[gmx-users] mdrun_mpi error
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Dec 10 15:32:32 CET 2011
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.Abraham at anu.edu.au
> <mailto: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
>> <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.pawar at gmail.com <mailto: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
>> <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.Abraham at anu.edu.au <mailto: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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