Hi John,
Are you on a 32 bit machine? Or an x86_64 machine running 32 bit Linux?
I have no problems on my x86_64 machine running Redhat EL4 x86_64 with the
x86_64 Intel compilers. Ptraj can read multiple gigabyte files. On a 32 bit
installation you would need to include the FILE_OFFSET and LARGEFILE_SOURCE
defines to get LFS support. In the AMBER 10 config_amber.h file we have:
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2
$(AMBERBUILDFLAGS)
Which turns it on. However, ptraj is now built as part of AmberTools using
config.h and I do not see these defines in there. Hence you could try
editing config.h and change:
CFLAGS= -m64 -DBINTRAJ $(AMBERBUILDFLAGS)
OCFLAGS=-O3 -m64 -DBINTRAJ $(AMBERBUILDFLAGS)
To
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -DBINTRAJ
$(AMBERBUILDFLAGS)
OCFLAGS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O3 -m64 -DBINTRAJ
$(AMBERBUILDFLAGS)
Then do:
make -f Makefile_at clean
make -f Makefile_at
and then try it again. If it works please let me know your machine specs,
compiler, OS version and if it is 32 bit etc and I'll make sure the
AmberTools configure script gets updated for the upcoming release.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Beale, John
> Sent: Thursday, October 15, 2009 5:40 AM
> To: amber.ambermd.org
> Subject: [AMBER] Large File Support
>
> Is large file support enabled by default in Amber 10? I am running a
> 2,000,000-step MD simulation of a protein in TIP3P water. I mistakenly
> set my ntwx too low, and the .mdcrd file has grown to 2.9 gigabytes. I
> am unable to run ptraj with such a large .mdcrd file. Ptraj won't
> accept
> it as the trajin file.
>
>
>
> I read in the archive that to enable large file support it is necessary
> to add the following: " -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE" to
> CFLAGS. Should this be necessary for Amber 10?
>
>
>
> John
>
>
>
>
>
>
>
>
>
>
>
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Received on Thu Oct 15 2009 - 11:30:05 PDT
