Re: mail reg Namd compilation

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Tue May 29 2018 - 11:38:42 CDT

Dear Vidhya,

The compiler is not seeing your FFTW header files. Probably the linker will have similar issues.

Try defining the path with the --fftw-prefix option when you do ./config to produce your NAMD build directory. You can also manually edit the Make.config file to fix directory paths and compiler options.

Best regards,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801
dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/
> On May 28, 2018, at 3:06 AM, Vidhya Sankar <vidhyasankar7928_at_REMOVE_yahoo.com> wrote:
> 
> Dear namd user when i compile Namd2.9 i got the following error  i am using fftw-2.15
> 
> 
> 
> src/ComputePme.C:19:19: error: sfftw.h: No such file or directory
> src/ComputePme.C:20:20: error: srfftw.h: No such file or directory
> src/ComputePme.C:355: error: 'fftw_plan' does not name a type
> src/ComputePme.C:356: error: 'rfftwnd_plan' does not name a type
> src/ComputePme.C:357: error: ISO C++ forbids declaration of 'fftw_complex' with no type
> src/ComputePme.C:357: error: expected ';' before '*' token
> src/ComputePme.C: In constructor 'ComputePmeMgr::ComputePmeMgr()':
> src/ComputePme.C:484: error: 'work' was not declared in this scope
> src/ComputePme.C: In member function 'void ComputePmeMgr::initialize(CkQdMsg*)':
> src/ComputePme.C:1193: error: 'work' was not declared in this scope
> src/ComputePme.C:1193: error: expected type-specifier before 'fftw_complex'
> src/ComputePme.C:1193: error: expected ';' before 'fftw_complex'
> src/ComputePme.C:1197: error: 'forward_plan_yz' was not declared in this scope
> src/ComputePme.C:1197: error: 'FFTW_REAL_TO_COMPLEX' was not declared in this scope
> src/ComputePme.C:1198: error: 'FFTW_ESTIMATE' was not declared in this scope
> src/ComputePme.C:1198: error: 'FFTW_MEASURE' was not declared in this scope
> src/ComputePme.C:1199: error: 'FFTW_IN_PLACE' was not declared in this scope
> src/ComputePme.C:1199: error: 'FFTW_USE_WISDOM' was not declared in this scope
> src/ComputePme.C:1199: error: 'rfftwnd_create_plan_specific' was not declared in this scope
> src/ComputePme.C:1203: error: 'forward_plan_x' was not declared in this scope
> src/ComputePme.C:1203: error: 'FFTW_FORWARD' was not declared in this scope
> src/ComputePme.C:1204: error: 'FFTW_ESTIMATE' was not declared in this scope
> src/ComputePme.C:1204: error: 'FFTW_MEASURE' was not declared in this scope
> src/ComputePme.C:1205: error: 'FFTW_IN_PLACE' was not declared in this scope
> src/ComputePme.C:1205: error: 'FFTW_USE_WISDOM' was not declared in this scope
> src/ComputePme.C:1205: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:1205: error: expected primary-expression before ')' token
> src/ComputePme.C:1206: error: 'fftw_create_plan_specific' was not declared in this scope
> src/ComputePme.C:1210: error: 'backward_plan_x' was not declared in this scope
> src/ComputePme.C:1210: error: 'FFTW_BACKWARD' was not declared in this scope
> src/ComputePme.C:1211: error: 'FFTW_ESTIMATE' was not declared in this scope
> src/ComputePme.C:1211: error: 'FFTW_MEASURE' was not declared in this scope
> src/ComputePme.C:1212: error: 'FFTW_IN_PLACE' was not declared in this scope
> src/ComputePme.C:1212: error: 'FFTW_USE_WISDOM' was not declared in this scope
> src/ComputePme.C:1212: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:1212: error: expected primary-expression before ')' token
> src/ComputePme.C:1213: error: 'fftw_create_plan_specific' was not declared in this scope
> src/ComputePme.C:1217: error: 'backward_plan_yz' was not declared in this scope
> src/ComputePme.C:1217: error: 'FFTW_COMPLEX_TO_REAL' was not declared in this scope
> src/ComputePme.C:1218: error: 'FFTW_ESTIMATE' was not declared in this scope
> src/ComputePme.C:1218: error: 'FFTW_MEASURE' was not declared in this scope
> src/ComputePme.C:1219: error: 'FFTW_IN_PLACE' was not declared in this scope
> src/ComputePme.C:1219: error: 'FFTW_USE_WISDOM' was not declared in this scope
> src/ComputePme.C:1219: error: 'rfftwnd_create_plan_specific' was not declared in this scope
> src/ComputePme.C: In destructor 'virtual ComputePmeMgr::~ComputePmeMgr()':
