Dear all,
I tried to compile ambertools using "./configure gnu", but when I enter "make install" command, it comes out many error related to fftw3:
Included at fftw3.F90:10 end subroutine fftwl_export_wisdom_to_file 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1735 Included at fftw3.F90:10 type(C_PTR) function fftwl_export_wisdom_to_string() bind(C, name='fftwl_ex 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1736 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1737 Included at fftw3.F90:10 end function fftwl_export_wisdom_to_string 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1739 Included at fftw3.F90:10 subroutine fftwl_export_wisdom(write_char,data) bind(C, name='fftwl_export_ 1Error: Syntax error in SUBROUTINE statement at (1) In file fftw3.f03:1740 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1741 Included at fftw3.F90:10 type(C_FUNPTR), value :: write_char 1Error: Derived type 'c_funptr' at (1) is being used before it is defined In file fftw3.f03:1742 Included at fftw3.F90:10 type(C_PTR), value :: data 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1743 Included at fftw3.F90:10 end subroutine fftwl_export_wisdom 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1745 Included at fftw3.F90:10 integer(C_INT) function fftwl_import_system_wisdom() bind(C, name='fftwl_im 1Error: Parameter 'c_int' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1746 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1747 Included at fftw3.F90:10 end function fftwl_import_system_wisdom 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1749 Included at fftw3.F90:10 integer(C_INT) function fftwl_import_wisdom_from_filename(filename) bind(C, 1Error: Parameter 'c_int' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1750 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1751 Included at fftw3.F90:10 character(C_CHAR), dimension(*), intent(in) :: filename 1Error: Unexpected data declaration statement in INTERFACE block at (1) In file fftw3.f03:1752 Included at fftw3.F90:10 end function fftwl_import_wisdom_from_filename 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1754 Included at fftw3.F90:10 integer(C_INT) function fftwl_import_wisdom_from_file(input_file) bind(C, n 1Error: Parameter 'c_int' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1755 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1756 Included at fftw3.F90:10 type(C_PTR), value :: input_file 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1757 Included at fftw3.F90:10 end function fftwl_import_wisdom_from_file 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1759 Included at fftw3.F90:10 integer(C_INT) function fftwl_import_wisdom_from_string(input_string) bind( 1Error: Parameter 'c_int' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1760 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1761 Included at fftw3.F90:10 character(C_CHAR), dimension(*), intent(in) :: input_string 1Error: Unexpected data declaration statement in INTERFACE block at (1) In file fftw3.f03:1762 Included at fftw3.F90:10 end function fftwl_import_wisdom_from_string 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1764 Included at fftw3.F90:10 integer(C_INT) function fftwl_import_wisdom(read_char,data) bind(C, name='f 1Error: Parameter 'c_int' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1765 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1766 Included at fftw3.F90:10 type(C_FUNPTR), value :: read_char 1Error: Derived type 'c_funptr' at (1) is being used before it is defined In file fftw3.f03:1767 Included at fftw3.F90:10 type(C_PTR), value :: data 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1768 Included at fftw3.F90:10 end function fftwl_import_wisdom 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1770 Included at fftw3.F90:10 subroutine fftwl_fprint_plan(p,output_file) bind(C, name='fftwl_fprint_plan 1Error: Syntax error in SUBROUTINE statement at (1) In file fftw3.f03:1771 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1772 Included at fftw3.F90:10 type(C_PTR), value :: p 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1773 Included at fftw3.F90:10 type(C_PTR), value :: output_file 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1774 Included at fftw3.F90:10 end subroutine fftwl_fprint_plan 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1776 Included at fftw3.F90:10 subroutine fftwl_print_plan(p) bind(C, name='fftwl_print_plan') 1Error: Syntax error in SUBROUTINE statement at (1) In file fftw3.f03:1777 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1778 Included at fftw3.F90:10 type(C_PTR), value :: p 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1779 