[gmx-users] Failure in MD run without any error

Mark Abraham mark.j.abraham at gmail.com
Mon Oct 28 21:49:19 CET 2013


Hard to know. LAM was discontinued over 4 years ago. You could have a flaky
file system. Unless you're trying to run a jobsover both machines over
network like Infiniband, you don't even want to use an external MPI library
- single-node performance with built-in thread-MPI will give much better


On Mon, Oct 28, 2013 at 9:12 PM, niloofar niknam
<niloofae_niknam at yahoo.com>wrote:

>  DearGromacs users
> I have encountered something strange. I have installed Red
> Hat Enterprise Linux 6.1 & 6.2 on two machines recently and then lam 7.1.4,
> fftw 3.3.2 and Gromacs 4.5.5 .
> During linux installation, everything went well I didn`t
> face any complain or receiving any error, as well as in lam, fftw and
> Gromacs
> installation, But when I run an MD job on both of these machines, at first
> everything seems normal but after some steps ( usually multi thousands
> steps), the
> job doesn`t proceed. Log file does not show any change or there is no
> error.
> Obviously the job is stopped while terminal shows all the processors are
> 100%
> busy.
> I have also reinstalled the linux and the mentioned programs
> too but it did not solve the problem. I don`t have any idea what the
> problem
> is. Any comment or suggestion would be highly appreciated.
> Thanks in advance,
> Niloofar
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list