[gmx-users] mdrun_mpi error

aiswarya pawar aiswarya.pawar at gmail.com
Sat Dec 10 09:54:25 CET 2011 

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
 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', needed by `
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 -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
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.Abraham at 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', 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
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>
>>
>
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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> Please search the archive at
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