[gmx-users] Gromacs 4.5.5

[Emmanuel, Alaina]

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. 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