<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 10/12/2011 7:54 PM, aiswarya pawar wrote:
<blockquote
cite="mid:CAEa6cRB_i4tmPCZKfbot5v63DGmJYQfLM239_1a4rjvQDdKbFg@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEa6cRB_i4tmPCZKfbot5v63DGmJYQfLM239_1a4rjvQDdKbFg@mail.gmail.com"
type="cite">
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
moz-do-not-send="true" href="http://libgmx_mpi.la">libgmx_mpi.la</a>',
needed by `<a moz-do-not-send="true" 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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://libmd_mpi.la">libmd_mpi.la</a> -lnsl -lm <br>
libtool: link: cannot find the library `../mdlib/<a
moz-do-not-send="true" href="http://libmd_mpi.la">libmd_mpi.la</a>'
or unhandled argument `../mdlib/<a moz-do-not-send="true"
href="http://libmd_mpi.la">libmd_mpi.la</a>'<br>
make[1]: *** [<a moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
href="http://libgmx_mpi.la/" target="_blank">libgmx_mpi.la</a>',
needed by `<a moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://libmd_mpi.la/" target="_blank">libmd_mpi.la</a>
-lnsl -lm <br>
libtool: link: cannot find the library `../mdlib/<a
moz-do-not-send="true" href="http://libmd_mpi.la/"
target="_blank">libmd_mpi.la</a>' or unhandled
argument `../mdlib/<a moz-do-not-send="true"
href="http://libmd_mpi.la/" target="_blank">libmd_mpi.la</a>'<br>
make[1]: *** [<a moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
href="http://libgmx_mpi.la" target="_blank">libgmx_mpi.la</a>',
needed by `<a moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
href="http://libmd_mpi.la" target="_blank">libmd_mpi.la</a>
-lnsl -lm <br>
libtool: link: cannot find the library `../mdlib/<a
moz-do-not-send="true"
href="http://libmd_mpi.la" target="_blank">libmd_mpi.la</a>'
or unhandled argument `../mdlib/<a
moz-do-not-send="true"
href="http://libmd_mpi.la" target="_blank">libmd_mpi.la</a>'<br>
make[1]: *** [<a moz-do-not-send="true"
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
moz-do-not-send="true"
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>
gmx-users mailing list <a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe
requests to the list. Use the www
interface or send it to <a
moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></span></blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div>
</div>
</div>
<br>
--<br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>