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Re: [ESPResSo-users] Running in Parallel.


From: Rudolf Weeber
Subject: Re: [ESPResSo-users] Running in Parallel.
Date: Tue, 23 Jan 2018 16:42:31 +0100
User-agent: Mutt/1.5.24 (2015-08-30)

Hi,
On Tue, Jan 23, 2018 at 03:11:44PM +0000, Rhys Goodall wrote:
> Hello,
> 
> I've made a remote install of Espresso on a centrally managed system, after
> many trials and tribulation we've managed to configure the right environment
> to get it to compile. However when I run the same python script that i've
> tested locally (also in parallel) I get an error saying:
> 
> Executing command:
> ==================
> mpirun -npernode 2 -np 2 /home/reag2/espresso2/build/pypresso
> ~/lj-correlation.py
> 
> --------------------------------------------------------------------------
> An MPI process has executed an operation involving a call to the
> "fork()" system call to create a child process.  Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your MPI job may hang, crash, or produce silent
> data corruption.  The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
> 
> The process that invoked fork was:
> 
>   Local host:          cpu-e-50 (PID 440257)
>   MPI_COMM_WORLD rank: 0
> 
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/home/reag2/lj-correlation.py", line 78, in <module>
>     system.non_bonded_inter.set_force_cap(lj_cap)
> AttributeError: 'espressomd.interactions.NonBondedInteractions' object has
> no attribute 'set_force_cap'
Is this with the current "python" branch from github.com/espressomd/espresso?
If not, please use that. 
In the current code, the forcecap is an attribute of the system class.
s=espressomd.System()
s.force_cap=10

Hope that helps!
Regards, Rudolf

--

Dr. Rudolf Weeber
Institute for Computational Physics
Universit├Ąt Stuttgart
Allmandring 3
70569 Stuttgart
Germany
Phone: +49(0)711/685-67717
Email: address@hidden
http://www.icp.uni-stuttgart.de/~icp/Rudolf_Weeber




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