Included at fftw3.F90:10 end subroutine fftwl_print_plan 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1781 Included at fftw3.F90:10 type(C_PTR) function fftwl_malloc(n) bind(C, name='fftwl_malloc') 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1782 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1783 Included at fftw3.F90:10 integer(C_SIZE_T), value :: n 1Error: Parameter 'c_size_t' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1784 Included at fftw3.F90:10 end function fftwl_malloc 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1786 Included at fftw3.F90:10 type(C_PTR) function fftwl_alloc_real(n) bind(C, name='fftwl_alloc_real') 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1787 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1788 Included at fftw3.F90:10 integer(C_SIZE_T), value :: n 1Error: Parameter 'c_size_t' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1789 Included at fftw3.F90:10 end function fftwl_alloc_real 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1791 Included at fftw3.F90:10 type(C_PTR) function fftwl_alloc_complex(n) bind(C, name='fftwl_alloc_compl 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1792 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1793 Included at fftw3.F90:10 integer(C_SIZE_T), value :: n 1Error: Parameter 'c_size_t' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1794 Included at fftw3.F90:10 end function fftwl_alloc_complex 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1796 Included at fftw3.F90:10 subroutine fftwl_free(p) bind(C, name='fftwl_free') 1Error: Syntax error in SUBROUTINE statement at (1) In file fftw3.f03:1797 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1798 Included at fftw3.F90:10 type(C_PTR), value :: p 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1799 Included at fftw3.F90:10 end subroutine fftwl_free 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1801 Included at fftw3.F90:10 subroutine fftwl_flops(p,add,mul,fmas) bind(C, name='fftwl_flops') 1Error: Syntax error in SUBROUTINE statement at (1) In file fftw3.f03:1802 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1803 Included at fftw3.F90:10 type(C_PTR), value :: p 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1804 Included at fftw3.F90:10 real(C_DOUBLE), intent(out) :: add 1Error: Parameter 'c_double' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1805 Included at fftw3.F90:10 real(C_DOUBLE), intent(out) :: mul 1Error: Parameter 'c_double' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1806 Included at fftw3.F90:10 real(C_DOUBLE), intent(out) :: fmas 1Error: Parameter 'c_double' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1807 Included at fftw3.F90:10 end subroutine fftwl_flops 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1809 Included at fftw3.F90:10 real(C_DOUBLE) function fftwl_estimate_cost(p) bind(C, name='fftwl_estimate 1Error: Parameter 'c_double' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1810 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1811 Included at fftw3.F90:10 type(C_PTR), value :: p 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1812 Included at fftw3.F90:10 end function fftwl_estimate_cost 1Error: Expecting END INTERFACE statement at (1) In file fftw3.f03:1814 Included at fftw3.F90:10 real(C_DOUBLE) function fftwl_cost(p) bind(C, name='fftwl_cost') 1Error: Parameter 'c_double' at (1) has not been declared or is a variable, which does not reduce to a constant expression In file fftw3.f03:1815 Included at fftw3.F90:10 import 1Error: Unclassifiable statement at (1) In file fftw3.f03:1816 Included at fftw3.F90:10 type(C_PTR), value :: p 1Error: Derived type 'c_ptr' at (1) is being used before it is defined In file fftw3.f03:1817 Included at fftw3.F90:10 end function fftwl_cost 1Error: Expecting END INTERFACE statement at (1)make[2]: *** [fftw3.o] Error 1make[2]: Leaving directory `/software/amber12/AmberTools/src/pbsa'make[1]: *** [serial] Error 2make[1]: Leaving directory `/software/amber12/AmberTools/src'make: *** [install] Error 2
so I recompile it with "./configure -nofftw3 gnu", and this time "make install" command seems successful, and "make test" all passed. However, does anyone know what is the effect of the "-nofftw3" flag on ambertools function? Would it affects the input parameter file preparation and makes similation fail? By using the .top and .crd files prepared by ambertools, I find the simulation system collapsed rapidly during minimization. Is it related to the fftw3 problem? Thanks!
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
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Received on Sat Sep 14 2013 - 10:30:03 PDT
