[gmx-users] gromacs-localp-3.0.2 local pressure installation

Mon Jul 26 00:58:34 CEST 2010

kambiz yaghmaei wrote:
> Hi all
> 
>  
> 
> I tried to install "gromacs-localp-3.0.2" on Fedora 11.
> 
> First, I successfully run ./configure:
> 
>  
> 
> …………………………………………………………………………………………..
> 
> …………………………………………………………………………………………..
> 
> config.status: creating man/Makefile
> 
> config.status: creating man/man1/Makefile
> 
> config.status: creating src/config.h
> 
>  
> 
> GROMACS / LOCALPRESSURE is ready to compile.
> 
>  
> 
> * Binaries and libraries for this host will be installed in
> 
>     /usr/local/gromacs-localp/i686-pc-linux-gnu/bin
> 
>     /usr/local/gromacs-localp/i686-pc-linux-gnu/lib
> 
>   and shared data will placed in
> 
>     /usr/local/gromacs-localp/share
> 
>   (You can set this with --prefix, --exec-prefix and --datadir)
> 
>  
> 
> * You are compiling a double precision version of the package -
> 
>   program names will be suffixed with _d to avoid overwriting single
> 
>   precision files. You can override it with --program-suffix
> 
>  
> 
>  
> 
>  
> 
> But after making make-distclean followed by make command,
> 
> I am facing this error message:
> 

Running "make distclean" prior to "make" is likely not the sequence of commands 
you want.  See the following for general installation instructions:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions

-Justin

>  
> 
>  
> 
> ……………………………………………………………………………………………………….
> 
> ………………………………………………………………………………………………………
> 
> cc -DHAVE_CONFIG_H -I. -I. -I../../src  -I../../include 
> -DGMXLIBDIR=\"/usr/local/gromacs-localp/share/top\"   -O6 
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double 
> -funroll-all-loops -o mkinl mkinl.o mkinl_declarations.o 
> mkinl_outerloop.o mkinl_innerloop.o mkinl_calcdist.o mkinl_invsqrt.o 
> mkinl_recip.o mkinl_interactions.o metacode.o
> 
> ./mkinl c
> 
>> >> This is the GROMACS innerloop code generator
> 
>> >> It will generate double precision C code in file innerc.c
> 
>> >> Using gromacs invsqrt code
> 
>> >> Inlining gromacs invsqrt and/or reciprocal code
> 
>> >> Using normal solvent optimized loops
> 
>> >> Prefetching coordinates in loops: none
> 
>> >> Prefetching forces in loops: none
> 
>> >> Nonthreaded inner loops
> 
>> >> Vectorizing invsqrt in loops:none
> 
>  
> 
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>> >> Generated 29303 lines of code in 78 functions
> 
> (innerc.c may take a while to compile)
> 
>  
> 
> source='innerc.c' object='innerc.lo' libtool=yes \
> 
>      depfile='.deps/innerc.Plo' tmpdepfile='.deps/innerc.TPlo' \
> 
>      depmode=gcc3 /bin/sh ../../config/depcomp \
> 
>      /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. 
> -I../../src  -I../../include 
> -DGMXLIBDIR=\"/usr/local/gromacs-localp/share/top\"   -O6 
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double 
> -funroll-all-loops -c -o innerc.lo `test -f innerc.c || echo './'`innerc.c
> 
> cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include 
> -DGMXLIBDIR=\"/usr/local/gromacs-localp/share/top\" -O6 
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double 
> -funroll-all-loops -c innerc.c -MT innerc.lo -MD -MP -MF 
> .deps/innerc.TPlo -o innerc.o
> 
> In file included from ../../include/typedefs.h:53,
> 
>                  from innerc.c:8:
> 
> ../../include/sysstuff.h:46:2: warning: #ident is a deprecated GCC 
> extension
> 
> In file included from ../../include/types/graph.h:40,
> 
>                  from ../../include/typedefs.h:66,
> 
>                  from innerc.c:8:
> 
> ../../include/fatal.h:46:2: warning: #ident is a deprecated GCC extension
> 
> In file included from ../../include/vec.h:100,
> 
>                  from innerc.c:10:
> 
> ../../include/maths.h:46:2: warning: #ident is a deprecated GCC extension
> 
> In file included from ../../include/vec.h:103,
> 
>                  from innerc.c:10:
> 
> ../../include/macros.h:46:2: warning: #ident is a deprecated GCC extension
> 
> innerc.c:25018:7: error: invalid suffix "a" on integer constant
> 
> innerc.c: In function 'inl3302':
> 
> innerc.c:25018: error: expected ';' before ')' token
> 
> innerc.c:25018: error: expected statement before ')' token
> 
> innerc.c:25018: error: expected expression before '=' token
> 
> innerc.c:27591:7: error: invalid suffix "a" on integer constant
> 
> innerc.c: In function 'inl3402':
> 
> innerc.c:27591: error: expected ';' before ')' token
> 
> innerc.c:27591: error: expected statement before ')' token
> 
> innerc.c:27591: error: expected expression before '=' token
> 
> make[3]: *** [innerc.lo] Error 1
> 
> make[3]: Leaving directory `/home/Yaghmaei/gromacs-localp-3.0.2/src/gmxlib'
> 
> make[2]: *** [all-recursive] Error 1
> 
> make[2]: Leaving directory `/home/Yaghmaei/gromacs-localp-3.0.2/src'
> 
> make[1]: *** [all] Error 2
> 
> make[1]: Leaving directory `/home/Yaghmaei/gromacs-localp-3.0.2/src'
> 
> make: *** [all-recursive] Error 1
> 
>  
> 
>  
> 
> Could anybody help me ??
> 
> Kambiz
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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