[gmx-users] Installation problem on gromacs 3.3.1 during the step make install

[maria goranovic]

Hi,

I am trying to install a serial version of 3.3.1 on my suse 10.2 linux box.
I am attempting this installation on my home directory, and do not have root
access.

I think I have followed all the steps exactly and get an error while doing
the final make install. The final part of the log file is attached below.

PS1: I do use make distclean before each new attempt at ./configure
PS2: my home directory is /people/mail/mariag

Help, please ?

Thank you very much,

-Maria

########################################
....
....
Making install in man1
make[2]: Entering directory `/people/mail/mariag/gromacs-3.3.1/man/man1'
make[3]: Entering directory `/people/mail/mariag/gromacs-3.3.1/man/man1'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/people/mail/mariag/gromacs-3.3.1/man/man1" || mkdir -p --
"/people/mail/mariag/gromacs-3.3.1/man/man1"
 /usr/bin/install -c -m 644 './anadock.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/anadock.1'
/usr/bin/install: `./anadock.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/anadock.1'
are the same file
 /usr/bin/install -c -m 644 './g_cluster.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_cluster.1'
/usr/bin/install: `./g_cluster.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_cluster.1'
are the same file
 /usr/bin/install -c -m 644 './g_filter.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_filter.1'
/usr/bin/install: `./g_filter.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_filter.1'
are the same file
 /usr/bin/install -c -m 644 './g_potential.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_potential.1'
/usr/bin/install: `./g_potential.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_potential.1'
are the same file
 /usr/bin/install -c -m 644 './g_velacc.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_velacc.1'
/usr/bin/install: `./g_velacc.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_velacc.1'
are the same file
 /usr/bin/install -c -m 644 './ngmx.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/ngmx.1'
/usr/bin/install: `./ngmx.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/ngmx.1'
are the same file
 /usr/bin/install -c -m 644 './cdist.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/cdist.1'
/usr/bin/install: `./cdist.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/cdist.1'
are the same file
 /usr/bin/install -c -m 644 './g_clustsize.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_clustsize.1'
/usr/bin/install: `./g_clustsize.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_clustsize.1'
are the same file
 /usr/bin/install -c -m 644 './g_gyrate.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_gyrate.1'
/usr/bin/install: `./g_gyrate.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_gyrate.1'
are the same file
 /usr/bin/install -c -m 644 './g_rama.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_rama.1'
/usr/bin/install: `./g_rama.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_rama.1'
are the same file
 /usr/bin/install -c -m 644 './g_wham.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_wham.1'
/usr/bin/install: `./g_wham.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_wham.1'
are the same file
 /usr/bin/install -c -m 644 './pdb2gmx.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/pdb2gmx.1'
/usr/bin/install: `./pdb2gmx.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/pdb2gmx.1'
are the same file
 /usr/bin/install -c -m 644 './disco.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/disco.1'
/usr/bin/install: `./disco.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/disco.1'
are the same file
 /usr/bin/install -c -m 644 './g_confrms.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_confrms.1'
/usr/bin/install: `./g_confrms.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_confrms.1'
are the same file
 /usr/bin/install -c -m 644 './g_h2order.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_h2order.1'
/usr/bin/install: `./g_h2order.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_h2order.1'
are the same file
 /usr/bin/install -c -m 644 './g_rdf.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_rdf.1'
/usr/bin/install: `./g_rdf.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_rdf.1'
are the same file
 /usr/bin/install -c -m 644 './genbox.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/genbox.1'
/usr/bin/install: `./genbox.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/genbox.1'
are the same file
 /usr/bin/install -c -m 644 './protonate.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/protonate.1'
/usr/bin/install: `./protonate.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/protonate.1'
are the same file
 /usr/bin/install -c -m 644 './do_dssp.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/do_dssp.1'
/usr/bin/install: `./do_dssp.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/do_dssp.1'
are the same file
 /usr/bin/install -c -m 644 './g_covar.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_covar.1'
/usr/bin/install: `./g_covar.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_covar.1'
are the same file
 /usr/bin/install -c -m 644 './g_hbond.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_hbond.1'
/usr/bin/install: `./g_hbond.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_hbond.1'
are the same file
 /usr/bin/install -c -m 644 './g_rms.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_rms.1'
/usr/bin/install: `./g_rms.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_rms.1'
are the same file
 /usr/bin/install -c -m 644 './genconf.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/genconf.1'
/usr/bin/install: `./genconf.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/genconf.1'
are the same file
 /usr/bin/install -c -m 644 './tpbconv.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/tpbconv.1'
/usr/bin/install: `./tpbconv.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/tpbconv.1'
are the same file
