On Jun 16, 2013 7:58 PM, "Emmanuel, Alaina" <[email protected]> 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
