On 10/12/2011 7:54 PM, aiswarya pawar wrote:
i used the option still i get the error as=
/bin/sh ../../libtool --tag=CC --mode=compile mpCC -DHAVE_CONFIG_H
-I. -I../../src -I../../include
-DGMXLIBDIR=\"/home/staff/sec/secdpal/soft/gromacs/share/top\"
-I/home/staff/sec/secdpal/soft/include -O3 -qarch=ppc64 -qtune=pwr5
-c -o vmdio.lo vmdio.c
This is a build failure optimizing for POWER5. The configure line you
gave below was optimizing for BlueGene/P. We can't help if we don't know
what your context is. Start a new email and describe one single problem
fully in it.
Mark
mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\"/home/staff/sec/secdpal/soft/gromacs/share/top\"
-I/home/staff/sec/secdpal/soft/include -O3 -qarch=ppc64 -qtune=pwr5 -c
vmdio.c -o vmdio.o
1506-503 (W) Option "-qlongdouble / -qldbl128" is not supported for
LINUX for Power.
"/usr/include/glob.h", line 166.34: 1506-276 (S) Syntax error:
possible missing identifier?
"/usr/include/glob.h", line 166.12: 1506-033 (S) Function
__REDIRECT_NTH is not valid. Function cannot return a function.
"/usr/include/glob.h", line 166.12: 1506-282 (S) The type of the
parameters must be specified in a prototype.
"/usr/include/glob.h", line 169.35: 1506-334 (S) Identifier glob_t has
already been defined on line 113 of "/usr/include/glob.h".
"/usr/include/glob.h", line 169.42: 1506-277 (S) Syntax error:
possible missing ';' or ','?
"/usr/include/glob.h", line 171.39: 1506-276 (S) Syntax error:
possible missing identifier?
"/usr/include/glob.h", line 171.13: 1506-282 (S) The type of the
parameters must be specified in a prototype.
"/usr/include/glob.h", line 171.13: 1506-343 (S) Redeclaration of
__REDIRECT_NTH differs from previous declaration on line 166 of
"/usr/include/glob.h".
"/usr/include/glob.h", line 171.13: 1506-050 (I) Return type "void" in
redeclaration is not compatible with the previous return type
"int(const char*,int)".
"/usr/include/glob.h", line 171.58: 1506-160 (S) Object globfree64
cannot be declared as type void.
"/usr/include/glob.h", line 175.12: 1506-343 (S) Redeclaration of
glob64 differs from previous declaration on line 169 of
"/usr/include/glob.h".
"/usr/include/glob.h", line 175.12: 1506-382 (I) The type "int(const
char* restrict,int,int(*)(const char*,int),struct {...}* restrict)" of
identifier glob64 differs from previous type "int".
make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 8.8e+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/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in
the future
/bin/sh ../../libtool --tag=CC --mode=link mpCC -O3 -qarch=ppc64
-qtune=pwr5 -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
make[1]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'
make: warning: Clock skew detected. Your build may be incomplete.
On Sat, Dec 10, 2011 at 1:05 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
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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