On May 7, 2014, at 4:32 AM, M. Reza Ganjalikhany <ganjalikhany.gmail.com> wrote:
> Dear Amber Users,
>
> I got the following error while I was installing parallel amber12 +
> ambertools13 with MPICH2 3.0.4 on ubuntu 14.04 x86_64. Configuration step
> passed successfully but the error appeared during the installation:
>
> ./configure -mpi gnu
> Checking for updates...
> Checking for available patches online. This may take a few seconds...
>
> Available AmberTools 13 patches:
>
> No patches available
>
> Available Amber 12 patches:
>
> No patches available
> Searching for python2... Found python2.7: /usr/bin/python2.7
>
> Obtaining the gnu suite version:
> gcc -v
> The version is 4.8.2
>
> Testing the gcc compiler:
> gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> testp.c
> OK
>
> Testing the gfortran compiler:
> gfortran -O0 -o testp testp.f
> OK
>
> Testing mixed C/Fortran compilation:
> gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o
> testp.c.o testp.c
> gfortran -O0 -c -o testp.f.o testp.f
> gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> testp.c.o testp.f.o -lgfortran -w
> OK
>
> Testing pointer size:
> gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o
> test_pointer_size test_pointer_size.c
> Detected 64 bit operating system.
>
> Testing flex: OK
> Testing Amber's NetCDF... OK.
>
> Checking for zlib: OK
>
> Checking for libbz2: OK
>
> Configuring fftw-3.3 (may be time-consuming)...
>
> fftw-3.3 configure succeeded.
>
> Configuring XBLAS (may be time-consuming)...
>
> XBLAS configure succeeded.
>
> Configuring MTK++ (may be time-consuming)...
>
> MTK++-0.2.0 configure succeeded.
>
> The configuration file, config.h, was successfully created.
>
> The next step is to type 'make install'
>
> Cleaning the src directories. This may take a few moments.
> Configure complete.
>
>
>
> make install:
> .
> .
> .
>
> (cd cifparse && make install )
> make[2]: Entering directory `/opt/amber12/AmberTools/src/cifparse'
> flex -t cifparse.l | sed 's/yy/cifp/g' > lex.cif.c
> /opt/amber12/bin/yacc -v -d cifparse.y
> sed 's/yy/cifp/g' < y.tab.c > cifp.tab.c
> sed 's/yy/cifp/g' < y.tab.h > cifp.tab.h
> rm -f y.tab.c y.tab.h
> mpicc -c -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> -DHASGZ -DHASBZ2 -DMPI lex.cif.c
> mpicc -c -Dflex -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI cifp.tab.c
> mpicc -c -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> -DHASGZ -DHASBZ2 -DMPI cifparse.c
> cifparse.c: In function ‘ndb_cif_print_item_value’:
> cifparse.c:180:7: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(fp, null_char);
> ^
> cifparse.c: In function ‘ndb_cif_print_formatted_item_value’:
> cifparse.c:422:2: warning: embedded ‘\0’ in format [-Wformat-contains-nul]
> sprintf(tmpstring, " %s\0", value);
> ^
> cifparse.c:428:2: warning: embedded ‘\0’ in format [-Wformat-contains-nul]
> sprintf(tmpstring, " \'%s\'\0", value);
> ^
> cifparse.c:430:2: warning: embedded ‘\0’ in format [-Wformat-contains-nul]
> sprintf(tmpstring, "\'%s\'\0", value);
> ^
> cc1: some warnings being treated as errors
I can't reproduce these problems. The failures is being caused because somewhere the compiler flag "-Werror=format-security" is being used which translates what used to be a simple warning into a hard compiler error. I suspect this is done implicitly by the "mpicc" compiler wrapper.
What do you get when you run the command:
mpicc -show
? Do you see -Werror=format-security in the listing of flags there?
This may be something we want to 'fix' (although cifparse is not a library that any developer wrote)...
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 07 2014 - 05:30:02 PDT
