘/mnt/c/WSL/cns\_solve\_1.3/intel-x86\_64bit-linux/source’ make[1]: Entering directory ‘/mnt/c/WSL/cns\_solve\_1.3/intel-x86\_64bit-linux/source’ 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[1]: \*\*\* [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[1]: \*\*\* [Makefile:64: fault] Error 1 /bin/sh: 2: Syntax error: “(” unexpected make[1]: \*\*\* [Makefile:64: (core] Error 2 /bin/sh: 2: Syntax error: “)” unexpected make[1]: \*\*\* [Makefile:64: dumped)] Error 2 make[1]: Target ‘../bin/cns\_solve’ not remade because of errors. make[1]: Leaving directory ‘/mnt/c/WSL/cns\_solve\_1.3/intel-x86\_64bit-linux/source’ make: \*\*\* [Makefile:59: cns\_solve] Error 2 Can you help me on this? And thank you so much for spending your time to help me solve this. Hope to get your help soon. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [August 23, 2025, 8:05am UTC](https://ask.bioexcel.eu/t/error-when-trying-to-install-cns-make-install-compiler-gfortran/5806/6 "2025-08-23T08:05:05Z")
It looks like you are compiling it under a Window Linux subsystem, correct? Did you simply try a `pip install` - this would install a CNS executable. Check the installation and development instructions in the haddock3 directory