[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/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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