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On 23/02/2011 3:35 PM, Justin Kat wrote:
<blockquote
cite="mid:AANLkTimcrY=RjErx5xAvwUjfUEJp1udDOBW8WbyeGBvZ@mail.gmail.com"
type="cite">
<pre>Im not quite sure if this is the right place to analyze, but a bit before the part in the config.log where it states the error of "cannot compuete sizeof (off_t)", there is this:
configure:25048: checking size of off_t
configure:25053: /usr/local/bin/mpicc -o conftest -O3 -fomit-frame-pointer -fin
line-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -I/usr/loc
al/include -L/usr/local/lib conftest.c -lnsl -lm >&5
configure:25053: $? = 0
configure:25053: ./conftest
./conftest: error while loading shared libraries: libmpi.so.0: cannot open share
d object file: No such file or directory
configure:25053: $? = 127
configure: program exited with status 127
</pre>
</blockquote>
<br>
That looks like the right part to examine. So during configure, your
shared-library environment is such that executables compiled with
mpicc can't be run. Running some other MPI test program will
establish whether the problem is with your MPI install/environment
(likely IMO), or with what configure is doing.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTimcrY=RjErx5xAvwUjfUEJp1udDOBW8WbyeGBvZ@mail.gmail.com"
type="cite">
<pre>configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.3"
| #define PACKAGE_STRING "gromacs 4.5.3"
| #define PACKAGE_BUGREPORT "<a moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.3"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
Also before this there a multiple chunks of such
configure:25019: $? = 0
configure:25019: ./conftest
./conftest: error while loading shared libraries: libmpi.so.0: cannot open share
d object file: No such file or directory
configure:25019: $? = 127
configure: program exited with status 127
configure: failed program was:
| /* confdefs.h */
parts all over the place.
It seems like I am missing some files somewhere?
On Feb 20, 2011, at 9:30 PM, Justin Kat wrote:
><i> Dear experts,
</i>><i>
</i>><i> I am still unable to overcome this error during the configuration:
</i>><i>
</i>><i> configure: error: cannot compute sizeof (off_t)
</i>><i> See `config.log' for more details.
</i>So what does config.log say about "cannot compute sizeof (off_t) ?"
Carsten
><i>
</i>><i> I came across this thread with the exact same setup as I have:
</i>><i>
</i>><i> <a moz-do-not-send="true" href="http://lists.gromacs.org/pipermail/gmx-users/2011-February/058369.html">http://lists.gromacs.org/pipermail/gmx-users/2011-February/058369.html</a>
</i>><i>
</i>><i> I have tried uninstalling openmpi 1.4.4 and installing the more stable openmpi1.4.3 but I am still experiencing the same error.
</i>><i>
</i>><i> ./configure --enable-mpi --program-suffix=_mpi MPICC=/usr/local/bin/mpicc --with-fft=fftw3
</i>><i>
</i>><i> I have also tried to explicitly provide the path to mpicc as above but it still gives me the same error.
</i>><i>
</i>><i> This may or may not be relevant but at the end of the config.log there is also this line:
</i>><i>
</i>><i> configure: exit 77
</i>><i>
</i>><i> Does that mean anything?
</i>><i>
</i>><i> Any help at all is appreciated!
</i>><i>
</i>><i> Thanks,
</i>><i> Justin--
</i>><i> gmx-users mailing list <a moz-do-not-send="true" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">gmx-users at gromacs.org</a>
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</i>
--
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
<a moz-do-not-send="true" href="http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne">http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne</a>
</pre>
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