On 23/02/2011 3:35 PM, Justin Kat wrote:
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
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.
Mark
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 "gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>"
| #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:
>/ Dear experts,
/>/
/>/ I am still unable to overcome this error during the configuration:
/>/
/>/ configure: error: cannot compute sizeof (off_t)
/>/ See `config.log' for more details.
/So what does config.log say about "cannot compute sizeof (off_t) ?"
Carsten
>/
/>/ I came across this thread with the exact same setup as I have:
/>/
/>/ http://lists.gromacs.org/pipermail/gmx-users/2011-February/058369.html
/>/
/>/ I have tried uninstalling openmpi 1.4.4 and installing the more stable
openmpi1.4.3 but I am still experiencing the same error.
/>/
/>/ ./configure --enable-mpi --program-suffix=_mpi MPICC=/usr/local/bin/mpicc
--with-fft=fftw3
/>/
/>/ I have also tried to explicitly provide the path to mpicc as above but it
still gives me the same error.
/>/
/>/ This may or may not be relevant but at the end of the config.log there is
also this line:
/>/
/>/ configure: exit 77
/>/
/>/ Does that mean anything?
/>/
/>/ Any help at all is appreciated!
/>/
/>/ Thanks,
/>/ Justin--
/>/ gmx-users mailing listgmx-users at gromacs.org
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
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--
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
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