[gmx-users] Installation Question - Large Files and Inner Loops

Joanne Hanna J.F.Hanna at warwick.ac.uk
Wed Aug 31 21:55:54 CEST 2005


I have just done a reinstall of gromacs and have actually paid attention to the output as it installs!
There are two points that I am unsure about, I was wondering if anyone could explain or confirm whether or not these are okay?

1. at the make stage the following lines. Should I be finding a special C compiler for large files, or is this something I need to define? 

chchecking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGE_FILES value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... 1
checking for fseeko... yes
checking for _doprnt... no
checking if malloc debugging is wanted... no
checking for X... no
checking for libXext and libXp... no
checking for only libXext... no

2. should Prefetching forces in loops and Vectorizing invsqrt in loops be equaling zero? Is there a 'correct' number of lines of code to be generated?
Joanne Hanna
Department of Chemistry
University of Warwick

J.F.Hanna at warwick.ac.uk
>>> This is the GROMACS code generator for MD & MC inner loops
>>> It will generate single precision C code in file innerc.c
>>> Using fast inline assembly gcc/x86 truncation. Since we are changing
    the control word this might affect the numerical result slightly.
>>> Using gromacs invsqrt code
>>> Inlining gromacs invsqrt code
>>> Using normal solvent optimized loops
>>> Prefetching forces in loops: none
>>> Nonthreaded inner loops
>>> Vectorizing invsqrt in loops:none
>>> Generated 42963 lines of code in 156 functions
(innerc.c may take a while to compile)

Sorry if these are very obvious or trivial questions. Any advice would be much appreciated.


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