On a fresh checkout I have following problem with
gcc 4.4.1 on opensuse 11.2
cd $AMBERHOME/src
./configure gnu
make -f Makefile_at
[...]
make
[...]
ranlib libsqm.a
mv libsqm.a /home/agoetz/TMP/amber11/lib
make[2]: Leaving directory `/home/agoetz/TMP/amber11/src/sqm'
gfortran -o sander 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/agoetz/TMP/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/agoetz/TMP/amber11/lib/arpack.a
/home/agoetz/TMP/amber11/lib/lapack.a
/home/agoetz/TMP/amber11/lib/blas.a ../lib/nxtsec.o ../lib/sys.a
../netcdf/lib/libnetcdf.a
/home/agoetz/TMP/amber11/lib/arpack.a(dsaupd.o): In function `dsaupd_':
dsaupd.f:(.text+0x29d): undefined reference to `second_'
dsaupd.f:(.text+0x4df): undefined reference to `second_'
/home/agoetz/TMP/amber11/lib/arpack.a(dsaup2.o): In function `dsaup2_':
dsaup2.f:(.text+0x144): undefined reference to `second_'
dsaup2.f:(.text+0x338): undefined reference to `second_'
dsaup2.f:(.text+0x4a2): undefined reference to `second_'
/home/agoetz/TMP/amber11/lib/arpack.a(dsaup2.o):dsaup2.f:(.text+0x6a0):
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 have no idea where the object second_ should be. Quick fix for me to
continue working is to switch back to carpack/f2c. But this should be fixed.
All the best,
Andy
--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Sun Feb 28 2010 - 05:30:02 PST
