i used the option still i get the error as=<br><br>/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<br>
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<br>1506-503 (W) Option "-qlongdouble / -qldbl128" is not supported for LINUX for Power.<br>
"/usr/include/glob.h", line 166.34: 1506-276 (S) Syntax error: possible missing identifier?<br>"/usr/include/glob.h", line 166.12: 1506-033 (S) Function __REDIRECT_NTH is not valid. Function cannot return a function.<br>
"/usr/include/glob.h", line 166.12: 1506-282 (S) The type of the parameters must be specified in a prototype.<br>"/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".<br>
"/usr/include/glob.h", line 169.42: 1506-277 (S) Syntax error: possible missing ';' or ','?<br>"/usr/include/glob.h", line 171.39: 1506-276 (S) Syntax error: possible missing identifier?<br>
"/usr/include/glob.h", line 171.13: 1506-282 (S) The type of the parameters must be specified in a prototype.<br>"/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".<br>
"/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)".<br>"/usr/include/glob.h", line 171.58: 1506-160 (S) Object globfree64 cannot be declared as type void.<br>
"/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".<br>"/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".<br>
make[2]: *** [vmdio.lo] Error 1<br>make[2]: Leaving directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'<br>make[1]: *** [all-recursive] Error 1<br>make[1]: Leaving directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'<br>
(cd ./src/mdlib && make ; exit 0)<br>make[1]: Entering directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'<br>make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in the future<br>
make[1]: *** No rule to make target `../gmxlib/<a href="http://libgmx_mpi.la">libgmx_mpi.la</a>', needed by `<a href="http://libmd_mpi.la">libmd_mpi.la</a>'. Stop.<br>make[1]: Leaving directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'<br>
(cd ./src/kernel && make mdrun ; exit 0)<br>make[1]: Entering directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'<br>make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in the future<br>
/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 <a href="http://libgmxpreprocess_mpi.la">libgmxpreprocess_mpi.la</a> -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/<a href="http://libmd_mpi.la">libmd_mpi.la</a> -lnsl -lm <br>
libtool: link: cannot find the library `../mdlib/<a href="http://libmd_mpi.la">libmd_mpi.la</a>' or unhandled argument `../mdlib/<a href="http://libmd_mpi.la">libmd_mpi.la</a>'<br>make[1]: *** [<a href="http://libgmxpreprocess_mpi.la">libgmxpreprocess_mpi.la</a>] Error 1<br>
make[1]: Leaving directory `/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'<br>make: warning: Clock skew detected. Your build may be incomplete.<br><br><br><div class="gmail_quote">On Sat, Dec 10, 2011 at 1:05 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 10/12/2011 6:31 PM, aiswarya pawar wrote:
<blockquote type="cite"><br>
Hi,<br>
<br>
I tried giving this-<br>
<br>
<br>
./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"<br>
<br>
and the configure process ran well.<br>
<br>
but when i gave make mdrun, i get an error which says=<br>
<br>
make[2]: *** [vmdio.lo] Error 1<br>
</blockquote>
<br></div>
The first error happened above this line, so we can't tell what is
wrong. As a wild guess, use --without-dlopen with configure.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><br>
<br>
<blockquote type="cite">make[2]: Leaving directory
`/home/soft/gromacs-4.5.5/src/
<div>gmxlib'<br>
make[1]: *** [all-recursive] Error 1<br>
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'<br>
(cd ./src/mdlib && make ; exit 0)<br>
make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'<br>
make[1]: Warning: File `Makefile' has modification time 7.6e+02
s in the future<br>
make[1]: *** No rule to make target `../gmxlib/<a href="http://libgmx_mpi.la/" target="_blank">libgmx_mpi.la</a>', needed by `<a href="http://libmd_mpi.la/" target="_blank">libmd_mpi.la</a>'. Stop.<br>
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'<br>
(cd ./src/kernel && make mdrun ; exit 0)<br>
