Hi, I tried giving this-
./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 --enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 -qarch=450d -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d -qtune=450" and the configure process ran well. but when i gave make mdrun, i get an error which says= make[2]: *** [vmdio.lo] Error 1 make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/ gmxlib' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib' (cd ./src/mdlib && make ; exit 0) make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib' make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the future make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by ` libmd_mpi.la'. Stop. make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib' (cd ./src/kernel && make mdrun ; exit 0) make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel' make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the future /bin/sh ../../libtool --tag=CC --mode=link mpcc -O3 -qarch=450d -qtune=450 -no-undefined -version-info 6:0:0 -L/home/soft/lib -o libgmxpreprocess_mpi.la -rpath /home/soft/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error 1 On Sat, Dec 10, 2011 at 1:01 PM, aiswarya pawar <aiswarya.pa...@gmail.com>wrote: > Hi, > > I tried giving this- > > > ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 > --enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 -qarch=450d > -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d -qtune=450" > > and the configure process ran well. > > but when i gave make mdrun, i get an error which says= > > make[2]: *** [vmdio.lo] Error 1 > make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib' > (cd ./src/mdlib && make ; exit 0) > make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib' > make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the > future > make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by ` > libmd_mpi.la'. Stop. > make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib' > (cd ./src/kernel && make mdrun ; exit 0) > make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel' > make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the > future > /bin/sh ../../libtool --tag=CC --mode=link mpcc -O3 -qarch=450d > -qtune=450 -no-undefined -version-info 6:0:0 > -L/home/staff/sec/secdpal/soft/lib -o libgmxpreprocess_mpi.la -rpath > /home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo > convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo > gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo > readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo > topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo > vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm > libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or > unhandled argument `../mdlib/libmd_mpi.la' > make[1]: *** [libgmxpreprocess_mpi.la] Error 1 > > > > On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 8/12/2011 6:35 PM, aiswarya pawar wrote: >> >>> Hi users, >>> >>> Am running the mdrun_mpi on cluster with the md.mdp parameters as- >>> >>> ; VARIOUS PREPROCESSING OPTIONS >>> title = Position Restrained Molecular Dynamics >>> >>> >>> ; RUN CONTROL PARAMETERS >>> constraints = all-bonds >>> integrator = md >>> dt = 0.002 ; 2fs ! >>> nsteps = 2500000 ; total 5000 ps. >>> nstcomm = 10 >>> nstxout = 500 ; collect data every 1 ps >>> nstxtcout = 500 >>> nstvout = 0 >>> nstfout = 0 >>> nstlist = 10 >>> ns_type = grid >>> rlist = 1.0 >>> coulombtype = PME >>> rcoulomb = 1.0 >>> vdwtype = cut-off >>> rvdw = 1.4 >>> pme_order = 4 >>> ewald_rtol = 1e-5 >>> optimize_fft = yes >>> DispCorr = no >>> ; Berendsen temperature coupling is on >>> Tcoupl = v-rescale >>> tau_t = 0.1 0.1 >>> tc-grps = protein non-protein >>> ref_t = 300 300 >>> ; Pressure coupling is on >>> Pcoupl = parrinello-rahman >>> Pcoupltype = isotropic >>> tau_p = 1.0 >>> compressibility = 4.5e-5 >>> ref_p = 1.0 >>> ; Generate velocites is on at 300 K. >>> gen_vel = yes >>> gen_temp = 300.0 >>> gen_seed = -1 >>> >>> >>> The grompp runs fine. but when i run the mdrun_mpi i get an error such >>> as- >>> >>> Child exited abnormally! >>> Killing remote processes...DONE >>> >> >> There's no information here upon which one can diagnose anything. Look at >> the stderr, stdout and .log files and consult the errors page on the >> GROMACS website for clues. >> >> Mark >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >
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