Re: installation of namd without tcl and fftw

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue May 11 2010 - 05:16:01 CDT

Hi Ipsita,

There is one thing you can check. Go to the NAMD build directory, and
extract an object file from the Tcl library:
ar xv .rootdir/tcl/lib/libtcl8.3.a tclVar.o
file tclVar.o
file obj/common.o

You can see whether the two object files have the same type. If yes,
it might be a problem with incompatible versions of the compilers. You
could try recompiling Tcl: their build system is really nice and
straightforward.

Jerome

On 11 May 2010 11:00, ipsita basu <ibasu788_at_gmail.com> wrote:
> But I downloaded tcl-linux-x86_64.tar.gz which is specified in the
> notes.txt for 64 bit linux machine. Could you please tell me then
> which tcl is suitable for my machine?
>
>
> On 5/11/10, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>> The linker says your Tcl static library is "incompatible", which
>>  probably means that it is compiled for the wrong architecture (32 bit
>>  instead of 64 bit?).
>>
>>  Jerome
>>
>>
>>  On 11 May 2010 07:40, ipsita basu <ibasu788_at_gmail.com> wrote:
>>  > Thanks for your reply. I can understand now. Actually I installed namd
>>  > in all the linux machine in our lab with tcl and fftw,just following
>>  > the notes.txt distributed with namd library except in a machine whose
>>  > configuration is:
>>  > Linux localhost.localdomain 2.6.9-55.EL #1 SMP Fri Apr 20 16:33:09 EDT
>>  > 2007 ppc64 ppc64 ppc64 GNU/Linux
>>  > Here I tried NAMD_2.7b1,NAMD2.7b2 etc. But at the last step when I
>>  > enter the " make " command, it gives error. This output I attach
>>  > herewith.
>>  > But if I tried it without compiling tcl and fftw, then installation is done.
>>  > So can you tell me how solve the installation problem?
>>  >
>>  > Thank you.
>>  > On 5/10/10, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>>  >> Hi Ipsita,
>>  >>
>>  >>  Not having Tcl support will limit what you can do with the config
>>  >>  script. You can set only one parameter per line (without semicolon at
>>  >>  the end of the line). The error message also tells you that some
>>  >>  commands (e.g. "run") are not available. You can only request one
>>  >>  minimization, OR one MD run, with a single temperature, pressure
>>  >>  (etc.) setting. So yes, life is easier with Tcl enabled.
>>  >>
>>  >>  Jerome
>>  >>
>>  >>  PS: note to anyone with CVS commit rights who happens to be reading -
>>  >>  can you please commit the following:
>>  >>
>>  >>  RCS file: /namd/cvsroot/namd2/src/ParseOptions.C,v
>>  >>  retrieving revision 1.1022
>>  >>  diff -r1.1022 ParseOptions.C
>>  >>  841c841
>>  >>  <                   << "configuation file but were not needed" << "\n" << endi;
>>  >>  ---
>>  >>  >                   << "configuration file but were not needed" << "\n" << endi;
>>  >>
>>  >>
>>  >>
>>  >>
>>  >>
>>  >>  On 10 May 2010 13:11, ipsita basu <ibasu788_at_gmail.com> wrote:
>>  >>  > Hi,
>>  >>  >    I have installed NAMD_2.7b2_Source for a linux ppc 64 machine
>>  >>  > without TCL and FFTW as I am not able to install with TCL and FFTW.
>>  >>  > Now when I am going to run a simulation script in that machine, it is
>>  >>  > aborted giving error like this:
>>  >>  > ERROR:   in the configuration file are not allowed
>>  >>  > ERROR: Could not understand units ';' in option 'LangevinPistonTarget
>>  >>  > = 1.01325 ;
>>  >>  > ERROR: Multiple definitions of 'fixedatoms'
>>  >>  > ERROR:   in the configuration file are not allowed
>>  >>  > Warning: The following variables were set in the
>>  >>  > Warning: configuation file but were not needed
>>  >>  > Warning:    langevinTemp
>>  >>  > Warning:    langevinDamping
>>  >>  > Warning:    langevinHydrogen
>>  >>  > ERROR: The following variables were set in the
>>  >>  > ERROR: configuration file but are NOT VALID
>>  >>  > ERROR:    run
>>  >>  > ERROR:    output
>>  >>  > ERROR:    minimize
>>  >>  > FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>  >>  > [0] Stack Traceback:
>>  >>  >  [0] .CmiAbort+0x90  [0x1062222c]
>>  >>  >  [1] ._Z8NAMD_diePKc+0x64  [0x1011c320]
>>  >>  >  [2] ._ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0xec
>>  >>  >  [0x1051af58]
>>  >>  >  [3] ._ZN9NamdState14configListInitEP10ConfigList+0x24c  [0x10493174]
>>  >>  >  [4] ._ZN9ScriptTcl3runEPc+0x104  [0x104fc184]
>>  >>  > Whereas the same script is running well in other linux machine where
>>  >>  > namd is installed with TCL and FFTW.
>>  >>  > I would like to know is there anyone to help me.
>>  >>  >
>>  >>  >
>>  >>  >                   Thanking You
>>  >>  >
>>  >>  >                      Ipsita
>>  >>  > --
>>  >>  > Ipsita Basu
>>  >>  > Research Fellow
>>  >>  > c/o : Dr. Chaitali Mukhopadhyay
>>  >>  > Rajabazar Science College
>>  >>  > 92 APC Road
>>  >>  > Kolkata - 700009
>>  >>  >
>>  >>  >
>>  >>
>>  >
>>  >
>>  > --
>>  > Ipsita Basu
>>  > Research Fellow
>>  > c/o : Dr. Chaitali Mukhopadhyay
>>  > Rajabazar Science College
>>  > 92 APC Road
>>  > Kolkata - 700009
>>  >
>>
>
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
>

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