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Cannot Compute Sizeof Gromacs

yeschecking size of int... Message #30 received at [email protected] (full text, mbox, reply): From: Manuel Prinz To: Nicholas Breen Cc: [email protected] Subject: Re: Bug#456860: gromacs: FTBFS: checking size of int... Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson. [gmx-users] configure: error: cannot compute sizeof (off_t) Justin Kat justin.kat at mail.mcgill.ca Wed Feb 23 05:35:50 CET 2011 Previous I'dtrouble-shoot your mpicc first.MarkPost by Justin KatI cant seem to find anything in the config.log file that might pointme in the right direction../configure --enable-mpi --program-suffix=_mpiMPICC=/usr/lib64/openmpi/1.4-gcc/bin/mpicc/usr/lib64/openmpi/1.4-gcc/include/usr/lib64/openmpi/1.4-gcc/But it seems to have no effect http://electrictricycle.net/cannot-compute/cannot-compute-sizeof-int-gromacs.html

yes > checking for string.h... configure: error: cannot compute sizeof (int)" If I remove the --enable-mpi all goes well, but I need to run gromacs in Parallel.I would like to know how I can install gromacs Files: 2464e6277acf15c1e87997164f3ab3db 1166 science extra gromacs_3.3.2-3.dsc 2ae597147dfa24e6b963c1ea0aacf7cc 1743596 science extra gromacs_3.3.2-3.diff.gz e8e3703bd6e0ffce00dac68add261fb0 2712458 doc extra gromacs-doc_3.3.2-3_all.deb abbbc9317bcfff1f52d7e073d9f5576e 6394512 science extra gromacs_3.3.2-3_i386.deb ed21f4345f1571518c4d7ab61cd2f8d1 14351364 devel extra gromacs-dev_3.3.2-3_i386.deb 47c2ca5508ffc9059eb14de8c16ee5e9 3318676 science extra gromacs-mpich_3.3.2-3_i386.deb I'll keep this bug open until then. -- Nicholas Breen [email protected] Information forwarded to [email protected], Nicholas Breen : Bug#456860; Package gromacs. click to read more

Reported by: Lucas Nussbaum Date: Tue, 18 Dec 2007 09:04:38 UTC Severity: serious Found in version gromacs/3.3.2-2 Fixed in version gromacs/3.3.2-3 Done: Nicholas Breen Bug is archived. About the archive rebuild: The rebuild was done on about 50 AMD64 nodes of the Grid'5000 platform, using a clean chroot containing a sid i386 environment. Send a report that this bug log contains spam.

Read http://www.gromacs.org/Support/Mailing_Lists Previous message View by thread View by date Next message [gmx-users] configure: error: cannot compute sizeof (off_t... configure: error: cannot compute sizeof (int) Date: Tue, 18 Dec 2007 16:39:52 -0800 On Wed, Dec 19, 2007 at 12:47:55AM +0100, Manuel Prinz wrote: > I just finished to develop a So I hope we'll have a fixed openmpi package in a few days. > I'll keep you informed about the progress! vferrario Re: [gmx-users] configure: error: cannot compute size...

Building GROMACS against sid works like a charm, and binaries end up in gromacs-openmpi. This is collateral damage from #456721, and should be corrected by a re-rebuild once that's been closed. Carsten KutznerMax Planck Institute for Biophysical ChemistryTheoretical and Computational BiophysicsAm Fassberg 11, 37077 Goettingen, GermanyTel. +49-551-2012313, Fax: +49-551-2012302http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne Justin Kat 2011-02-23 04:35:50 UTC PermalinkRaw Message Im not quite sure if this https://www.mail-archive.com/[email protected]/msg38261.html Use the www interface or send it to [email protected]

Justin Kat Re: [gmx-users] configure: error: cannot compute ... Read http://www.gromacs.org/Support/Mailing_Lists*--Dr. configure: error: cannot compute sizeof (int) > See `config.log' for more details. > make: *** [build-openmpi] Error 77 > dpkg-buildpackage: failure: debian/rules build gave error exit status 2 The full build yes > checking for sys/stat.h...

Copy sent to Nicholas Breen . https://bugs.debian.org/456860 yes > checking whether mpicc.openmpi accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops... I'll do more tomorrow and will include > GROMACS. 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

Please don't post (un)subscribe requests to the list. More about the author After configuring and making openmpi i started to configure gromacs. Message #20 received at [email protected] (full text, mbox, reply): From: [email protected] (Nicholas Breen) To: Manuel Prinz Cc: [email protected] Subject: Re: Bug#456860: gromacs: FTBFS: checking size of int... Nicholas Breen (supplier of updated gromacs package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators

Also available in: Atom PDF Loading... If you still have problems - once you are sure the MPI test works - you can reopen the bug by attaching both the MPI test program that works as well yes > checking whether byte ordering is bigendian... check my blog URL: Previous message: [gmx-users] Re:gmx-users Digest, Vol 82, Issue 168 Next message: [gmx-users] configure: error: cannot compute sizeof (off_t) Messages sorted by: [ date ] [ thread ] [ subject

Best regards Manuel [signature.asc (application/pgp-signature, inline)] Tags added: pending Request was from [email protected] (Nicholas Breen) to [email protected] (Thu, 27 Dec 2007 04:51:05 GMT) Full text and rfc822 format available. Justin Kat Re: [gmx-users] configure: error: cannot compute ... configure: error: cannot compute sizeof (int) Date: Thu, 20 Dec 2007 16:42:19 +0100 [Message part 1 (text/plain, inline)] Am Mittwoch, den 19.12.2007, 00:47 +0100 schrieb Manuel Prinz: > I just finished

yes > checking whether mpicc.openmpi accepts -funroll-all-loops...

Full text and rfc822 format available. Mark Abraham Reply via email to Search the site The Mail Archive home gmx-users - all messages gmx-users - about the list Expand Previous message Next message The Mail Archive home You're welcome to contribute! yes > checking for strings.h...

Full text and rfc822 format available. So I hope we'll have a fixed openmpi package in a few days. > I'll keep you informed about the progress! Mark Abraham [gmx-users] configure: error: cannot compute sizeof (... news Acknowledgement sent to [email protected] (Nicholas Breen): Extra info received and forwarded to list.

no > checking for sys/types.h... No further changes may be made. Read http://www.gromacs.org/Support/Mailing_Lists * -- Dr. Use the www interface or send it to [email protected]

Make sure toucan compile and run a simple MPI test program first. It seems like I am missing some files somewhere? Acknowledgement sent to Lucas Nussbaum : New Bug report received and forwarded. yes > checking for unistd.h...

Notification sent to Lucas Nussbaum : Bug acknowledged by developer. Added Vcs-Browser, Vcs-Svn fields. - Increase Standards-Version to 3.7.3. Read http://www.gromacs.org/Support/Mailing_Lists * -- Dr. Full text and rfc822 format available.

Thank you for reporting the bug, which will now be closed. Full text and rfc822 format available. http://bugzilla.gromacs.org/show_bug.cgi?id=179) * debian/gromacs-doc.doc-base: remove extraneous spaces. Message #37 received at [email protected] (full text, mbox, reply): From: Nicholas Breen To: [email protected] Subject: Bug#456860: fixed in gromacs 3.3.2-3 Date: Sat, 29 Dec 2007 03:47:05 +0000 Source: gromacs Source-Version: