AMBER Archive (2006)

Subject: Re: AMBER: Problem with file size of sander outputs

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Wed Feb 22 2006 - 14:58:00 CST

I have little experience about it, not related to sander but other
program. At first I compiled that program using ifort9. The program died
with "filesize limit exceeded " displayed when the produced file reached
2.1GB. Intel announced that intel compiler automatically enable "large
file support", but I don't know why my program still has the 2GB
limitation.

Then I use PGI compiler with -Mlfs flag for the compiliation. The
re-compiled program can now overcome the 2GB limitation. Maybe you also
can try using PGI compiler with -Mlfs flag to re-compile sander. Hope this
helps!

On Wed, 22 Feb 2006 05:49:49 -0500, german <gsciaini_at_qi.fcen.uba.ar> wrote:

> Try to divide your calculation into different output files restarting
> them with NTX=5, and IREST=1...
>
> Good look
> G.
>
>
>
> At 11:54 p.m. 21/02/2006 -0800, you wrote:
>
>> Dear amber community,
>>
>> I have been running a PME explicit solvent molecular
>> dynamics for a 20 KDa protein and its ligand using the
>> sander module of AMBER8.
>> I set nstlim=40000 and ntpr=10. After a couple of
>> hours , my MD run stopped at nstep =9970 giving me the
>> following error message:
>>
>> Filesize limit exceeded
>>
>> My trajectory file size has reached to 2 GB, the MD
>> output is 666 Kb and the coordinate output is 6.6 MB.
>>
>> I believe I will have to recompile sander changing
>> some codes to increase the file size in sander. Could
>> someone please let me know what codes in sander should
>> be modified?
>>
>> cheers,
>>
>> jenk.
>>
>>
>>
>>
>>
>>
>> --- Ross Walker <ross_at_rosswalker.co.uk> wrote:
>>
>> >
>> > > ./configure -mpi ifort
>> > > make parallel
>> >
>> > -mpi means native MPI libraries as provided by the
>> > operating system. This is
>> > the option to use for things like an SGI altix. For
>> > a regular PC running
>> > redhat you need to provide an mpi installation
>> > either MPICH or LAM. This MPI
>> > installation needs to be compiled with the same
>> > compiler as you are using
>> > for compiling Amber. Hence the lam that is often
>> > installed by default with
>> > redhat will not work as it is compiled with GCC.
>> >
>> > So, download either Lam or MPICH, compile it with
>> > ifort and chech your PATH
>> > is correct so that the correct installation is being
>> > used.
>> >
>> > E.g. which lamboot
>> >
>> > should return /usr/local/lam/lamboot (or similar)
>> > rather than /usr/bin/lamboot
>> >
>> > Once this is done create a config.h for the lam or
>> > mpich:
>> >
>> > export LAM_HOME=/usr/local/lam..... (or where you
>> > installed it)
>> > ./configure -p4 -lam ifort
>> > or
>> > export MPICH_HOME=/usr/local/mpich.....
>> > ./configure -p4 -mpich ifort
>> >
>> > Then:
>> >
>> > make clean
>> > make parallel
>> >
>> > You should then not get the undefined references you
>> > are seeing.
>> >
>> > All the best
>> > Ross
>> >
>> > /\
>> > \/
>> > |\oss Walker
>> >
>> > | Department of Molecular Biology TPC15 |
>> > | The Scripps Research Institute |
>> > | Tel: +1 858 784 8889 | EMail:-
>> > ross_at_rosswalker.co.uk |
>> > | http://www.rosswalker.co.uk | PGP Key available on
>> > request |
>> >
>> > Note: Electronic Mail is not secure, has no
>> > guarantee of delivery, may not
>> > be read every day, and should not be used for urgent
>> > or sensitive issues.
>> >
>> >
>> >
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>>
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>
> 

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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