[gmx-users] Gromacs 4.5.5

Emmanuel, Alaina A.E.Emmanuel at warwick.ac.uk
Mon Jun 17 11:55:06 CEST 2013 

Thank you Mark.


Sent from my Ultrafast Samsung Galaxy S4 on Three



-------- Original message --------
From: Mark Abraham <mark.j.abraham at gmail.com>
Date: 17/06/2013 08:02 (GMT+00:00)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Gromacs 4.5.5


On Jun 16, 2013 7:58 PM, "Emmanuel, Alaina" <A.E.Emmanuel at warwick.ac.uk>
wrote:
>
> Dear All,
>
> I've had to re-install my gromacs on my computer and I'm having issues
getting past the "Making all in Man7" during the "make" stage.

There is no error in the output you show. Grepping for "error" doesn't
really help when there is a tool called g_pme_error.

I think you are misunderstanding your instruction to your shell to run make
in a background process. By design, that does not explicitly tell you that
make had finished correctly.

Mark

> Below (at the end) are 2 copies of different outputs I get during my
installation. The first copy is from the "make.log" file. The second copy
is from typing "grep -i error make.log".
>
> The stages that I have followed so far are:
>
> 1) tar -xvf gromacs-4.5.5.tar.gz
> 2) cd gromacs-4.5.5
> 3) ./configure --prefix=/home/user/name/gromacs --disable-float
> 4) make > make.log &
> 5) grep -i error make.log
>
> If I delete the "man7" folder in the second stage, I have no problem
completing the installation of gromacs. Unfourtunately this means that I am
only able to use about half of the g_analysis_tools available.  In addition
to this I'm only able to use them whilst in the same directory.
>
>
> Output from "make > make.log"
>
> make[3]: Leaving directory
`/home/chem/msrhcf/gromacs-4.5.5/share/template'
> make[2]: Leaving directory
`/home/chem/msrhcf/gromacs-4.5.5/share/template'
> Making all in html
> make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/share/html'
> Making all in .
> make[3]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/share/html'
> make[3]: Nothing to be done for `all-am'.
> make[3]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share/html'
> Making all in images
> make[3]: Entering directory
`/home/chem/msrhcf/gromacs-4.5.5/share/html/images'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory
`/home/chem/msrhcf/gromacs-4.5.5/share/html/images'
> Making all in online
> make[3]: Entering directory
`/home/chem/msrhcf/gromacs-4.5.5/share/html/online'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory
`/home/chem/msrhcf/gromacs-4.5.5/share/html/online'
> make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share/html'
> make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/share'
> make[2]: Nothing to be done for `all-am'.
> make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share'
> make[1]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share'
> Making all in man
> make[1]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/man'
> Making all in man1
> make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/man/man1'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/man/man1'
> Making all in man7
> make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/man/man7'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/man/man7'
> make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/man'
> make[2]: Nothing to be done for `all-am'.
> make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/man'
> make[1]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/man'
> make[1]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5'
> make[1]: Nothing to be done for `all-am'.
> make[1]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5'
>
>
> Lengthy output for "grep -i error make.log":
