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
make[2]: *** [cifparse.o] Error 1
make[2]: Leaving directory `/opt/amber12/AmberTools/src/cifparse'
make[1]: *** [parallel] Error 2
make[1]: Leaving directory `/opt/amber12/AmberTools/src'
make: *** [install] Error 2
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Received on Wed May 07 2014 - 02:00:02 PDT
