[gmx-developers] compiling from tarball on ubuntu

[René Pool]

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 CFLAGS="-O2");
* Rebuilding the above .deb package from source also yields working 
binaries;
* 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??

Cheers,
René
=====================================================
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.
> 
> --
> Szilárd
> 
> 
> 
> On Tue, Oct 19, 2010 at 4:41 PM, Anton Feenstra <feenstra at few.vu.nl> wrote:
>> Hi!
>>
>>
>> We're having problems here compiling gromacs from source (tarballs). We're
>> 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 on
>> the gromacs pages, of this issue. Stock ubuntu mdrun does run on the same
>> tpr. Tried it on ubuntu 9.10 (karmic) and 10.04 (lucid).
>>
>> Can anyone confirm this problem, and any hint on how to proceed?
>>
>>
>> --
>> Groetjes,
>>
>> Anton
>>  _____________ _______________________________________________________
>> |             |                                                       |
>> |  _   _  ___,| 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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