Debugging a MPI application is sometimes like finding a needle in a haystack

-
I am running some tests as usual before releasing a new version of Ray. This time, I will be releasing Ray 2.3.0.

My job 10446216 on colosse (colossus in English) -- the supercomputer of Laval University operated by Calcul Québec (Compute Quebec in English) -- failed, and I did not know why.

All the jobs that run on colosse are automatically profiled by a formidable array of tools. And the nice thing is that I don't need to do anything fancy to get these runtime profiles.

All I need is my job identifier. With my job identifier, I then go to https://www.clumeq.ca/users/common/report/myjobs/10446216/0/#

Below, the runtime report automatically generated for me by Calcul Québec is shown. The job was a 512-core job, running on 64 8-core machines.
Just from the first figure, one can see that one of the machine crashed (the blue line). Such an event may be caused by a software bug in the software I used (in this case, a development version of Ray).

Basically, for each machine, I get 4 metrics sampled throughout the computation:


  • CPU usage, 
  • Memory usage, 
  • Input/Output usage, and 
  • Communication.

We can see that something strange happened to r101-n57 (# 19).

Usage status overview

Job status and usage overview

Informations

Job ID: 10446216
Task ID: 0
Project identifier (RAPI): nne-790-ac
Number of cores: 512
Queue: med
Wallclock: 11h 19m 24s
Submit time: 2013-09-04 16:06:50
Start time: 2013-09-04 20:36:48
End time: 2013-09-05 07:56:12
Submit script: Click to show
#PBS -W x=ENVREQUESTED:TRUE
#PBS -q med
#PBS -S /bin/bash
#PBS -N HiSeq-2500-NA12878-demo-2x150-1
#PBS -o HiSeq-2500-NA12878-demo-2x150-1.stdout
#PBS -e HiSeq-2500-NA12878-demo-2x150-1.stderr
#PBS -A nne-790-ac
#PBS -l walltime=02:00:00:00

#PBS -l nodes=64:ppn=8
 
 cd $PBS_O_WORKDIR

module use /rap/nne-790-ab/modulefiles
module load nne-790-ab/Ray/2.3.0-devel-b3e6b07764f71318408de5fbe632a41ae29c2105-1


mpiexec -n 512 \
Ray -k 31 \
-o HiSeq-2500-NA12878-demo-2x150-1 \
-read-write-checkpoints HiSeq-2500-NA12878-demo-2x150.SavedState \
-route-messages \
-detect-sequence-files HiSeq-2500-NA12878-demo-2x150 \



Comments

Post a Comment

Popular posts from this blog

Learning to solve the example 1 of puzzle 3aa6fb7a in the ARC prize

-
Image
Hi dear reader, Puzzle rules The example 1 of the puzzle 3aa6fb7a of the ARC prize looks like this: A playout starts with an blank board of width 7 and of height 7. There are therefore 49 cells. Each cell can be blank or can contain one of the 10 possible colors. The colors are identified from 0 to 9.  I added a rule. This rule is that each cell has to be changed exactly once.  The game ends when all cells have been changed. The player wins if all the cell colors match the cell colors in the expected output. Some numbers: Each cell has 11 possible values: 10 colors + blank state There are 49! ( 6.0828186e+62) distinct possible orders of cell changes in a playout.  There are 49!*10 ( 6.0828186e+63) 49 * 10 = 490 possible actions for the first action.  There are 11^49 ( 1.0671896e+51) possible board states The number of possible pairs (s, a) is even larger and upper-bounded by 11^49 * 49 * 10 = 5.2292289e+53 . Given a board state s and a proposed action a, an actio...
Read more

The Thorium actor engine is operational now, we can start to work on actor applications for metagenomics

-
I have been very busy during the last months. In particular, I completed my doctorate on April 10th, 2014 and we moved from Canada to the United States on April 15th, 2014. I started a new occupation on April 21st, 2014 at Argonne National Laboratory (a U.S. Department of Energy laboratory). But the biggest change, perhaps, was not one listed in the enumeration above. The biggest change was to stop working on Ray. Ray is built on top of RayPlatform, which in turn uses MPI for the parallelism and distribution. But this approach is not an easy way of devising applications because message passing alone is a very leaky, not self-contained, abstraction. Ray usually works fine, but it has some bugs . The problem with leaky abstractions is that they lack simplicity and are way too complex to scale out. For example, it is hard to add new code to an existing code base without breaking anything. This is the case because MPI only offers a fixed number of ranks. Sure, the MPI standard has s...
Read more

The source code of SOAPdenovo2 sits in the shadows

-
Update 2012-12-28: SOAPdenovo 2.04-r223 source code was posted online on 2012-12-28. Some minor concerns: 1. The tarball suffers from the bundled library problem (libbam.a and libbammac.a are shipped precompiled). This is incompatible with the GPLv3 license. 2. The Makefile is not portable with its hard-coded paths to compilers (/opt/blc/gcc-4.5.0/bin/gcc should just be gcc). The SOAPdenovo2 article was published today under the terms of the Creative Commons Attribution License. Here are the Availability and requirements for SOAPdenovo2 as reported in the article: Availability and requirements Project name: SOAPdenovo2 Project home page: http://soapdenovo2.sourceforge.net/ Operating system(s): e.g. Platform independent Programming language: C, C++ Other requirements: GCC version ≥ 4.5.0 License: GNU General Public License version 3.0 (GPLv3) Any restrictions to use by non-academics: none Contact: bgi-soap@googlegroups.com I fired up my browser and in a ...
Read more