From: Lea Thøgersen (lea_at_birc.au.dk)
Date: Wed Mar 29 2006 - 06:27:09 CST
Can it really be that I have lost everything because the file got larger
than 2Gb???
I cannot read in any way the DCD file from a 2ns simulation executed
with the precompiled binary called NAMD_2.6b1_AIX-POWER-MPI on an IBM
rs6000 pSeries 690 with AIX5.1D OS and tcl8.3.
During the simulation I have frequently copied the dcd-file to my
workstation (AMD64), used flipdcd, and studied the progress. However,
since the size of the dcd-file got lager than 2Gb I haven't been able to
open it in any way. Of course every time I copied the dcd-file to my
workstation, the older version was overwritten (stupid, stupid me) so
when the file suddenly gave me problems, I had no backup.
When trying to use flipdcd on my workstation it gave the following:
>flipdcd dmpc_sol2.eq.dcd
dmpc_sol2.eq.dcd is not in DCD format
I can understand it will give problems since I only have 2Gb memory on
my workstation and flipdcd uses an amount of memory corresponding to the
filesize (as far as I understand).
When trying to use catdcd on my workstation it gave the following:
>catdcd dmpc_sol2.eq.dcd
CatDCD 4.0
read_dcdheader returned -6
Error: could not open file 'dmpc_sol2.eq.dcd' for reading.
I guessed that maybe catdcd need it to be in native endian? Anyhow, I
found some previous post on this list about problems with large dcd
files from AIX:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3332.html
Thereby inspired I got the latest cvs version of the plugin-tree for vmd
and compiled a 64bit version of catdcd on the machine where the
simulation was executed.
However, whether I compile catdcd with gmake AIX5 or AIX5_64, I get the
following output when trying to use it on my file:
>catdcd dmpc_sol2.eq.dcd
CatDCD 4.0
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) read_dcdheader: corruption or unrecognized file structure
Error: could not open file 'dmpc_sol2.eq.dcd' for reading.
When trying to use flipdcd on the AIX machine I get the following
>flipdcd dmpc_sol2.eq.dcd
Can't stat dmpc_sol2.eq.dcd
So again I ask you: Can it really be that I have lost everything because
the file got larger than 2Gb???
Thank you for any help
Lea
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