Charm++ parallel programming system

[Eric Bohm <ebohm AT illinois.edu>]

Hello,

The issue with OpenAtom is that you need to explicitly move or remove the output files before it will run.  That safety measure is in place to ensure that experimental results are not overwritten.

That is usually accomplished by a script, typically named "tidy"
prefix your execution line an invocation of that to clear away output from a prior run.
 
./tidy water;


On 03/24/2016 09:15 AM, Kale, Laxmikant V wrote:

I am forwarding this to the charm++ mailing list for a speedy response. — -Sanjay

From: "Lukasz Orlowski (ACRC)" <lukasz-o AT acrc.a-star.edu.sg>
Date: Thursday, March 24, 2016 at 4:59 AM
To: Laxmikant Kale <kale AT illinois.edu>
Cc: "Marek T Michalewicz (ACRC)" <Michalewiczm AT acrc.a-star.edu.sg>
Subject: Requesting help running OpenAtom on Power8 platform

Hi Kale,

I’m working with Dr Marek Michalewicz, I’m having problems running OpenAtom on Power8 platform and he recommended I contact you, describing what problems I’m running into.

I compile charm++ with the following command:

$ ./build charm++ mpi-linux-ppc --with-production -j80

charm++ compiles properly. Then I follow the instruction to test a sample program:

$ cd mpi-linux-ppc/tests/charm++/simplearrayhello

$ make

$ ./charmrun ./hello

I get a message from setarch, that the ppc64le architecture is unrecognised. I am however able to run the sample program with:

$ mpirun -np 1  ./hello

Charm-FFT and OpenAtom compile properly again, but when I run a test as described on OpenAtom’s web page: http://charm.cs.illinois.edu/OpenAtom/download.shtml, I get the following warnings and seg fault at the end:

$ mpirun -np 4 ../../build-O3/OpenAtom tests/simple_minimization/cpaimd_config.p1 tests/simple_minimization/water.input 
Charm++> Running on MPI version: 3.0Michalewiczm AT acrc.a-star.edu.sg
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE)
Charm++> Running in non-SMP mode: numPes 4
Converse/Charm++ Commit ID: v6.7.0-1-gca55e1d
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.  
CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 unique compute nodes (160-way SMP).
Charm++> cpu topology info is gathered in 5.012 seconds.
Executing OpenAtom: BINARY - ../../build-O3/OpenAtom Binary produced from source-tree at commit: 07b6e34e4f67d922fa4cfb2a5c288b4dddd6a5ac

============================================================================== Starting Cpaimd-Charm-Driver Setup Phase
------------------------------------------------------------------------------   Cpaimd-Charm-Driver running on 4 processors.  At the beginning of the run user mem 345.875000 MB   Reading Physics input from tests/simple_minimization/water.input

==============================================================================Michalewiczm AT acrc.a-star.edu.sg Invoking PINY Interface
------------------------------------------------------------------------------

============================================================================== Reading simulation input file tests/simple_minimization/water.input
------------------------------------------------------------------------------
Simulation param. allocation: 0.0024 Mbytes; Total memory: 0.0024 Mbytes
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$$$$$$ The recommended range of cp_nonloc_pme_order is 4-8  $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ You are in danger! Your cp_min_update is off! 
Are you debugging some CS code? 
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ The true cp_mass_tau is 1581.14. The value set 25 is scaled by sqrt(cmass_cut_def/1000)=44.7214.
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ You have requested more than 1000 spline points    Are you certain this is what you would like to do? $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ You have requested a cp run tolerence greater than   10000 times the minimization tolerence 5 0.0001  Are you certain this is what you would like to do? $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ You have requested a write inst freq > 2000 steps  Are you certain this is what you would like to do? $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ You have requested a write position freq > 2000 steps  Are you certain this is what you would like to do? $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ You have requested a write velocity freq > 2000 steps  Are you certain this is what you would like to do? $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ For CP calculations, interatomic PE should be 
Calculated every step.  Setting the frequency to 1 $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$Michalewiczm AT acrc.a-star.edu.sg$$ $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ Restart types other than restart_all employed
in parallel may effect comparisons with simulations  performed in scalar or with different numbers of procs $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ CP-Restart types other than restart_all employed in parallel may effect comparisons with simulations  performed in scalar or with different numbers of procs $$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$ @@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@ ERROR: water already exists! (exiting)
@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@ [Partition 0][Node 0] End of program
-------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 33283 on node firestone exited on signal 11 (Segmentation fault). --------------------------------------------------------------------------

As you see I don’t use charmrun due to the issue with ppc64le, but rather mpirun by hand.

Michalewiczm AT acrc.a-star.edu.sgMichalewiczm@acrc.a-star.edu.sg

Would you be able to tell me what might be the issue or to whom should I talk about it?

Regards,

Lukasz Orlowski

Computational Scientist

A*STAR Computational Resource Centre

Email: lukasz-o AT acrc.a-star.edu.sg

Phone: +65 6419 1306