[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
>         -- 
>         gmx-users mailing list gmx-users at gromacs.org
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>
>
>
>
>

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