[gmx-developers] pedantic change to gmx_chi.c (3.3.1) suggested

[David van der Spoel]

chris.neale at utoronto.ca wrote:
> The following change to the source code of 3.3.1 gmx_chi.c was required 
> on a new machine on which I have recently compiled the code. I believe 
> that the error here is in a perl script that the sysadmin has written to 
> wrap 'cc' for equivalent usage on different architectures. In any event 
> the change to the source code should not hurt gromacs and may avoid a 
> similar problem in the future for other users. I do realize that it 
> makes no sense that this affects compilation. The difference is removal 
> of a double semicolon in the first line and removal of a space before 
> the semicolon in the second line. I am not sure which one didn't react 
> well with the in-house 'cc' perl script.

The double semicolon had already been removed from the CVS versions. The 
space shouldn't make a difference. Thanks for reporting.

> 
> $ diff tools/gmx_chi_original.c tools/gmx_chi.c
> 1030,1031c1030,1031
> <   static bool 
> bNormHisto=TRUE,bChiProduct=FALSE,bHChi=FALSE,bRAD=FALSE,bPBC=TRUE;;
> <   static real core_frac=0.5 ;
> ---
>>   static bool 
>> bNormHisto=TRUE,bChiProduct=FALSE,bHChi=FALSE,bRAD=FALSE,bPBC=TRUE;
>>   static real core_frac=0.5;
> 
> Here is the last few lines of output from the make install command 
> before I made the change:
> 
> ...
> 
> Making install in tools
> make[2]: Entering directory `/home/cneale/exe/gromacs-3.3.1/src/tools'
> source='gmx_chi.c' object='gmx_chi.lo' libtool=yes \
> DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
> /bin/sh ../../libtool --tag=CC --mode=compile ccc -DHAVE_CONFIG_H -I. 
> -I. -I../../src -I/usr/X11R6/include  -I../../include 
> -DGMXLIBDIR=\"/home/cneale/exe/gromacs-3.3.1/exec/share/top\" 
> -I/home/cneale/exe/fftw-3.1.2/exec/include  -std1 -fast -O4 -no_ifo 
> -arch ev6 -unroll 2 -fp_reorder -c -o gmx_chi.lo gmx_chi.c
>  ccc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include 
> -I../../include 
> -DGMXLIBDIR=\"/home/cneale/exe/gromacs-3.3.1/exec/share/top\" 
> -I/home/cneale/exe/fftw-3.1.2/exec/include -std1 -fast -O4 -no_ifo -arch 
> ev6 -unroll 2 -fp_reorder -c gmx_chi.c -o gmx_chi.o
> cc: Error: gmx_chi.c, line 1031: Invalid statement. (badstmt)
>   static real core_frac=0.5 ;
> --^
> cc: Error: gmx_chi.c, line 1032: Missing ";". (nosemi)
>   t_pargs pa[] = {
> ----------^
> cc: Error: gmx_chi.c, line 1033: Invalid expression. (badexpr)
>     { "-r0",  FALSE, etINT, {&r0},
> ----------------------------^
> 
> ...
> 
> #####
> 
> Manufacturer: Compaq
> Operating system: Red Hat Linux 7.2
> Interconnect: Quadrics Elan3
> 
> $ gcc --version
> 2.96
> $ f77 --version
> 2.96
> 
> $which cc
> /opt/compile/bin/cc
> $ ls -l /opt/compile/bin/cc
> lrwxrwxrwx    1 root     root            7 Mar  7  2007 
> /opt/compile/bin/cc -> compile
> $ ls -l /opt/compile/bin/compile
> -rwxr-xr-x    1 root     root        13153 Mar  7  2007 
> /opt/compile/bin/compile
> 
> compile is a perl script written in-house by the maintainers of our cluster
> 
> $head -30 compile
> #!/usr/bin/perl
> #
> # wrapper to do several things:
> #       - arrange for sensible defaults, since users often forget -O
> #       - optionally log compiler usage (timestamp, user, flags)
> #       - hide ugly library stuff, especially MPI
> #       - address these across different langs, systems, compilers, MPI's.
> # the goal is to make it possible for a user to compile everywhere
> # without changing their makefile/etc, using the obvious switches.
> # they could put all this intelligence in the makefile, and we could
> # factor the intelligence into a system-specific make include,
> # but putting it in one place and using perl is more powerful.
> #
> # records each invocation to syslog.  it is installed with several
> # aliases (symlinks in the bin directory) to make it run whenever someone
> # uses a generic cc/c++/f77/f90/mpicc/etc command.
> #
> # written by XXXXXXX--hidden by C. Neale (without premission)-XXXXX
> #
> 
> use strict;
> use User::pwent;
> use Sys::Syslog;
> use Pod::Usage;
> 
> =head1 NAME
> 
>     compile - compile, with intelligence about language, mpi, etc.
> 
> =head1 SYNOPSIS
> 
> 
> 
> Thanks,
> Chris.
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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