[gmx-users] configure: error: cannot compute sizeof (off_t)

[Mark Abraham]

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 at gromacs.org  <mailto:gmx-users at 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>
>
>
> />/  http://lists.gromacs.org/mailman/listinfo/gmx-users
> />/  Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/Search  before posting!
>
>
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>
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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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