>
> /bin/sh ../../libtool --tag=CC   --mode=compile cc  -DHAVE_CONFIG_H -I.
-I../../src -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/home/chem/msrhcf/gromacs_from455/share/top\"   -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -pthread -I./include -MT gmx_pme_error.lo -MD
-MP -MF .deps/gmx_pme_error.Tpo -c -o gmx_pme_error.lo gmx_pme_error.c
>  cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
-I../../include -DGMXLIBDIR=\"/home/chem/msrhcf/gromacs_from455/share/top\"
-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -pthread -I./include -MT gmx_pme_error.lo -MD
-MP -MF .deps/gmx_pme_error.Tpo -c gmx_pme_error.c  -fPIC -DPIC -o
.libs/gmx_pme_error.o
>  cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
-I../../include -DGMXLIBDIR=\"/home/chem/msrhcf/gromacs_from455/share/top\"
-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -pthread -I./include -MT gmx_pme_error.lo -MD
-MP -MF .deps/gmx_pme_error.Tpo -c gmx_pme_error.c -o gmx_pme_error.o
>/dev/null 2>&1
> mv -f .deps/gmx_pme_error.Tpo .deps/gmx_pme_error.Plo
> /bin/sh ../../libtool --tag=CC   --mode=link cc   -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -pthread -I./include -no-undefined
-version-info 6:0:0   -o libgmxana_d.la -rpath
/home/chem/msrhcf/gromacs_from455/lib geminate.lo autocorr.lo expfit.lo
polynomials.lo levenmar.lo anadih.lo pp2shift.lo dlist.lo eigio.lo cmat.lo
eigensolver.lo nsc.lo hxprops.lo fitahx.lo gmx_analyze.lo gmx_anaeig.lo
gmx_bar.lo gmx_angle.lo gmx_bond.lo gmx_bundle.lo gmx_chi.lo gmx_cluster.lo
gmx_confrms.lo gmx_covar.lo gmx_current.lo gmx_dos.lo gmx_density.lo
gmx_densmap.lo gmx_dih.lo gmx_dielectric.lo gmx_kinetics.lo gmx_spatial.lo
gmx_dipoles.lo gmx_disre.lo gmx_dist.lo gmx_dyndom.lo gmx_enemat.lo
gmx_energy.lo gmx_lie.lo gmx_filter.lo gmx_gyrate.lo gmx_h2order.lo
gmx_hbond.lo gmx_helix.lo gmx_mindist.lo gmx_msd.lo gmx_morph.lo
gmx_nmeig.lo gmx_nmens.lo gmx_order.lo gmx_principal.lo gmx_polystat.lo
gmx_potential.lo gmx_rama.lo gmx_rdf.lo gmx_rms.lo gmx_rmsdist.lo
gmx_rmsf.lo gmx_rotacf.lo gmx_rotmat.lo gmx_saltbr.lo gmx_sas.lo
gmx_select.lo gmx_pme_error.lo gmx_options.lo gmx_sgangle.lo gmx_sorient.lo
gmx_spol.lo gmx_tcaf.lo gmx_traj.lo gmx_velacc.lo gmx_helixorient.lo
gmx_clustsize.lo gmx_mdmat.lo gmx_wham.lo correl.lo gmx_sham.lo
gmx_nmtraj.lo gmx_trjconv.lo gmx_trjcat.lo gmx_trjorder.lo gmx_xpm2ps.lo
gmx_editconf.lo gmx_genbox.lo gmx_genion.lo gmx_genconf.lo gmx_genpr.lo
gmx_eneconv.lo gmx_vanhove.lo gmx_wheel.lo addconf.lo gmx_tune_pme.lo
gmx_membed.lo calcpot.lo edittop.lo dens_filter.lo powerspect.lo
gmx_densorder.lo gmx_hydorder.lo binsearch.lo ../gmxlib/libgmx_d.la
 ../mdlib/libmd_d.la      -lnsl -lm
> cc  -shared  .libs/geminate.o .libs/autocorr.o .libs/expfit.o
.libs/polynomials.o .libs/levenmar.o .libs/anadih.o .libs/pp2shift.o
.libs/dlist.o .libs/eigio.o .libs/cmat.o .libs/eigensolver.o .libs/nsc.o
.libs/hxprops.o .libs/fitahx.o .libs/gmx_analyze.o .libs/gmx_anaeig.o
.libs/gmx_bar.o .libs/gmx_angle.o .libs/gmx_bond.o .libs/gmx_bundle.o
.libs/gmx_chi.o .libs/gmx_cluster.o .libs/gmx_confrms.o .libs/gmx_covar.o
.libs/gmx_current.o .libs/gmx_dos.o .libs/gmx_density.o .libs/gmx_densmap.o
.libs/gmx_dih.o .libs/gmx_dielectric.o .libs/gmx_kinetics.o
.libs/gmx_spatial.o .libs/gmx_dipoles.o .libs/gmx_disre.o .libs/gmx_dist.o
.libs/gmx_dyndom.o .libs/gmx_enemat.o .libs/gmx_energy.o .libs/gmx_lie.o
.libs/gmx_filter.o .libs/gmx_gyrate.o .libs/gmx_h2order.o .libs/gmx_hbond.o
.libs/gmx_helix.o .libs/gmx_mindist.o .libs/gmx_msd.o .libs/gmx_morph.o
.libs/gmx_nmeig.o .libs/gmx_nmens.o .libs/gmx_order.o .libs/gmx_principal.o
.libs/gmx_polystat.o .libs/gmx_potential.o .libs/gmx_rama.o .libs/gmx_rdf.o
