[gmx-developers] compiling from tarball on ubuntu
szilard.pall at cbr.su.se
Fri Oct 22 17:13:31 CEST 2010
This all sounds _very_ strange. I only have 64 bit systems around, but
on those (Ubuntu 10.04 and 9.10 with gcc 4.4.3/4.3/4 and 4.3.4
respectively) gromacs 4.0.5 runs just fine.
I didn't use any magic while compiling either:
$ ../configure --prefix=/home/pszilard/tmp/gromacs-4.0.5-install &&
make -j4 && make install
I'll look around and see if I can find a 32 bit system and check.
On Thu, Oct 21, 2010 at 12:38 PM, René Pool <r.pool at few.vu.nl> wrote:
> Hi all,
> I mentioned that Anton's system was 64 bit, but I just found out that it's
> 32 bit.
> Szilárd, your system is 64 bit, so maybe this is a clue??
> René Pool
> IBIVU/Bioinformatics, Vrije Universiteit Amsterdam
> De Boelelaan 1081a, 1081HV AMSTERDAM, the Netherlands
> Room P120
> E: r.pool at few.vu.nl
> T: +31 20 59 83714
> F: +31 20 59 87653
> René Pool wrote:
>> Hi all,
>> I have got mdrun working from the 4.0.5 tarball!
>> Some important issues though:
>> * Compilation from tarball using standard configure options (optimization
>> level O3) results in mdrun segfaulting;
>> * The gromacs 4.0.5 package from ubuntu 9.10 works (It was compiled using
>> * Rebuilding the above .deb package from source also yields working
>> * Complilation from the 4.0.5 tarball from the gromacs website using
>> CFLAGS="-O2" yields a working mdrun.
>> The above means that gromacs (at least the 4.0.5 version) cannot be
>> optimized to level 3 on my ubuntu 9.10 (i686) installation and on Anton's
>> ubuntu 10.04 (x86_64) installation.
>> Anton used gcc version 4.4.3, my gcc version is 4.4.1.
>> I have also tried linking to a freshly compiled fftw3 lib instead of
>> linking to the ubuntu fftw3 lib, giving the same results as above.
>> Any ideas on this issue??
>> René Pool
>> IBIVU/Bioinformatics, Vrije Universiteit Amsterdam
>> De Boelelaan 1081a, 1081HV AMSTERDAM, the Netherlands
>> Room P120
>> E: r.pool at few.vu.nl
>> T: +31 20 59 83714
>> F: +31 20 59 87653
>> Szilárd Páll wrote:
>>> Hi Anton,
>>> I've just tried on Ubuntu 10.04 x86_64 with gcc 4.4.3 and gcc 4.3.4 as
>>> well. Compiled from the 4.0.5 tarball from the website, ran a
>>> simulations with a few systems (including SPC/E water box) and
>>> everything worked just fine.
>>> On Tue, Oct 19, 2010 at 4:41 PM, Anton Feenstra <feenstra at few.vu.nl>
>>>> We're having problems here compiling gromacs from source (tarballs).
>>>> trying 4.0.5 since that matches our local development tree. Compilation
>>>> seems to go fine, but mdrun segfaults at step 0 (in nsgrid_core), and it
>>>> also fails on the water tutorial (same segv).
>>>> I wasn't able to find any confirmation on the mailing lists, or anywhere
>>>> the gromacs pages, of this issue. Stock ubuntu mdrun does run on the
>>>> tpr. Tried it on ubuntu 9.10 (karmic) and 10.04 (lucid).
>>>> Can anyone confirm this problem, and any hint on how to proceed?
>>>> _____________ _______________________________________________________
>>>> | | |
>>>> | _ _ ___,| K. Anton Feenstra |
>>>> | / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |
>>>> |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands |
>>>> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
>>>> | | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
>>>> | | "Your Country Needs YOU" (U.S. Army) |
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