> src/ComputePme.C:1344: error: 'work' was not declared in this scope
> src/ComputePme.C: In member function 'void ComputePmeMgr::gridCalc1()':
> src/ComputePme.C:1439: error: 'forward_plan_yz' was not declared in this scope
> src/ComputePme.C:1440: error: 'rfftwnd_real_to_complex' was not declared in this scope
> src/ComputePme.C: In member function 'void ComputePmeMgr::gridCalc2()':
> src/ComputePme.C:1606: error: 'forward_plan_x' was not declared in this scope
> src/ComputePme.C:1606: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:1606: error: expected primary-expression before ')' token
> src/ComputePme.C:1607: error: 'work' was not declared in this scope
> src/ComputePme.C:1607: error: 'fftw' was not declared in this scope
> src/ComputePme.C: In member function 'void ComputePmeMgr::gridCalc2R()':
> src/ComputePme.C:1668: error: 'backward_plan_x' was not declared in this scope
> src/ComputePme.C:1668: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:1668: error: expected primary-expression before ')' token
> src/ComputePme.C:1669: error: 'work' was not declared in this scope
> src/ComputePme.C:1669: error: 'fftw' was not declared in this scope
> src/ComputePme.C: In member function 'void ComputePmeMgr::gridCalc3()':
> src/ComputePme.C:1837: error: 'backward_plan_yz' was not declared in this scope
> src/ComputePme.C:1838: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:1838: error: expected primary-expression before ')' token
> src/ComputePme.C:1839: error: 'rfftwnd_complex_to_real' was not declared in this scope
> src/ComputePme.C: In destructor 'PmePencil<T>::~PmePencil()':
> src/ComputePme.C:3108: error: there are no arguments to 'fftw_free' that depend on a template parameter, so a declaration of 'fftw_free' must be available
> src/ComputePme.C:3108: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> src/ComputePme.C: At global scope:
> src/ComputePme.C:3161: error: 'rfftwnd_plan' does not name a type
> src/ComputePme.C:3212: error: 'fftw_plan' does not name a type
> src/ComputePme.C:3263: error: 'fftw_plan' does not name a type
> src/ComputePme.C: In member function 'void PmeZPencil::fft_init()':
> src/ComputePme.C:3304: error: 'fftw_malloc' was not declared in this scope
> src/ComputePme.C:3334: error: 'forward_plan' was not declared in this scope
> src/ComputePme.C:3334: error: 'FFTW_REAL_TO_COMPLEX' was not declared in this scope
> src/ComputePme.C:3335: error: 'FFTW_ESTIMATE' was not declared in this scope
> src/ComputePme.C:3335: error: 'FFTW_MEASURE' was not declared in this scope
> src/ComputePme.C:3336: error: 'FFTW_IN_PLACE' was not declared in this scope
> src/ComputePme.C:3336: error: 'FFTW_USE_WISDOM' was not declared in this scope
> src/ComputePme.C:3336: error: 'rfftwnd_create_plan_specific' was not declared in this scope
> src/ComputePme.C:3337: error: 'backward_plan' was not declared in this scope
> src/ComputePme.C:3337: error: 'FFTW_COMPLEX_TO_REAL' was not declared in this scope
> src/ComputePme.C: In member function 'void PmeYPencil::fft_init()':
> src/ComputePme.C:3364: error: 'fftw_malloc' was not declared in this scope
> src/ComputePme.C:3393: error: 'forward_plan' was not declared in this scope
> src/ComputePme.C:3393: error: 'FFTW_FORWARD' was not declared in this scope
> src/ComputePme.C:3394: error: 'FFTW_ESTIMATE' was not declared in this scope
> src/ComputePme.C:3394: error: 'FFTW_MEASURE' was not declared in this scope
> src/ComputePme.C:3395: error: 'FFTW_IN_PLACE' was not declared in this scope
> src/ComputePme.C:3395: error: 'FFTW_USE_WISDOM' was not declared in this scope
> src/ComputePme.C:3395: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:3395: error: expected primary-expression before ')' token
> src/ComputePme.C:3396: error: expected primary-expression before ')' token
> src/ComputePme.C:3396: error: 'fftw_create_plan_specific' was not declared in this scope
> src/ComputePme.C:3397: error: 'backward_plan' was not declared in this scope
> src/ComputePme.C:3397: error: 'FFTW_BACKWARD' was not declared in this scope
> src/ComputePme.C:3399: error: expected primary-expression before ')' token
> src/ComputePme.C:3400: error: expected primary-expression before ')' token
> src/ComputePme.C: In member function 'void PmeXPencil::fft_init()':
