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 *
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Received on Sun Aug 05 2018 - 00:30:02 PDT
