Re: mail reg Namd compilation

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Mon May 28 2018 - 04:14:34 CDT

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Hello,

Well, maybe they need it for some reason (e.g. some sort of modified
source code that only exists for 2.9).

In any case, S.Vidhyasankar, you should probably use the FFTW version
that the NAMD developers themselves use, rather than any other version,
i.e. the one they suggest you download from their own website:

http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz

Most likely, the NAMD compilation scheme tries to find stuff that exist
in their own fftw-linux version but not in your fftw-2.15

The same probably applies to tcl, download and use the library from
ks.uiuc.edu website:

http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz

Hope this helps,
Fotis

On 05/28/2018 11:58 AM, Ajasja Ljubetič wrote:
> Any reason why you are trying to compile such an old version (It's
> been six years since the release of NAMD 2.9)?
> I would try to compile the latest version if possible.
>
> Best,
> Ajasja
>
> On Mon, 28 May 2018 at 10:08, Vidhya Sankar
> <vidhyasankar7928_at_remove_yahoo.com
> <mailto: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
>
>

-- 
*******************************************
Fotis A. Baltoumas
Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology, National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
*******************************************

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