[gmx-users] mdrun_mpi error

[aiswarya pawar]

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.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', 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.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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>
>
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