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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