One note that has escaped me. Before, I didn't test AT before trying
to compile amber. Now, when testing AT, I get plenty of errors related
to the multiple definition of _csqrt during NAB testing, like the
following:
test$ ./test_at_serial.sh
[...]
=====================================================
Running test to compute Langevin modes:
/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
/home/seabra/local/amber/amber11/lib/libnab.a(newton.o):newton.c:(.text+0xd50):
undefined reference to `_dposv_'
collect2: ld returned 1 exit status
cc failed!
make[1]: *** [nmode3_test] Error 1
=====================================================
[...]
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7450 Ext. 5021
On Mon, Mar 1, 2010 at 3:18 PM, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
> 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?
>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon Mar 01 2010 - 11:00:03 PST