.libs/gmx_rms.o .libs/gmx_rmsdist.o .libs/gmx_rmsf.o .libs/gmx_rotacf.o
.libs/gmx_rotmat.o .libs/gmx_saltbr.o .libs/gmx_sas.o .libs/gmx_select.o
.libs/gmx_pme_error.o .libs/gmx_options.o .libs/gmx_sgangle.o
.libs/gmx_sorient.o .libs/gmx_spol.o .libs/gmx_tcaf.o .libs/gmx_traj.o
.libs/gmx_velacc.o .libs/gmx_helixorient.o .libs/gmx_clustsize.o
.libs/gmx_mdmat.o .libs/gmx_wham.o .libs/correl.o .libs/gmx_sham.o
.libs/gmx_nmtraj.o .libs/gmx_trjconv.o .libs/gmx_trjcat.o
.libs/gmx_trjorder.o .libs/gmx_xpm2ps.o .libs/gmx_editconf.o
.libs/gmx_genbox.o .libs/gmx_genion.o .libs/gmx_genconf.o .libs/gmx_genpr.o
.libs/gmx_eneconv.o .libs/gmx_vanhove.o .libs/gmx_wheel.o .libs/addconf.o
.libs/gmx_tune_pme.o .libs/gmx_membed.o .libs/calcpot.o .libs/edittop.o
.libs/dens_filter.o .libs/powerspect.o .libs/gmx_densorder.o
.libs/gmx_hydorder.o .libs/binsearch.o  -Wl,--rpath
-Wl,/home/chem/msrhcf/gromacs-4.5.5/src/gmxlib/.libs -Wl,--rpath
-Wl,/home/chem/msrhcf/gromacs-4.5.5/src/mdlib/.libs -Wl,--rpath
-Wl,/home/chem/msrhcf/gromacs_from455/lib
-L/home/chem/msrhcf/gromacs-4.5.5/src/gmxlib/.libs
../gmxlib/.libs/libgmx_d.so ../mdlib/.libs/libmd_d.so
-L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/ -lnsl -lm  -msse2
-pthread -Wl,-soname -Wl,libgmxana_d.so.6 -o .libs/libgmxana_d.so.6.0.0
> ar cru .libs/libgmxana_d.a  geminate.o autocorr.o expfit.o polynomials.o
levenmar.o anadih.o pp2shift.o dlist.o eigio.o cmat.o eigensolver.o nsc.o
hxprops.o fitahx.o gmx_analyze.o gmx_anaeig.o gmx_bar.o gmx_angle.o
gmx_bond.o gmx_bundle.o gmx_chi.o gmx_cluster.o gmx_confrms.o gmx_covar.o
gmx_current.o gmx_dos.o gmx_density.o gmx_densmap.o gmx_dih.o
gmx_dielectric.o gmx_kinetics.o gmx_spatial.o gmx_dipoles.o gmx_disre.o
gmx_dist.o gmx_dyndom.o gmx_enemat.o gmx_energy.o gmx_lie.o gmx_filter.o
gmx_gyrate.o gmx_h2order.o gmx_hbond.o gmx_helix.o gmx_mindist.o gmx_msd.o
gmx_morph.o gmx_nmeig.o gmx_nmens.o gmx_order.o gmx_principal.o
gmx_polystat.o gmx_potential.o gmx_rama.o gmx_rdf.o gmx_rms.o gmx_rmsdist.o
gmx_rmsf.o gmx_rotacf.o gmx_rotmat.o gmx_saltbr.o gmx_sas.o gmx_select.o
gmx_pme_error.o gmx_options.o gmx_sgangle.o gmx_sorient.o gmx_spol.o
gmx_tcaf.o gmx_traj.o gmx_velacc.o gmx_helixorient.o gmx_clustsize.o
gmx_mdmat.o gmx_wham.o correl.o gmx_sham.o gmx_nmtraj.o gmx_trjconv.o
gmx_trjcat.o gmx_trjorder.o gmx_xpm2ps.o gmx_editconf.o gmx_genbox.o
gmx_genion.o gmx_genconf.o gmx_genpr.o gmx_eneconv.o gmx_vanhove.o
gmx_wheel.o addconf.o gmx_tune_pme.o gmx_membed.o calcpot.o edittop.o
dens_filter.o powerspect.o gmx_densorder.o gmx_hydorder.o binsearch.o
> cc  -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
-I../../include -DGMXLIBDIR=\"/home/chem/msrhcf/gromacs_from455/share/top\"
  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -pthread -I./include -MT g_pme_error.o -MD
-MP -MF .deps/g_pme_error.Tpo -c -o g_pme_error.o g_pme_error.c
> mv -f .deps/g_pme_error.Tpo .deps/g_pme_error.Po
> /bin/sh ../../libtool --tag=CC   --mode=link cc   -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -pthread -I./include   -o g_pme_error
g_pme_error.o libgmxana_d.la ../mdlib/libmd_d.la ../gmxlib/libgmx_d.la-lnsl -lm
> cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -pthread -I./include -o .libs/g_pme_error
g_pme_error.o  ./.libs/libgmxana_d.so
/home/chem/msrhcf/gromacs-4.5.5/src/mdlib/.libs/libmd_d.so
../mdlib/.libs/libmd_d.so -lfftw3 /usr/lib64/libxml2.so -lz
/home/chem/msrhcf/gromacs-4.5.5/src/gmxlib/.libs/libgmx_d.so
../gmxlib/.libs/libgmx_d.so -ldl -lnsl -lm  -Wl,--rpath
-Wl,/home/chem/msrhcf/gromacs_from455/lib
> creating g_pme_error
>
>
> Thank you for your help.
>
> Kind Regards,
>
> Alaina
>
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