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compilation problem with CNS

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  • stella.joe13
    Dear cnsbb, How to use pre-compiled linux(32-bit; with bash shell) binaries to get the compilers to work in CNS ver 1.21. Please see below the complete process
    Message 1 of 2 , Jun 1, 2009
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      Dear cnsbb,

      How to use pre-compiled linux(32-bit; with bash shell) binaries to get the compilers to work in CNS ver 1.21.

      Please see below the complete process done and suggest.

      # cd cns
      # ls
      cns_solve_1.21 cns_solve_1.21_all-mp.tar
      # cd cns_solve_1.21
      # ls

      bin cns_solve_original inputs License Readme utils
      Changes doc instlib Makefile source
      cns_solve_env helplib libraries modules test

      # nedit cns_solve_env
      # make install

      Installation directory: cns_solve_1.21/intel-i686-linux
      copying files in instlib directory linux to intel-i686-linux
      0read.me
      Makefile.header.1.ifort
      Makefile.header.2.gfortran
      Makefile.header.3.pgf95
      Makefile.header.4.ifort_mp
      arch_env
      machine_c.c
      machine_f.f
      Using Makefile template for compiler: gfortran
      making source directory in intel-i686-linux
      making bin directory in intel-i686-linux
      making utils directory in intel-i686-linux
      making test directory in intel-i686-linux
      linking source files to intel-i686-linux/source
      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
      making compiler-test directory in intel-i686-linux
      testing Fortran and C compilers
      compiling: gcc -O -DCNS_ARCH_TYPE_LINUX
      C compiler passes test
      compiling: gfortran -w -O3 -malign-double -funroll-loops -ffast-math
      linking: gfortran -w
      Segmentation fault
      ***** ERROR: problem with Fortran compiler *****
      make[3]: *** [fortran-test] Error 2
      make[2]: *** [compiler-test] Error 2
      make[1]: *** [compiler-test] Error 2
      compiler problems - stopping installation
      please check compilers before retrying installation
      make: *** [install] Error 1

      # cd intel-i686-linux
      # ls

      0read.me machine_c.c Makefile.header.2.gfortran test
      arch_env machine_f.f Makefile.header.3.pgf95 utils
      bin Makefile.header Makefile.header.4.ifort_mp
      compiler-test Makefile.header.1.ifort source

      # nedit 0read.me

      # make install compiler=gfortran

      Installation directory: cns_solve_1.21/intel-i686-linux
      copying files in instlib directory linux to intel-i686-linux
      0read.me
      Makefile.header.1.ifort
      Makefile.header.2.gfortran
      Makefile.header.3.pgf95
      Makefile.header.4.ifort_mp
      arch_env
      machine_c.c
      machine_f.f
      Using Makefile template for compiler: gfortran
      removing old source files
      linking source files to intel-i686-linux/source
      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 -DCNS_ARCH_TYPE_LINUX
      C compiler passes test
      compiling: gfortran -w -O3 -malign-double -funroll-loops -ffast-math
      linking: gfortran -w
      Segmentation fault
      ***** ERROR: problem with Fortran compiler *****
      make[3]: *** [fortran-test] Error 2
      make[2]: *** [compiler-test] Error 2
      make[1]: *** [compiler-test] Error 2
      compiler problems - stopping installation
      please check compilers before retrying installation
      make: *** [install] Error 1
      ------------------------------------------------------
      Can anyone Now tell me How to proceed. Thanks in advance.
      Regards,
      stella joe
    • Axel Brunger
      Don t run the install script for the precompiled version as as explicitly stated in the download instructions and in the Installation instructions on the CNS
      Message 2 of 2 , Jun 1, 2009
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        Don't run the install script for the precompiled version
        as as explicitly stated in the download instructions
        and in the Installation instructions on the CNS website!


        On Jun 1, 2009, at 5:47 AM, stella.joe13 wrote:



        Dear cnsbb,

        How to use pre-compiled linux(32-bit; with bash shell) binaries to get the compilers to work in CNS ver 1.21. 

        Please see below the complete process done and suggest.

        # cd cns
        # ls
        cns_solve_1. 21 cns_solve_1. 21_all-mp. tar
        # cd cns_solve_1. 21
        # ls

        bin cns_solve_original inputs License Readme utils
        Changes doc instlib Makefile source
        cns_solve_env helplib libraries modules test

        # nedit cns_solve_env 
        # make install

        Installation directory: cns_solve_1. 21/intel- i686-linux
        copying files in instlib directory linux to intel-i686-linux
        0read.me
        Makefile.header. 1.ifort
        Makefile.header. 2.gfortran
        Makefile.header. 3.pgf95
        Makefile.header. 4.ifort_mp
        arch_env
        machine_c.c
        machine_f.f
        Using Makefile template for compiler: gfortran
        making source directory in intel-i686-linux
        making bin directory in intel-i686-linux
        making utils directory in intel-i686-linux
        making test directory in intel-i686-linux
        linking source files to intel-i686-linux/ source
        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
        making compiler-test directory in intel-i686-linux
        testing Fortran and C compilers
        compiling: gcc -O -DCNS_ARCH_TYPE_ LINUX 
        C compiler passes test
        compiling: gfortran -w -O3 -malign-double -funroll-loops -ffast-math 
        linking: gfortran -w 
        Segmentation fault
        ***** ERROR: problem with Fortran compiler *****
        make[3]: *** [fortran-test] Error 2
        make[2]: *** [compiler-test] Error 2
        make[1]: *** [compiler-test] Error 2
        compiler problems - stopping installation
        please check compilers before retrying installation
        make: *** [install] Error 1

        # cd intel-i686-linux
        # ls

        0read.me machine_c.c Makefile.header. 2.gfortran test
        arch_env machine_f.f Makefile.header. 3.pgf95 utils
        bin Makefile.header Makefile.header. 4.ifort_mp
        compiler-test Makefile.header. 1.ifort source

        # nedit 0read.me

        # make install compiler=gfortran

        Installation directory: cns_solve_1. 21/intel- i686-linux
        copying files in instlib directory linux to intel-i686-linux
        0read.me
        Makefile.header. 1.ifort
        Makefile.header. 2.gfortran
        Makefile.header. 3.pgf95
        Makefile.header. 4.ifort_mp
        arch_env
        machine_c.c
        machine_f.f
        Using Makefile template for compiler: gfortran
        removing old source files
        linking source files to intel-i686-linux/ source
        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 -DCNS_ARCH_TYPE_ LINUX 
        C compiler passes test
        compiling: gfortran -w -O3 -malign-double -funroll-loops -ffast-math 
        linking: gfortran -w 
        Segmentation fault
        ***** ERROR: problem with Fortran compiler *****
        make[3]: *** [fortran-test] Error 2
        make[2]: *** [compiler-test] Error 2
        make[1]: *** [compiler-test] Error 2
        compiler problems - stopping installation
        please check compilers before retrying installation
        make: *** [install] Error 1
        ------------ --------- --------- --------- --------- ------
        Can anyone Now tell me How to proceed. Thanks in advance.
        Regards,
        stella joe 


        Axel T. Brunger
        Investigator,  Howard Hughes Medical Institute
        Professor of Molecular and Cellular Physiology
        Stanford University

        Email:  brunger@...      
        Phone:  +1 650-736-1031
        Fax:    +1 650-745-1463






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