Re: NAMD 2.8 and PLUMED 1.3

From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Aug 31 2012 - 13:57:31 CDT

this sounds like a general unix problem. you need to ensure that directory
is included when the compiler is looking for header files. I'm not sure
exactly how this is done, maybe by setting a $INCLUDE_DIR variable in your
shell, or probably there is something you can add to the compile line, for
instance ./build [your stuff here] -I [directory where that file is].

Anyway, I think it's a simple enough problem, just needs some googling or
someone with more unix experience than me.

~Aron

On Thu, Aug 30, 2012 at 8:59 AM, candy deck <candy76_at_hotmail.co.uk> wrote:

>
>
> Dear NAMD user.
> I'm trying to install NAMD 2.8 and patching PLUMED1.3
> Here is what I've done :
>
> tar xzf NAMD_2.8_Source.tar.gz
> cd NAMD_2.8_Source
> tar xf charm-6.3.2.tar
> cd charm-6.3.2
>
> Build and test the Charm++/Converse library (network version):
> ./build charm++ net-linux-x86_64 --no-build-shared --with-production
> cd net-linux-x86_64/tests/charm++/megatest
> make pgm
> ./charmrun ++local +p4 ./pgm (also try running on multiple nodes)
> cd ../../../../..
>
>
> Download and install TCL and FFTW libraries:
> wget
> http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
> tar xzf fftw-linux-x86_64.tar.gz
> mv linux-x86_64 fftw
> wget
> http://www.ks.uiuc.edu/Research/namd/libraries/old_2010/tcl-linux-x86_64.tar.gz
> tar xzf tcl-linux-x86_64.tar.gz
> mv linux-x86_64 tcl
>
>
> Set up build directory and compile:
> network version: ./config Linux-x86_64-g++ --charm-arch net-linux-x86_64
>
> *apply the patch: ./plumedpatch_namd_2.8.sh -patch *
>
> cd Linux-x86_64-g++
> make
>
> And here, things like :
> src/ComputeMgr.C:83:21: fatal error: metadyn.h: No such file or directory
> compilation terminated
> are showing up...
>
>
> However, metadyn.h exists...
> if I do ls -l , I obtain :
>
> lrwxrwxrwx 1 candy candy 36 2012-08-30 13:55 metadyn.h ->
> ../plumed-1.3/common_files/metadyn.h
>
>
> Can someone help ??
> Thanks a lot
> Candy
>
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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