Charm++ parallel programming system

["Kale, Laxmikant V" <kale AT illinois.edu>]

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: 3.0
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

==============================================================================
Invoking PINY Interface
------------------------------------------------------------------------------


==============================================================================
Reading simulation input file tests/simple_minimization/water.input
------------------------------------------------------------------------------

Simulation param. allocation: 0.0024 Mbytes; Total memory: 0.0024 Mbytes
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$$$$$$
The recommended range of cp_nonloc_pme_order is 4-8 
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
You are in danger! Your cp_min_update is off! 
Are you debugging some CS code? 
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$

$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
The true cp_mass_tau is 1581.14. The value set 25
is scaled by sqrt(cmass_cut_def/1000)=44.7214.
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$

$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
You have requested more than 1000 spline points   
Are you certain this is what you would like to do?
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
You have requested a cp run tolerence greater than  
10000 times the minimization tolerence 5 0.0001 
Are you certain this is what you would like to do?
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
You have requested a write inst freq > 2000 steps 
Are you certain this is what you would like to do?
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
You have requested a write position freq > 2000 steps 
Are you certain this is what you would like to do?
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
You have requested a write velocity freq > 2000 steps 
Are you certain this is what you would like to do?
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
For CP calculations, interatomic PE should be 
Calculated every step.  Setting the frequency to 1
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
Restart types other than restart_all employed
in parallel may effect comparisons with simulations 
performed in scalar or with different numbers of procs
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
CP-Restart types other than restart_all employed
in parallel may effect comparisons with simulations 
performed in scalar or with different numbers of procs
$$$$$$$$$$$$$$$$$$$$_warning_$$$$$$$$$$$$$$$$$$$$
@@@@@@@@@@@@@@@@@@@@_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.

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