[gmx-developers] compiling from tarball on ubuntu
r.pool at few.vu.nl
Thu Oct 21 12:38:51 CEST 2010
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??
IBIVU/Bioinformatics, Vrije Universiteit Amsterdam
De Boelelaan 1081a, 1081HV AMSTERDAM, the Netherlands
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 CFLAGS="-O2");
> * 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 on
>>> 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) |
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> or send it to gmx-developers-request at gromacs.org.
More information about the gromacs.org_gmx-developers