[gmx-users] mdrun_mpi error
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Dec 10 08:35:11 CET 2011
On 10/12/2011 6:31 PM, aiswarya pawar 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
The first error happened above this line, so we can't tell what is
wrong. As a wild guess, use --without-dlopen with configure.
Mark
> 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
> <http://libgmx_mpi.la/>', needed by `libmd_mpi.la
> <http://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 <http://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 <http://libmd_mpi.la/> -lnsl -lm
> libtool: link: cannot find the library `../mdlib/libmd_mpi.la
> <http://libmd_mpi.la/>' or unhandled argument `../mdlib/libmd_mpi.la
> <http://libmd_mpi.la/>'
> make[1]: *** [libgmxpreprocess_mpi.la
> <http://libgmxpreprocess_mpi.la/>] Error 1
>
> On Sat, Dec 10, 2011 at 1:01 PM, aiswarya pawar
> <aiswarya.pawar at gmail.com <mailto:aiswarya.pawar at 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
> <http://libgmx_mpi.la>', needed by `libmd_mpi.la
> <http://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
> <http://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 <http://libmd_mpi.la> -lnsl -lm
> libtool: link: cannot find the library `../mdlib/libmd_mpi.la
> <http://libmd_mpi.la>' or unhandled argument
> `../mdlib/libmd_mpi.la <http://libmd_mpi.la>'
> make[1]: *** [libgmxpreprocess_mpi.la
> <http://libgmxpreprocess_mpi.la>] Error 1
>
>
>
> On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at 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
> --
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