Re: catDCD 32 bit Vs. 64 bit Version

From: juneja_at_speakeasy.net
Date: Fri Feb 01 2008 - 04:00:51 CST

Dear Peter,

I am producing this dcd from charmm on AMD Opteron(tm) Processor 2222 64bit machine. I try to get the number of frames in the dcd so I use the catDCD to find it (although I knew how many frames I will have in my charmm produced dcd). The output of catDCD is as follows:

- - - - - -
CatDCD 4.0
dcdplugin) detected CHARMM -i8 64-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) Warning: DCD header claims 525000 frames, file size indicates there are actually 554166 frames
dcdplugin) detected CHARMM -i8 64-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) Warning: DCD header claims 525000 frames, file size indicates there are actually 554166 frames
Opened file 'dyna.dcd' for reading.
Read 554166 frames from file dyna.dcd.
Total frames: 554166
CatDCD exited normally.
- - - - - -

If you look to the above output you will see the conflict. Actually in charmm I am producing 525000 frames however catDCD shows that there exists 554166 frames (which I believe is wrong). For the sake of check I converted this charmm generated 64bit dcd (dyna.dcd) to 32bit dcd (dyna_32bit.dcd) and then read it with catDCD and I figure out that everything goes fine and I get the following output:

- - - - - -
CatDCD 4.0
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Opened file 'dyna_32bit.dcd' for reading.
Read 525000 frames from file dyna_32bit.dcd.
Total frames: 525000
CatDCD exited normally.
- - - - - -

Best
-Alok


On Thu Jan 31 20:26 , Peter Freddolino sent:

Hi Alok,
I don't think this is likely to be the problem if you're just working on
an amd64; I routinely transition between dcds produced by 64-bit and
32-bit machines without difficulty. namd should write with the same
precision in either case. Could you specify where and how you produced
the dcd, where you're trying to read it, and what the expected and
actual number of frames are? The only time I'm aware of there being
portability problems with dcds is where there's a change in endianism
between machines, or when you're using AIX (see the discussion at
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3332.html).

Best,
Peter

Alok Juneja wrote:
> Hello Everybody,
>
> I have written 64 bit dcd file and now ask catDCD to figure out the
> details of the dcd file. Though catDCD reads the 64 bit dcd but shows
> wrong number of frames in contrast to the correct number of frames
> shown in the header of dcd. I believe this is all because of problems
> related to reading of 64 bit dcd file by 32 bit catDCD. Is there any
> way to solve this problem. Is 64 bit version of catDCD is available.
> Just to intimate that I am using AMD Athlon(tm) 64 Processor.
>
>
> Best Wishes,
> Alok


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