From: Buddhadev Maiti (bmaiti_at_gsu.edu)
Date: Fri Aug 31 2012 - 22:40:11 CDT
I am going to help you for PLUMED installation. Please let me know how are you going to install: one node multiple processors / multiple nodes multiple processors
Have a nice weekend,
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Aron Broom [broomsday_at_gmail.com]
Sent: Friday, August 31, 2012 2:57 PM
To: candy deck
Subject: Re: namd-l: NAMD 2.8 and PLUMED 1.3
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.
On Thu, Aug 30, 2012 at 8:59 AM, candy deck <candy76_at_hotmail.co.uk<mailto: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
tar xf charm-6.3.2.tar
Build and test the Charm++/Converse library (network version):
./build charm++ net-linux-x86_64 --no-build-shared --with-production
./charmrun ++local +p4 ./pgm (also try running on multiple nodes)
Download and install TCL and FFTW libraries:
tar xzf fftw-linux-x86_64.tar.gz
mv linux-x86_64 fftw
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<http://plumedpatch_namd_2.8.sh> -patch
And here, things like :
src/ComputeMgr.C:83:21: fatal error: metadyn.h: No such file or directory
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
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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