[AMBER] Error when compile ambertools15

From: amber amber <amberfmg.gmail.com>
Date: Thu, 7 May 2015 14:11:43 +0200

Dead Jason,

We tried that option, but didn't work. We have found that the problem is on
shared x64 libraries

We have modified the config.h in the C and C++ flag lines, adding the
option -mcmodel=large

$(AMBERBUILDFLAGS) -mcmodel=large
CXXOPTFLAGS=-fPIC -O3 -mcmodel=large

The reference about the problem is here:


Now the installation works perfectly!


> On Wed, 2015-05-06 at 13:32 +0200, amber amber wrote:
> 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
> 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
> 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_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_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_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/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
> 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?

Ack. The libraries need to get rebuilt (since AmberTools 14 did not
compile with -fPIC). Try the following commands:

make distclean

Then reconfigure and rebuild.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu May 07 2015 - 05:30:03 PDT
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