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On 8/04/2012 12:41 PM, bharat gupta wrote:
<blockquote
cite="mid:CAAh+zSUnCPpAitd4c7rYs_s24UQmjN0yOh71dKwNZfhq8ZLV=Q@mail.gmail.com"
type="cite">
<div class="gmail_quote">Hi,<br>
<br>
I am trying to enable mpi fro mdrun in an already installed
gromacs-4.5.5.</div>
</blockquote>
<br>
Using a freshly unpacked tarball will eliminate some sources of
problems. Shouldn't be necessary, of course, but since nobody can
warrant something hasn't been broken accidentally...<br>
<br>
<blockquote
cite="mid:CAAh+zSUnCPpAitd4c7rYs_s24UQmjN0yOh71dKwNZfhq8ZLV=Q@mail.gmail.com"
type="cite">
<div class="gmail_quote"> But while executing the command make
mdrun , I am getting the following errorn:-<br>
mv -f .deps/xlate.Tpo .deps/xlate.Plo<br>
/bin/sh ../../libtool --tag=CC --mode=link mpicc -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast
-no-undefined -version-info 6:0:0 -o <a
moz-do-not-send="true" href="http://libgmxpreprocess_mpi.la"
target="_blank">libgmxpreprocess_mpi.la</a> -rpath
/usr/local/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<br>
make[1]: Leaving directory `/usr/local/gromacs-4.5.5/src/kernel'<br>
</div>
</blockquote>
<br>
The original error occurred earlier - this error is triggered by
libmd not being built earlier because of some other problem.<br>
<br>
<blockquote
cite="mid:CAAh+zSUnCPpAitd4c7rYs_s24UQmjN0yOh71dKwNZfhq8ZLV=Q@mail.gmail.com"
type="cite">
<div class="gmail_quote"><br>
I used this command to configure , before issuing make mdrun :
./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3.
Also I have mpich2 installed in my system. So, what could be
reason for this error ??<span class="HOEnZb"><font
color="#888888"><br>
</font></span></div>
</blockquote>
<br>
Unknown at this stage.<br>
<br>
Mark<br>
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