 /usr/bin/install -c -m 644 './editconf.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/editconf.1'
/usr/bin/install: `./editconf.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/editconf.1'
are the same file
 /usr/bin/install -c -m 644 './g_density.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_density.1'
/usr/bin/install: `./g_density.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_density.1'
are the same file
 /usr/bin/install -c -m 644 './g_helix.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_helix.1'
/usr/bin/install: `./g_helix.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_helix.1'
are the same file
 /usr/bin/install -c -m 644 './g_rmsdist.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_rmsdist.1'
/usr/bin/install: `./g_rmsdist.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_rmsdist.1'
are the same file
 /usr/bin/install -c -m 644 './genion.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/genion.1'
/usr/bin/install: `./genion.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/genion.1'
are the same file
 /usr/bin/install -c -m 644 './trjcat.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/trjcat.1'
/usr/bin/install: `./trjcat.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/trjcat.1'
are the same file
 /usr/bin/install -c -m 644 './eneconv.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/eneconv.1'
/usr/bin/install: `./eneconv.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/eneconv.1'
are the same file
 /usr/bin/install -c -m 644 './g_dielectric.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_dielectric.1'
/usr/bin/install: `./g_dielectric.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_dielectric.1'
are the same file
 /usr/bin/install -c -m 644 './g_lie.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_lie.1'
/usr/bin/install: `./g_lie.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_lie.1'
are the same file
 /usr/bin/install -c -m 644 './g_rmsf.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_rmsf.1'
/usr/bin/install: `./g_rmsf.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_rmsf.1'
are the same file
 /usr/bin/install -c -m 644 './genpr.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/genpr.1'
/usr/bin/install: `./genpr.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/genpr.1'
are the same file
 /usr/bin/install -c -m 644 './trjconv.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/trjconv.1'
/usr/bin/install: `./trjconv.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/trjconv.1'
are the same file
 /usr/bin/install -c -m 644 './ffscan.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/ffscan.1'
/usr/bin/install: `./ffscan.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/ffscan.1'
are the same file
 /usr/bin/install -c -m 644 './g_dih.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_dih.1'
/usr/bin/install: `./g_dih.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_dih.1'
are the same file
 /usr/bin/install -c -m 644 './g_mdmat.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_mdmat.1'
/usr/bin/install: `./g_mdmat.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_mdmat.1'
are the same file
 /usr/bin/install -c -m 644 './g_rotacf.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_rotacf.1'
/usr/bin/install: `./g_rotacf.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_rotacf.1'
are the same file
 /usr/bin/install -c -m 644 './gmxcheck.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/gmxcheck.1'
/usr/bin/install: `./gmxcheck.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/gmxcheck.1'
are the same file
 /usr/bin/install -c -m 644 './trjorder.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/trjorder.1'
/usr/bin/install: `./trjorder.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/trjorder.1'
are the same file
 /usr/bin/install -c -m 644 './g_anaeig.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_anaeig.1'
/usr/bin/install: `./g_anaeig.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_anaeig.1'
are the same file
 /usr/bin/install -c -m 644 './g_dipoles.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_dipoles.1'
/usr/bin/install: `./g_dipoles.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_dipoles.1'
are the same file
 /usr/bin/install -c -m 644 './g_mindist.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_mindist.1'
/usr/bin/install: `./g_mindist.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_mindist.1'
are the same file
 /usr/bin/install -c -m 644 './g_saltbr.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_saltbr.1'
/usr/bin/install: `./g_saltbr.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_saltbr.1'
are the same file
 /usr/bin/install -c -m 644 './gmxdump.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/gmxdump.1'
/usr/bin/install: `./gmxdump.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/gmxdump.1'
are the same file
 /usr/bin/install -c -m 644 './wheel.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/wheel.1'
/usr/bin/install: `./wheel.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/wheel.1'
are the same file
 /usr/bin/install -c -m 644 './g_analyze.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_analyze.1'
/usr/bin/install: `./g_analyze.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_analyze.1'
are the same file
 /usr/bin/install -c -m 644 './g_disre.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_disre.1'
/usr/bin/install: `./g_disre.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_disre.1'
are the same file
 /usr/bin/install -c -m 644 './g_morph.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_morph.1'
/usr/bin/install: `./g_morph.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_morph.1'
are the same file
 /usr/bin/install -c -m 644 './g_sas.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_sas.1'
/usr/bin/install: `./g_sas.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_sas.1'
are the same file
 /usr/bin/install -c -m 644 './grompp.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/grompp.1'
