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 Sat Aug 04 2018 - 03:30:03 PDT
