OK, now that the issue with "second" is over, I can reproduce the same
error here:
$ uname -a
CYGWIN_NT-6.0 Home-Desktop 1.7.0(0.218/5/3) 2009-12-04 17:08 i686 Cygwin
$ gfortran -v
Using built-in specs.
Target: i686-pc-cygwin
Configured with:
/gnu/gcc/releases/packaging/4.3.4-3/gcc4-4.3.4-3/src/gcc-4.3.4/configure
--srcdir=/gnu/gcc/releases/packaging/4.3.4-3/gcc4-4.3.4-3/src/gcc-4.3.4
--prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin
--libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var
--sysconfdir=/etc --infodir=/usr/share/info --mandir=/usr/share/man
--datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man
-v --with-gmp=/usr --with-mpfr=/usr --enable-bootstrap
--enable-version-specific-runtime-libs --with-slibdir=/usr/bin
--libexecdir=/usr/lib --enable-static --enable-shared
--enable-shared-libgcc --disable-__cxa_atexit --with-gnu-ld
--with-gnu-as --with-dwarf2 --disable-sjlj-exceptions
--enable-languages=ada,c,c++,fortran,java,objc,obj-c++
--disable-symvers --enable-libjava --program-suffix=-4
--enable-libgomp --enable-libssp --enable-libada
--enable-threads=posix --with-arch=i686 --with-tune=generic
--enable-libgcj-sublibs CC=gcc-4 CXX=g++-4 CC_FOR_TARGET=gcc-4
CXX_FOR_TARGET=g++-4 GNATMAKE_FOR_TARGET=gnatmake
GNATBIND_FOR_TARGET=gnatbind AS=/opt/gcc-tools/bin/as.exe
AS_FOR_TARGET=/opt/gcc-tools/bin/as.exe LD=/opt/gcc-tools/bin/ld.exe
LD_FOR_TARGET=/opt/gcc-tools/bin/ld.exe
--with-ecj-jar=/usr/share/java/ecj.jar
Thread model: posix
gcc version 4.3.4 20090804 (release) 1 (GCC)
$ ./configure -cygwin gnu
[...]
$ make -f Makefile_at
[...]
$ make serial
[...]
cd mm_pbsa && make install
make[1]: Entering directory
`/cygdrive/c/Users/seabra/cygwin-home/local/amber/amber11/src/mm_pbsa'
gfortran -O0 -c -o make_crd_hg.o make_crd_hg.f
gfortran -o make_crd_hg.exe make_crd_hg.o ../lib/amopen.o ../lib/mexit.o
/home/seabra/local/amber/amber11/bin/nab -o mm_pbsa_nabnmode
mm_pbsa_nabnmode.nab
/home/seabra/local/amber/amber11/lib/libmc.a(cmplx.o):cmplx.c:(.text+0x592):
multiple definition of `_csqrt'
/usr/lib/gcc/i686-pc-cygwin/4.3.4/libgfortran.dll.a(d000775.o):(.text+0x0):
first defined here
collect2: ld returned 1 exit status
cc failed!
make[1]: *** [mm_pbsa_nabnmode.exe] Error 1
make[1]: Leaving directory
`/cygdrive/c/Users/seabra/cygwin-home/local/amber/amber11/src/mm_pbsa'
make: *** [serial] Error 2
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7450 Ext. 5021
On Sat, Feb 27, 2010 at 12:42 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Feb 27, 2010, Daniel Roe wrote:
>>
>> Compilers: gcc (GCC) 4.3.4 20090804 (release) 1, GNU Fortran (GCC) 4.3.4
>> 20090804 (release) 1
>> System: CYGWIN_NT-5.1 mojyt 1.7.1(0.218/5/3) 2009-12-07 11:48 i686 Cygwin
>> CVS Checkout Time: 2010-02-26 13:36
>
> Good: you can be our cygwin person.
>
>> Configure command: ./configure -cygwin -noX11 -nosleap gnu
>
> Do xleap and sleap not work??
>
>
>> /home/Dan/Amber/CVS/amber11/lib/libmc.a(cmplx.o):cmplx.c:(.text+0x592):
>> multiple definition of `_csqrt'
>
> You need to prevent cygwin compiling libmc.a. Go to line 669 of configure
> and have all platforms set c9xcomplex='skip'; i.e. comment out the "else"
> block there. That may break Langevin modes, however, but it's worth a try.
>
> ...dac
>
> p.s.: any grapevine news on NEB integration into Amber11?
>
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Mon Mar 01 2010 - 10:30:05 PST
