Re: [gmx-users] mdrun_mpi error
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.abra...@anu.edu.auwrote:
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
Re: [gmx-users] mdrun_mpi error
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
Re: [gmx-users] mdrun_mpi error
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.abra...@anu.edu.auwrote: 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 = 250 ; 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun_mpi error
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/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.pa...@gmail.comwrote: 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.abra...@anu.edu.auwrote: 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 = 250 ; 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
Re: [gmx-users] mdrun_mpi error
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 = 250 ; total 5000 ps. nstcomm = 10
Re: [gmx-users] mdrun_mpi error
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 = 250 ; 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun_mpi error
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 = 250 ; 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 Aiswarya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
Hi, you can check with ldd mdrun_mpi whether really all needed libraries were found. Is libimf.so in /opt/intel/fc/10.1.008/lib ? The intel compilers also come with files called iccvars.sh or ictvars.sh. If you do source /path/to/iccvars.sh everything should be set as needed. Check the Intel Compiler documentation. Carsten On Jul 8, 2010, at 10:52 AM, zhongjin wrote: Dear users, When I am using GROMACS 4.0.7 on the Compute node ，executing command: mpiexec -n 4 mdrun_mpi -deffnm SWNT66nvt /dev/null and then met a problem :mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory but I have added export LD_LIBRARY_PATH=/opt/intel/fc/10.1.008/lib in the .bash_profile, the libimf.so is in this directory. However,when executing command:mdrun -deffnm SWNT66nvt ，it's OK ! Anybody could help me? Thanks a lot! Zhongjin He -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
- Original Message - From: zhongjin zhongjin1...@yahoo.com.cn Date: Thursday, July 8, 2010 18:53 Subject: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory To: gmx-users@gromacs.org --- | Dear users, When I am using GROMACS 4.0.7 on the Compute node ，executing command: mpiexec -n 4 mdrun_mpi -deffnm SWNT66nvt /dev/null and then met a problem :mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory but I have added export LD_LIBRARY_PATH=/opt/intel/fc/10.1.008/lib in the .bash_profile, the libimf.so is in this directory. However,when executing command:mdrun -deffnm SWNT66nvt ，it's OK ! Anybody could help me? Thanks a lot! Looks like the either MPI compiler is doing things differently from the normal compiler, or your execution environment does not have access to that /opt path, or even the environment variable. Consider also the use of LD_RUN_PATH - see compiler docs. It also might help to use gcc as the underlying compiler for mpicc - it's about the same as Intel - but that depends on what the underlying problem is. Mark | --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault
User reported it's problem with input file. 2009/4/15 annalisa bordogna annalisa.bordo...@gmail.com: Hi, I received a similar error during an equilibration by steepest descent in which I had posed constraints on water, leaving the protein free to move. I suggest to control your mdp file... maybe you did the same thing and the system collapsed or exploded (you can see that reading the log file: if this is the cause, you should see problems regarding water). Cheers, Annalisa 2009/4/13 Justin A. Lemkul jalem...@vt.edu nam kim wrote: process crashes around 100 steps out of 1000 requested. Fine, but you still haven't answered my question. Do you receive any other messages? Do other systems run on the specific hardware you're using? You may just have some instability in this particular system that is causing a crash. Examine the trajectory, see what's going wrong, and post any other relevant error messages, if you receive any. Often times there is some output before a seg fault. -Justin On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: nam kim wrote: I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal: Segmentation fault (11) [rd:06790] Signal code: (128) [rd:06790] Failing at address: (nil) [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430] [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496] [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e] [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a] [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552] [rd:06790] [ 5] /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0] [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32] [rd:06790] *** End of error message *** Are there any other messages from mdrun? Anything printed to the screen (LINCS warnings, etc)? -Justin Thanks ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault
process crashes around 100 steps out of 1000 requested. On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: nam kim wrote: I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal: Segmentation fault (11) [rd:06790] Signal code: (128) [rd:06790] Failing at address: (nil) [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430] [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496] [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e] [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a] [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552] [rd:06790] [ 5] /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0] [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32] [rd:06790] *** End of error message *** Are there any other messages from mdrun? Anything printed to the screen (LINCS warnings, etc)? -Justin Thanks ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault
nam kim wrote: process crashes around 100 steps out of 1000 requested. Fine, but you still haven't answered my question. Do you receive any other messages? Do other systems run on the specific hardware you're using? You may just have some instability in this particular system that is causing a crash. Examine the trajectory, see what's going wrong, and post any other relevant error messages, if you receive any. Often times there is some output before a seg fault. -Justin On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: nam kim wrote: I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal: Segmentation fault (11) [rd:06790] Signal code: (128) [rd:06790] Failing at address: (nil) [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430] [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496] [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e] [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a] [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552] [rd:06790] [ 5] /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0] [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32] [rd:06790] *** End of error message *** Are there any other messages from mdrun? Anything printed to the screen (LINCS warnings, etc)? -Justin Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun_mpi error Signal: Segmentation fault
I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal: Segmentation fault (11) [rd:06790] Signal code: (128) [rd:06790] Failing at address: (nil) [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430] [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496] [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e] [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a] [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552] [rd:06790] [ 5] /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0] [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32] [rd:06790] *** End of error message *** Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault
nam kim wrote: I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal: Segmentation fault (11) [rd:06790] Signal code: (128) [rd:06790] Failing at address: (nil) [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430] [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496] [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e] [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a] [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552] [rd:06790] [ 5] /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0] [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32] [rd:06790] *** End of error message *** Are there any other messages from mdrun? Anything printed to the screen (LINCS warnings, etc)? -Justin Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