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'<br>
make[1]: Warning: File `Makefile' has modification time 7.5e+02
s in the future<br>
/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 <a href="http://libgmxpreprocess_mpi.la/" target="_blank">libgmxpreprocess_mpi.la</a>
-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/<a href="http://libmd_mpi.la/" target="_blank">libmd_mpi.la</a>
-lnsl -lm <br>
libtool: link: cannot find the library `../mdlib/<a href="http://libmd_mpi.la/" target="_blank">libmd_mpi.la</a>' or unhandled argument
`../mdlib/<a href="http://libmd_mpi.la/" target="_blank">libmd_mpi.la</a>'<br>
make[1]: *** [<a href="http://libgmxpreprocess_mpi.la/" target="_blank">libgmxpreprocess_mpi.la</a>]
Error 1</div>
<br>
<div class="gmail_quote">On Sat, Dec 10, 2011 at 1:01 PM, aiswarya
pawar <span dir="ltr"><<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi,<br>
<br>
I tried giving this-<br>
<br>
<br>
./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"<br>
<br>
and the configure process ran well.<br>
<br>
but when i gave make mdrun, i get an error which says=<br>
<br>
make[2]: *** [vmdio.lo] Error 1<br>
make[2]: Leaving directory
`/home/soft/gromacs-4.5.5/src/gmxlib'<br>
make[1]: *** [all-recursive] Error 1<br>
make[1]: Leaving directory
`/home/soft/gromacs-4.5.5/src/gmxlib'<br>
(cd ./src/mdlib && make ; exit 0)<br>
make[1]: Entering directory
`/home/soft/gromacs-4.5.5/src/mdlib'<br>
make[1]: Warning: File `Makefile' has modification time
7.6e+02 s in the future<br>
make[1]: *** No rule to make target `../gmxlib/<a href="http://libgmx_mpi.la" target="_blank">libgmx_mpi.la</a>', needed by `<a href="http://libmd_mpi.la" target="_blank">libmd_mpi.la</a>'. Stop.<br>
make[1]: Leaving directory
`/home/soft/gromacs-4.5.5/src/mdlib'<br>
(cd ./src/kernel && make mdrun ; exit 0)<br>
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'<br>
make[1]: Warning: File `Makefile' has modification time
7.5e+02 s in the future<br>
/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 <a href="http://libgmxpreprocess_mpi.la" target="_blank">libgmxpreprocess_mpi.la</a> -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/<a href="http://libmd_mpi.la" target="_blank">libmd_mpi.la</a> -lnsl -lm <br>
libtool: link: cannot find the library `../mdlib/<a href="http://libmd_mpi.la" target="_blank">libmd_mpi.la</a>' or unhandled argument
`../mdlib/<a href="http://libmd_mpi.la" target="_blank">libmd_mpi.la</a>'<br>
make[1]: *** [<a href="http://libgmxpreprocess_mpi.la" target="_blank">libgmxpreprocess_mpi.la</a>]
Error 1
<div>
<div><br>
<br>
<br>
<div class="gmail_quote">On Thu, Dec 8, 2011 at 5:32 PM,
Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>On 8/12/2011 6:35 PM, aiswarya pawar wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi users,<br>
<br>
Am running the mdrun_mpi on cluster with the
md.mdp parameters as-<br>
<br>
; VARIOUS PREPROCESSING OPTIONS<br>
title = Position Restrained
Molecular Dynamics<br>
<br>
<br>
; RUN CONTROL PARAMETERS<br>
constraints = all-bonds<br>
integrator = md<br>
dt = 0.002 ; 2fs !<br>
nsteps = 2500000 ; total 5000 ps.<br>
nstcomm = 10<br>
nstxout = 500 ; collect data every 1 ps<br>
nstxtcout = 500<br>
nstvout = 0<br>
nstfout = 0<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb = 1.0<br>
vdwtype = cut-off<br>
rvdw = 1.4<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
DispCorr = no<br>
; Berendsen temperature coupling is on<br>
Tcoupl = v-rescale<br>
tau_t = 0.1 0.1<br>
tc-grps = protein non-protein<br>
ref_t = 300 300<br>
; Pressure coupling is on<br>
Pcoupl = parrinello-rahman<br>
Pcoupltype = isotropic<br>
tau_p = 1.0<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = -1<br>
<br>
<br>
The grompp runs fine. but when i run the
mdrun_mpi i get an error such as-<br>
<br>
Child exited abnormally!<br>
Killing remote processes...DONE<br>
</blockquote>
<br>
</div>
</div>
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.<span><font color="#888888"><br>
<br>
Mark<br>
-- <br>
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</font></span></blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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