Dear amber users,
I updated to ambertools 15 without problem. The configuration is ok
according to the information obtained from ./configure gnu.
However, when I perform the compilation, I get the following error:
gfortran -shared -DBINTRAJ -DEMIL -fPIC -ffree-form -I../pbsa -I../sqm
-I../rism -I../../../include -I/usr/local/src/amber14//include
-I/usr/local/src/amber14//include -o
/usr/local/src/amber14//lib/libsander.so file_io_dat.o constants.o state.o
memory_module.o stack.o nose_hoover.o nose_hoover_init.o trace.o rmsgrd.o
lmod.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o egb.o remd.o findmask.o
relax_mat.o nmr.o multitmd.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o
printe.o runmin.o rdparm.API.o cpparm.o sander_lib.o mdread.o locmem.o
runmd.o getcor.o degcnt.o decnvh.o fastwt.API.o parallel.o shake.o ene.o
mdwrit.o minrit.o set.API.o dynlib.API.o mdfil.o nmlsrc.o ew_force.o
ew_setup.API.o ew_box.API.o ew_bspline.o ew_fft.o nonbond_list.API.o
short_ene.o ew_recip.o pcshift.o align.o csa.o rfree.o rgroup.o amopen.o
debug.API.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o mexit.o
new_time.API.o extra_pts.API.o thermo_int.o les.o matinv.o assert.o
erfcfun.o constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o emil.o
mdin_emil_dat.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
../rism/amber_rism_interface.SANDER.o AmberNetcdf.o bintraj.o binrestart.o
spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o
molecule.o xref.o dssp.o charmm.API.o crg_reloc.o amd.o scaledMD.o
barostats.o interface.o random.o qm_mm.API.o prmtop_type.o \
abfqmmm_module.o qm_ewald.o qmmm_vsolv.o qm2_extern_util_module.o
qm2_extern_module.o qm2_extern_adf_module.o qm2_read_adf_results.o
KFReader.o ArrayList.o qm2_extern_gms_module.o qm2_extern_tc_module.o
qm2_extern_gau_module.o qm2_extern_orc_module.o qm2_extern_nw_module.o
qm2_extern_qc_module.o qm2_extern_genmpi_module.o qmmm_adaptive_module.o
prn_qmmm_dipole.o sebomd_module.o sebomd_arrays.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 \
-L/usr/local/src/amber14//lib -lsqm \
ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o
ncsu-colvar.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o
ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-COM_ANGLE.o ncsu-cv-COM_DISTANCE.o
ncsu-cv-COM_TORSION.o ncsu-cv-COS_OF_DIHEDRAL.o ncsu-cv-DISTANCE.o
ncsu-cv-HANDEDNESS.o ncsu-cv-LCOD.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-lexer.o ncsu-parser.o ncsu-pmd-hooks.o ncsu-rmsd.o
ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-cv-PCA.o ncsu-read-pca.o
ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o mt19937.o
xray_fourier.o xray_globals.o xray_interface.o xray_real_space.o
xray_reciprocal_space.o xray_utils.o \
-lFpbsa ../lib/nxtsec.o /usr/local/src/amber14//lib/libemil.a
-lstdc++ \
../sebomd/sebomd.a \
../lib/sys.a /usr/local/src/amber14//lib/libnetcdff.a
/usr/local/src/amber14//lib/libnetcdf.a \
-lrism -lfftw3 -larpack -llapack -lblas -lxblas-amb \
Plumed.o -ldl -Wl,-export-dynamic
/usr/lib64/gcc/x86_64-slackware-linux/4.8.2/../../../../x86_64-slackware-linux/bin/ld:
/usr/local/src/amber14//lib/libnetcdff.a(fort-attio.o): relocation
R_X86_64_PC32 against undefined symbol `strlen..GLIBC_2.2.5' can not be
used when making a shared object; recompile with -fPIC
/usr/lib64/gcc/x86_64-slackware-linux/4.8.2/../../../../x86_64-slackware-linux/bin/ld:
link finale non riuscito: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [/usr/local/src/amber14//lib/libsander.so] Errore 1
make[2]: Leaving directory `/usr/local/src/amber14/AmberTools/src/sander'
make[1]: *** [serial] Errore 2
make[1]: Leaving directory `/usr/local/src/amber14/AmberTools/src'
make: *** [install] Errore 2
Some idea?
Thanks
Fernando
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Received on Wed May 06 2015 - 05:00:03 PDT
