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.pa...@gmail.com <mailto: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
<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.abra...@anu.edu.au <mailto: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
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