> src/ComputePme.C:3425: error: 'fftw_malloc' was not declared in this scope
> src/ComputePme.C:3449: error: 'forward_plan' was not declared in this scope
> src/ComputePme.C:3449: error: 'FFTW_FORWARD' was not declared in this scope
> src/ComputePme.C:3450: error: 'FFTW_ESTIMATE' was not declared in this scope
> src/ComputePme.C:3450: error: 'FFTW_MEASURE' was not declared in this scope
> src/ComputePme.C:3451: error: 'FFTW_IN_PLACE' was not declared in this scope
> src/ComputePme.C:3451: error: 'FFTW_USE_WISDOM' was not declared in this scope
> src/ComputePme.C:3451: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:3451: error: expected primary-expression before ')' token
> src/ComputePme.C:3452: error: expected primary-expression before ')' token
> src/ComputePme.C:3452: error: 'fftw_create_plan_specific' was not declared in this scope
> src/ComputePme.C:3453: error: 'backward_plan' was not declared in this scope
> src/ComputePme.C:3453: error: 'FFTW_BACKWARD' was not declared in this scope
> src/ComputePme.C:3455: error: expected primary-expression before ')' token
> src/ComputePme.C:3456: error: expected primary-expression before ')' token
> src/ComputePme.C: In member function 'void PmeZPencil::forward_fft()':
> src/ComputePme.C:3523: error: 'forward_plan' was not declared in this scope
> src/ComputePme.C:3524: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:3524: error: expected primary-expression before ')' token
> src/ComputePme.C:3524: error: 'rfftwnd_real_to_complex' was not declared in this scope
> src/ComputePme.C: In member function 'void PmeYPencil::forward_fft()':
> src/ComputePme.C:3637: error: 'forward_plan' was not declared in this scope
> src/ComputePme.C:3638: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:3638: error: expected primary-expression before ')' token
> src/ComputePme.C:3638: error: expected ')' before 'data'
> src/ComputePme.C: In member function 'void PmeXPencil::forward_fft()':
> src/ComputePme.C:3743: error: 'forward_plan' was not declared in this scope
> src/ComputePme.C:3744: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:3744: error: expected primary-expression before ')' token
> src/ComputePme.C:3744: error: expected ')' before 'data'
> src/ComputePme.C: In member function 'void PmeXPencil::backward_fft()':
> src/ComputePme.C:3780: error: 'backward_plan' was not declared in this scope
> src/ComputePme.C:3781: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:3781: error: expected primary-expression before ')' token
> src/ComputePme.C:3781: error: expected ')' before 'data'
> src/ComputePme.C: In member function 'void PmeYPencil::backward_fft()':
> src/ComputePme.C:3877: error: 'backward_plan' was not declared in this scope
> src/ComputePme.C:3878: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:3878: error: expected primary-expression before ')' token
> src/ComputePme.C:3878: error: expected ')' before 'data'
> src/ComputePme.C: In member function 'void PmeZPencil::backward_fft()':
> src/ComputePme.C:3972: error: 'backward_plan' was not declared in this scope
> src/ComputePme.C:3973: error: 'fftw_complex' was not declared in this scope
> src/ComputePme.C:3973: error: expected primary-expression before ')' token
> src/ComputePme.C:3973: error: 'rfftwnd_complex_to_real' was not declared in this scope
> src/ComputePme.C: In destructor 'PmePencil<T>::~PmePencil() [with T = CBaseT1<ArrayElementT<CkIndex3D>, CProxy_PmeZPencil>]':
> src/ComputePme.C:3143:   instantiated from here
> src/ComputePme.C:3108: error: 'fftw_free' was not declared in this scope
> src/ComputePme.C: In destructor 'PmePencil<T>::~PmePencil() [with T = CBaseT1<ArrayElementT<CkIndex3D>, CProxy_PmeYPencil>]':
> src/ComputePme.C:3198:   instantiated from here
> src/ComputePme.C:3108: error: 'fftw_free' was not declared in this scope
> src/ComputePme.C: In destructor 'PmePencil<T>::~PmePencil() [with T = CBaseT1<ArrayElementT<CkIndex3D>, CProxy_PmeXPencil>]':
> src/ComputePme.C:3251:   instantiated from here
> src/ComputePme.C:3108: error: 'fftw_free' was not declared in this scope
> make: *** [obj/ComputePme.o] Error 1
> 
> 
> 
> could any one please help me to solve the error 
> 
> 
> with regards
> S.Vidhyasankar
> 
> 

This archive was generated by hypermail 2.1.6 : Wed Dec 11 2019 - 23:19:55 CST