[gmx-users] compiling with gcc

[Joanne Hanna]

Hello
I have encountered warning messages when compiling on computers running either fedora core 3 or 4 which run gcc v 3.4 and v 4.0 respectively.
I have however succesfully compiled the same version of gmx 3.2.1 from the source code on machines running v 7.3 redhat which uses gcc v 2.96.

The warning messages are:

gcc 3.4

fedora core 3
index.c:63: warning: conflicting types for built-in function 'yn'
>>> 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)

x86_3dnow.s: Assembler messages:
x86_3dnow.s:3004: Warning: line numbers must be positive; line number 0 rejected
x86_3dnow.s:3369: Warning: line numbers must be positive; line number 0 rejected
x86_3dnow.s:5497: Warning: line numbers must be positive; line number 0 rejected
pme.c: In function `solve_pme':
pme.c:306: warning: dereferencing type-punned pointer will break strict-aliasing  rules
pppm.c: In function `convolution':
pppm.c:380: warning: dereferencing type-punned pointer will break strict-aliasin g rules
gmx_rdf.c: In function `extract_sq':
gmx_rdf.c:503: warning: dereferencing type-punned pointer will break strict-alia sing rules

gcc 4.0

index.c:63: warning: conflicting types for built-in function 'yn'
princ.c: In function 'orient_princ':
../../include/vec.h:231: warning: 'xcm[0]' is used uninitialized in this function
../../include/vec.h:232: warning: 'xcm[1]' is used uninitialized in this function
../../include/vec.h:233: warning: 'xcm[2]' is used uninitialized in this function
libxdrf.c: In function 'xdr3dfcoord':
libxdrf.c:685: warning: 'bitsizeint[0]' may be used uninitialized in this function
libxdrf.c:685: warning: 'bitsizeint[1]' may be used uninitialized in this function
libxdrf.c:685: warning: 'bitsizeint[2]' may be used uninitialized in this function
libxdrf.c:689: warning: 'prevcoord[0]' may be used uninitialized in this function
libxdrf.c:689: warning: 'prevcoord[1]' may be used uninitialized in this function
libxdrf.c:689: warning: 'prevcoord[2]' may be used uninitialized in this function
>>> This is the GROMACS code generator for MD & MC inner loops
>>> It will generate single precision C code in file innerc.c
>>> 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 42309 lines of code in 156 functions
(innerc.c may take a while to compile)

pme.c: In function 'solve_pme':
pme.c:306: warning: dereferencing type-punned pointer will break strict-aliasing rules
pppm.c: In function 'convolution':
pppm.c:380: warning: dereferencing type-punned pointer will break strict-aliasing rules
topio.c: In function ?do_top?:
topio.c:275: warning: ?comb? may be used uninitialized in this function
topio.c:597: warning: ?combination_rule? may be used uninitialized in this function
genhydro.c: In function ?add_h?:
genhydro.c:284: warning: ?jj? may be used uninitialized in this function
dlist.c: In function 'mk_dlist':
dlist.c:52: warning: 'atm.minO' may be used uninitialized in this function
hxprops.c: In function 'do_start_end':
hxprops.c:499: warning: 'hstart' may be used uninitialized in this function
hxprops.c:499: warning: 'hend' may be used uninitialized in this function
gmx_analyze.c: In function 'gmx_analyze':
gmx_analyze.c:768: warning: 'nset' may be used uninitialized in this function
gmx_analyze.c:768: warning: 'n' may be used uninitialized in this function
gmx_dipoles.c: In function 'gmx_dipoles':
gmx_dipoles.c:411: warning: 'gkrbin' may be used uninitialized in this function
gmx_h2order.c: In function 'calc_h2order':
gmx_h2order.c:73: warning: 'normal[0]' may be used uninitialized in this function
gmx_h2order.c:73: warning: 'normal[1]' may be used uninitialized in this function
gmx_h2order.c:73: warning: 'normal[2]' may be used uninitialized in this function
gmx_rdf.c: In function 'extract_sq':
gmx_rdf.c:503: warning: dereferencing type-punned pointer will break strict-aliasing rules
gmx_rmsdist.c: In function 'gmx_rmsdist':
gmx_rmsdist.c:544: warning: 'max1_6' may be used uninitialized in this function
gmx_rmsdist.c:544: warning: 'max1_3' may be used uninitialized in this function
eneconv.c: In function ?main?:
eneconv.c:411: warning: ?nremax? may be used uninitialized in this function
eneconv.c:415: warning: ?timestep? may be used uninitialized in this function
eneconv.c:411: warning: ?nset? may be used uninitialized in this function
discopar.c: In function ?disco_slave?:
discopar.c:231: warning: ?xcenter? may be used uninitialized in this function


Is this something that needs to be worried about? Any advice would be much appreciated!

Jo

Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL

(02476) 574623
J.F.Hanna at warwick.ac.uk