CNS install Error

[abiotik]

I got this error after "make install" I have followed all the install steps described above in the instruction. make install Installation directory: /home/nikola/Desktop/tik/haddock3/cns_solve_1.3//intel-x86_64bit-linux copying files in instlib directory intel-x86_64bit-linux to intel-x86_64bit-linux 0read.me arch_env machine_c.c machine_f.f 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 Using Makefile template for compiler: gfortran removing old source files linking source files to intel-x86_64bit-linux/source ln: failed to create symbolic link './cns_solve_env.sh': File exists 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 /bin/sh: 1: ../../bin/objects: Permission denied /bin/sh: 12: ../../bin/depend: Permission denied make[2]: [Makefile.proto:67: makefiles] Error 126 make[1]: [Makefile:131: makefiles] Error 2 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 -O3 -funroll-loops -ffast-math linking: gfortran -w 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[]) { | ^~~~ g++ -o cluster_struc -O cluster_struc.cpp -lm lex refloat.l gcc -O -o refloat lex.yy.c -lm -lfl make clean

flags: fortran -> [gfortran] -fdefault-integer-8 -w -O3 -funroll-loops -ffast-math c -> [gcc] -O -DINTEGER='long int' -DCNS_ARCH_TYPE_LINUX link -> [gfortran] -w

compiling: dmemory.c

compiling: machine_c.c

linking: cns_solve

/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/Scrt1.o: in function _start': (.text+0x17): undefined reference tomain' collect2: error: ld returned 1 exit status problems with new executable - old version retained (base) nikola@rack2:~/Desktop/tik/haddock3/cns_solve_1.3$ ^C (base) nikola@rack2:~/Desktop/tik/haddock3/cns_solve_1.3$ ^C (base) nikola@rack2:~/Desktop/tik/haddock3/cns_solve_1.3$ make install compilet=gfortran Installation directory: /home/nikola/Desktop/tik/haddock3/cns_solve_1.3//intel-x86_64bit-linux copying files in instlib directory intel-x86_64bit-linux to intel-x86_64bit-linux 0read.me arch_env machine_c.c machine_f.f 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 Using Makefile template for compiler: gfortran removing old source files linking source files to intel-x86_64bit-linux/source ln: failed to create symbolic link './cns_solve_env.sh': File exists 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 /bin/sh: 1: ../../bin/objects: Permission denied /bin/sh: 12: ../../bin/depend: Permission denied make[2]: [Makefile.proto:67: makefiles] Error 126 make[1]: [Makefile:131: makefiles] Error 2 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 -O3 -funroll-loops -ffast-math linking: gfortran -w 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[]) { | ^~~~ g++ -o cluster_struc -O cluster_struc.cpp -lm lex refloat.l gcc -O -o refloat lex.yy.c -lm -lfl make clean

flags: fortran -> [gfortran] -fdefault-integer-8 -w -O3 -funroll-loops -ffast-math c -> [gcc] -O -DINTEGER='long int' -DCNS_ARCH_TYPE_LINUX link -> [gfortran] -w

compiling: dmemory.c

compiling: machine_c.c

linking: cns_solve

/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/Scrt1.o: in function _start': (.text+0x17): undefined reference tomain' collect2: error: ld returned 1 exit status problems with new executable - old version retained

[amjjbonvin]

Which instructions are you following exactly? And on which system are you installing it?

Check: https://www.bonvinlab.org/haddock3/CNS.html

And make sure to edit the Makefile to have the proper options as described in the link above

[abiotik]

@amjjbonvin I am using debial linux I have modified the path variable on cns_solve_env file and changed it to .cns_colve_env_sh and got this error while doing make install make install CNS_SOLVE=/home/nikola/Desktop/tik/haddock3/cns_solve_1.3/: Command not found. Installation directory: /home/nikola/Desktop/tik/haddock3/cns_solve_1.3//intel-x86_64bit-linux copying files in instlib directory intel-x86_64bit-linux to intel-x86_64bit-linux 0read.me arch_env machine_c.c machine_f.f 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 Using Makefile template for compiler: gfortran removing old source files linking source files to intel-x86_64bit-linux/source ln: failed to create symbolic link './cns_solve_env.sh': File exists 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 /bin/sh: 1: ../../bin/objects: Permission denied /bin/sh: 12: ../../bin/depend: Permission denied make[2]: [Makefile.proto:67: makefiles] Error 126 make[1]: [Makefile:131: makefiles] Error 2 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 -O3 -funroll-loops -ffast-math linking: gfortran -w 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[]) { | ^~~~ g++ -o cluster_struc -O cluster_struc.cpp -lm lex refloat.l gcc -O -o refloat lex.yy.c -lm -lfl make clean

flags: fortran -> [gfortran] -fdefault-integer-8 -w -O3 -funroll-loops -ffast-math c -> [gcc] -O -DINTEGER='long int' -DCNS_ARCH_TYPE_LINUX link -> [gfortran] -w

compiling: dmemory.c

compiling: machine_c.c

linking: cns_solve

/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/Scrt1.o: in function _start': (.text+0x17): undefined reference tomain' collect2: error: ld returned 1 exit status problems with new executable - old version retained

[abiotik]

@amjjbonvin
Maybe after seting path variable I should delete all the "setenv" as I am using bash?

[amjjbonvin]

What about the questions I asked:

Which instructions are you following?

Check: https://www.bonvinlab.org/haddock3/CNS.html

Did you edit the Makefile to have the proper options as described in the link above?

[abiotik]

I didn't find any suggestions on editing make file. The only file editing process described in that link was editing .cns_solve_env_sh which I did. Maybe I am missing something? @amjjbonvin Should I delete the csh part of MakeFile code>?

[amjjbonvin]

Read further down on the page for the Troubleshooting and Makefile sections

[abiotik]

@amjjbonvin Here's what I did. I have gained the license and downloaded cns_1.3. I have copied the files from Haddock to /source of cns I have modified the .cns_solve_env_sh file's first line to the path that the cns is installed. Then I run make install and got this error make install compiler=gfortran environmental variable $CNS_SOLVE has been defined incorrectly this variable is set in cns_solve_env - modify this file make: *** [Makefile:38: install] Error 1

I have created Makefile.header.6.gfortran file in instlib/machine/supported/linux/ with the according codes and still got the same error It keeps refering to csh variables which I havn't edited

[amjjbonvin]

Check that there is not another already present Makefile.header.2.gfortran file - if that is the case it will be used first instead of your newly created one

[abiotik]

There are indeed Makefile.header.2 and 5 present. I have tried to install both with and without creating the new file, still the same error. BTW thanks for quick response!

[amjjbonvin]

Delete the old files and only use your new version

Alternatively go into the intel…/source directory and check/edit the content of the makefile there and then type in the same directory “make cns_solve”

[abiotik]

the/cns_solve_1.3/intel-x86_64bit-linux/source/ is empty

[amjjbonvin]

What about deleting this intel.. dir and trying again?And otherwise try simply to use the following for non-profit use executable:

https://surfdrive.surf.nl/files/index.php/s/EqEYBkc5ef2Drbc