Thank you everyone. We fixed the issue.
On Sun, 5 Aug 2018, 11:33 Kevin Keane (USD), <kkeane.sandiego.edu> wrote:
> I notice that according to your log, ld is in /usr/local/bin. That’s a
> very unusual location for a system program like that. Did your IT team
> maybe try to build your own tool chain? If so, that’s something I rarely
> recommend, unless you are trying to cross-compile – using the compilers
> from your operating system vendor is usually more reliable.
>
> Or is this another program that just happens to also be called ld?
>
> Sent from Mail for Windows 10
>
> From: maryam azimzadehirani
> Sent: Saturday, August 4, 2018 3:35 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Error for Amber16 and Amber tools 17 installation
>
> Dear Josh,
> Thank you for your reply. We tried to solve the issue. We are currently
> getting this error:
>
> r - getopts_c.o
> r - bspline.o
> r - fftw3.o
> ranlib /share/apps/Amber/amber16//lib/librism.a
> make[3]: Leaving directory `/share/apps/Amber/amber16/AmberTools/src/rism'
> gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> -DHASBZ2 -D__PLUMED_HAS_DLOPEN \
> -o Plumed.o Plumed.c
> gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I../pbsa -I../sqm -I../rism
> -I../../../include -I/share/apps/Amber/amber16//include
> -I/share/apps/Amber/amber16//include -o
> /share/apps/Amber/amber16//bin/sander 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 multisander.o sander.o trajene.o cshf.o
> nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o rdparm.o sander_lib.o
> mdread.o locmem.o runmd.o relaxmd.o quench.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 pol_gauss.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_bndpol.o ew_dipole_recip.o mexit.o new_time.o extra_pts.o thermo_int.o
> matinv.o assert.o erfcfun.o sinr_t.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.o crg_reloc.o
> amd.o scaledMD.o barostats.o random.o les.o abfqmmm_module.o qm_mm.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_mrcc_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/share/apps/Amber/amber16//lib -lsqm \
> nfe-abmd-hooks.o nfe-bbmd-ctxt.o nfe-bbmd-hooks.o nfe-colvar.o
> nfe-colvar-math.o nfe-colvar-type.o nfe-colvar-utils.o nfe-constants.o
> nfe-cv-ANGLE.o nfe-cv-COM_ANGLE.o nfe-cv-COM_DISTANCE.o
> nfe-cv-COM_TORSION.o nfe-cv-COS_OF_DIHEDRAL.o nfe-cv-DISTANCE.o
> nfe-cv-HANDEDNESS.o nfe-cv-LCOD.o nfe-cv-MULTI_RMSD.o nfe-cv-N_OF_BONDS.o
> nfe-cv-N_OF_STRUCTURES.o nfe-cv-R_OF_GYRATION.o nfe-cv-TORSION.o
> nfe-pmd-hooks.o nfe-rmsd.o nfe-sander-hooks.o nfe-sander-proxy.o
> nfe-stsm-hooks.o nfe-cv-PCA.o nfe-read-pca.o nfe-cv-SIN_OF_DIHEDRAL.o
> nfe-cv-PAIR_DIHEDRAL.o nfe-cv-PATTERN_DIHEDRAL.o nfe-cv-DF_COM_DISTANCE.o
> nfe-smd-hooks.o nfe-umbrella.o nfe-utils.o nfe-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 /share/apps/Amber/amber16//lib/libemil.a -lstdc++ \
> ../sebomd/sebomd.a \
> ../lib/sys.a /share/apps/Amber/amber16//lib/libnetcdff.a
> /share/apps/Amber/amber16//lib/libnetcdf.a \
> -lrism /share/apps/Amber/amber16//lib/libfftw3.a -larpack -llapack -lblas
> -lxblas-amb \
> Plumed.o -ldl -Wl,-export-dynamic
> collect2: ld terminated with signal 11 [Segmentation fault]
> /usr/local/bin/ld: make[2]: *** [/share/apps/Amber/amber16//bin/sander]
> Error 1
> make[2]: Leaving directory
> `/share/apps/Amber/amber16/AmberTools/src/sander'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/share/apps/Amber/amber16/AmberTools/src'
> make: *** [install] Error 2
>
>
>
> Thank you very much
>
> On Sat, Aug 4, 2018 at 12:04 AM, Josh Berryman <
> the.real.josh.berryman.gmail.com> wrote:
>
> > if "gzopen64" is missing then that would seem to indicate that you are
> > missing basic system libraries for file compression, probably called zlib
> > or libz.
> >
> > The fix for this depends on your OS, most systems should have this stuff
> by
> > default, or at least make it easily available.
> >
> >
> > On 3 August 2018 at 14:16, maryam azimzadehirani <maryamai1988.gmail.com
> >
> > wrote:
> >
> > > Dear Amber users,
> > > We are trying to install Amber16 with Amber tools 17. I have recieved a
> > > list of errors from the IT person in the lab (attached here). Can you
> > > please give us a hint on what is wrong? None of us installed amber
> > before.
> > > We are only users.
> > > Thank you very much in advance
> > > Maryam
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> *Maryam Azimzadeh Irani*
>
>
> *PhD in Computational Structural Biology *
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 07 2018 - 06:00:02 PDT
