On Sun, Feb 28, 2010 at 10:06 AM, Andreas Goetz <agoetz.sdsc.edu> wrote:
> On a fresh checkout I have following problem with
> gcc 4.4.1 on opensuse 11.2
> dsaup2.f:(.text+0x144): undefined reference to `second_'
> dsaup2.f:(.text+0x338): undefined reference to `second_'
> dsaup2.f:(.text+0x4a2): undefined reference to `second_'
> more undefined references to `second_' follow
> collect2: ld returned 1 exit status
> make[1]: *** [sander] Error 1
> make[1]: Leaving directory `/home/agoetz/TMP/amber11/src/sander'
> make: *** [serial] Error 2
I'm getting the same error on Cygwin (see below). It's good to see
this report though, I was already blaming Cygwin for it...
Gustavo.
==> Error on Cygwin: <===
$ uname -a
CYGWIN_NT-6.0 Delenn 1.7.1(0.218/5/3) 2009-12-07 11:48 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
[...] OK
$ make -f Makefile_at
[...] OK
[AmberTools testing uns OK, with few failures]
$ make serial
[...]
make[2]: Leaving directory
`/cygdrive/c/Users/seabra/Cygwin-home/local/amber11/src/sqm'
gfortran -o sander.exe constants.o memory_module.o stack.o
nose_hoover.o nose_hoover_vars.o nose_hoover_init.o qmmm_module.o
trace.o lmod.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o egb.o
remd.o findmask.o pb_force.o pb_exmol.o pb_mpfrc.o pb_direct.o
pb_lsolver.o pb_nlsolver.o dsvdc.o pb_list.o np_force.o sa_driver.o
relax_mat.o nmr.o multitmd.o multisander.o sander.o trajene.o cshf.o
nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o rdparm.o mdread.o
locmem.o runmd.o getcor.o degcnt.o decnvh.o fastwt.o parallel.o
shake.o ene.o mdwrit.o minrit.o set.o dynlib.o mdfil.o nmlsrc.o
ew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o nonbond_list.o
short_ene.o ew_recip.o pcshift.o align.o csa.o rfree.o rgroup.o
amopen.o debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o
mexit.o new_time.o extra_pts.o thermo_int.o matinv.o assert.o mmtsb.o
mmtsb_client.o erfcfun.o pb_read.o pb_write.o pb_init.o constantph.o
prn_dipoles.o ips.o sglds.o iwrap2.o amoeba_valence.o
amoeba_multipoles.o amoeba_recip.o amoeba_interface.o amoeba_direct.o
amoeba_mdin.o amoeba_adjust.o amoeba_self.o amoeba_vdw.o
amoeba_induced.o amoeba_runmd.o bintraj.o spatial_recip.o
spatial_fft.o parms.o softcore.o mbar.o molecule.o xref.o dssp.o
charmm.o qm_mm.o qm_ewald.o qm2_variable_solvent.o \
pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o cmd_matrix.o
lscivr_vars.o lsc_init.o lsc_xp.o force.o
/home/seabra/local/amber11/lib/libsqm.a \
mt19937.o ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o
ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar-math.o ncsu-colvar-type.o
ncsu-colvar-utils.o ncsu-colvar.o ncsu-constants.o ncsu-cv-ANGLE.o
ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o ncsu-cv-MULTI_RMSD.o
ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o ncsu-cv-R_OF_GYRATION.o
ncsu-cv-TORSION.o ncsu-cv-LCOD.o ncsu-cv-COS_OF_DIHEDRAL.o
ncsu-lexer.o ncsu-parser.o ncsu-pmd-hooks.o ncsu-rmsd.o
ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-smd-hooks.o
ncsu-umbrella.o ncsu-utils.o ncsu-value.o \
/home/seabra/local/amber11/lib/arpack.a
/home/seabra/local/amber11/lib/lapack.a
/home/seabra/local/amber11/lib/blas.a ../lib/nxtsec.o ../lib/sys.a
../netcdf/lib/libnetcdf.a
/home/seabra/local/amber11/lib/arpack.a(dsaupd.o):dsaupd.f:(.text+0x29):
undefined reference to `_second_'
/home/seabra/local/amber11/lib/arpack.a(dsaupd.o):dsaupd.f:(.text+0x3be):
undefined reference to `_second_'
/home/seabra/local/amber11/lib/arpack.a(dsaup2.o):dsaup2.f:(.text+0xde):
undefined reference to `_second_'
/home/seabra/local/amber11/lib/arpack.a(dsaup2.o):dsaup2.f:(.text+0x2a8):
undefined reference to `_second_'
/home/seabra/local/amber11/lib/arpack.a(dsaup2.o):dsaup2.f:(.text+0x3f7):
undefined reference to `_second_'
/home/seabra/local/amber11/lib/arpack.a(dsaup2.o):dsaup2.f:(.text+0x5d8):
more undefined references to `_second_' follow
collect2: ld returned 1 exit status
make[1]: *** [sander.exe] Error 1
make[1]: Leaving directory
`/cygdrive/c/Users/seabra/Cygwin-home/local/amber11/src/sander'
make: *** [serial] Error
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Received on Sun Feb 28 2010 - 06:00:11 PST
