From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Sat Jan 21 2006 - 13:22:11 CST
Hi Jorge and Others,
This goes along with previous messages from Jorge concerning writing large
(>2GB) dcd files on AIX operating systems.
We determined that compiling a 64 bit version of NAMD fixes this problem.
SDSC has a 64 bit version now compiled in their software directory for
those that are interested as of 1/20/2006 I believe. I have since run
simulations and indeed you can now write > 2 GB files.
I discovered another problem. When I used the 32 bit version of catdcd,
it did not work in reading dcd files written from the 64 bit NAMD. My
other fortran programs compiled in 32 bit and 64 bit do work however in
reading the dcd files. This confused me. However, I downloaded the
latest CVS plugin tree from vmd and was able to compile a 64 bit version
of catdcd. This works perfectly!
On AIX 5.2, I did this by using the default AIX5_64 flags along with
setenv OBJECT_MODE=64
setenv TCLINC=-I(tcl path to tcl include files for version 8.4.5)
setenv TCLLIB=-L(tcl path to tcl library files for version 8.4.5)
Then
gmake AIX5_64
I did need to modify the Makefile-arch as given in this mailing list (but
I am using libtcl8.4.so:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5574.html
Here are the compiling flags from the Makefile-arch file from the plugin
tree from CVS:
AIX5_64:
$(MAKE) dynlibs staticlibs bins \
"ARCH = AIX5_64" \
"COPTO = -o " \
"LOPTO = -o " \
"CC = xlc" \
"CXX = xlC" \
"CCFLAGS = -w -qinlglue -q64 -qarch=com -qtune=pwr4" \
"CXXFLAGS = -w -qstrict -Q -q64 -qarch=com -qtune=pwr4" \
"LDFLAGS = -q64 -qarch=com -qtune=pwr4" \
"TCLLDFLAGS = /(path to tcl 8.4.5 library libtcl8.4.so file)" \
"AR = ar -X64" \
"NM = nm -B" \
"RANLIB = touch" \
"SHLD = xlC -bM:SRE -bnoentry -bexpall -lm -q64 -qarch=com
-qtune=pwr4"
Hope this helps someone if they also have this problem.
Josh
On Wed, January 11, 2006 10:06 am, Jorge Pikunic wrote:
> Hi Michel,
>
> Gracias.
>
>> Regarding the first question, you shouldn't have any problem at loading
>> dcd files in either 32 or 64-bit machines. For example, I usually run my
> It seems to be a problem with the NAMD implementation on AIX (see Joshua's
> e-mail in this thread), which is used in the machine in which I ran the
> simulations.
>
>> Second, what do you mean with "recover" a part of the trajectory?
> The resulting dcd files are unreadable by most programs that can read dcd
> files. I was wondering if I can somehow recover the trajectories stored in
> these files. I think that the answer is no, after a couple of replies that
> I
> have received.
>
> Thank you,
>
> Jorge
>
>
>
>
>
>
--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
--------------------------------------------------
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