/usr/bin/install: `./grompp.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/grompp.1'
are the same file
 /usr/bin/install -c -m 644 './x2top.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/x2top.1'
/usr/bin/install: `./x2top.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/x2top.1'
are the same file
 /usr/bin/install -c -m 644 './g_angle.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_angle.1'
/usr/bin/install: `./g_angle.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_angle.1'
are the same file
 /usr/bin/install -c -m 644 './g_dist.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_dist.1'
/usr/bin/install: `./g_dist.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_dist.1'
are the same file
 /usr/bin/install -c -m 644 './g_msd.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_msd.1'
/usr/bin/install: `./g_msd.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_msd.1'
are the same file
 /usr/bin/install -c -m 644 './g_sgangle.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_sgangle.1'
/usr/bin/install: `./g_sgangle.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_sgangle.1'
are the same file
 /usr/bin/install -c -m 644 './highway.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/highway.1'
/usr/bin/install: `./highway.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/highway.1'
are the same file
 /usr/bin/install -c -m 644 './xpm2ps.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/xpm2ps.1'
/usr/bin/install: `./xpm2ps.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/xpm2ps.1'
are the same file
 /usr/bin/install -c -m 644 './g_bond.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_bond.1'
/usr/bin/install: `./g_bond.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_bond.1'
are the same file
 /usr/bin/install -c -m 644 './g_dyndom.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_dyndom.1'
/usr/bin/install: `./g_dyndom.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_dyndom.1'
are the same file
 /usr/bin/install -c -m 644 './g_nmeig.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_nmeig.1'
/usr/bin/install: `./g_nmeig.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_nmeig.1'
are the same file
 /usr/bin/install -c -m 644 './g_sorient.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_sorient.1'
/usr/bin/install: `./g_sorient.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_sorient.1'
are the same file
 /usr/bin/install -c -m 644 './make_ndx.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/make_ndx.1'
/usr/bin/install: `./make_ndx.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/make_ndx.1'
are the same file
 /usr/bin/install -c -m 644 './xrama.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/xrama.1'
/usr/bin/install: `./xrama.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/xrama.1'
are the same file
 /usr/bin/install -c -m 644 './g_bundle.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_bundle.1'
/usr/bin/install: `./g_bundle.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_bundle.1'
are the same file
 /usr/bin/install -c -m 644 './g_enemat.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_enemat.1'
/usr/bin/install: `./g_enemat.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_enemat.1'
are the same file
 /usr/bin/install -c -m 644 './g_nmens.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_nmens.1'
/usr/bin/install: `./g_nmens.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_nmens.1'
are the same file
 /usr/bin/install -c -m 644 './g_tcaf.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_tcaf.1'
/usr/bin/install: `./g_tcaf.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_tcaf.1'
are the same file
 /usr/bin/install -c -m 644 './mdrun.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/mdrun.1'
/usr/bin/install: `./mdrun.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/mdrun.1'
are the same file
 /usr/bin/install -c -m 644 './g_chi.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_chi.1'
/usr/bin/install: `./g_chi.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_chi.1'
are the same file
 /usr/bin/install -c -m 644 './g_energy.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_energy.1'
/usr/bin/install: `./g_energy.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_energy.1'
are the same file
 /usr/bin/install -c -m 644 './g_order.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_order.1'
/usr/bin/install: `./g_order.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_order.1'
are the same file
 /usr/bin/install -c -m 644 './g_traj.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_traj.1'
/usr/bin/install: `./g_traj.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_traj.1'
are the same file
 /usr/bin/install -c -m 644 './mk_angndx.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/mk_angndx.1'
/usr/bin/install: `./mk_angndx.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/mk_angndx.1'
are the same file
 /usr/bin/install -c -m 644 './g_densmap.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/g_densmap.1'
/usr/bin/install: `./g_densmap.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_densmap.1'
are the same file
 /usr/bin/install -c -m 644 './g_sham.1' '/people/mail/mariag/gromacs-3.3.1
/man/man1/g_sham.1'
/usr/bin/install: `./g_sham.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/g_sham.1'
are the same file
 /usr/bin/install -c -m 644 './make_edi.1' '/people/mail/mariag/gromacs-
3.3.1/man/man1/make_edi.1'
/usr/bin/install: `./make_edi.1' and
`/people/mail/mariag/gromacs-3.3.1/man/man1/make_edi.1'
are the same file
make[3]: *** [install-man1] Error 1
make[3]: Leaving directory `/people/mail/mariag/gromacs-3.3.1/man/man1'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/people/mail/mariag/gromacs-3.3.1/man/man1'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/people/mail/mariag/gromacs-3.3.1/man'
make: *** [install-recursive] Error 1
########################################
-- 
Maria G.
Technical University of Denmark
Copenhagen
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