Error running beagle_GPU

[Atila]

Hi,

I'm trying to run BEAST with CUDA. I have tried ../../bin/beast -
beagle_GPU -overwrite benchmark2.xml both with BEAST1.6.2 and 1.7.0
and get the following error:


Using BEAGLE TreeLikelihood
Branch rate model used: strictClockBranchRates
Using BEAGLE resource 1: GeForce GTX 480
Global memory (MB): 1536
Clock speed (Ghz): 1.50
Number of cores: 480
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH
EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE
PROCESSOR_GPU
Ignoring ambiguities in tree likelihood.
With 5565 unique site patterns.
Using rescaling scheme : dynamic
Creating the MCMC chain:
chainLength=100000
autoOptimize=true
autoOptimize delayed for 1000 steps
full evaluation test off
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007fb9f020d83d, pid=23711,
tid=140436735981312
#
# JRE version: 7.0_03-b04
# Java VM: Java HotSpot(TM) 64-Bit Server VM (22.1-b02 mixed mode
linux-amd64 compressed oops)
# Problematic frame:
# C [libhmsbeagle-cuda.so.1+0x1283d]
beagle::gpu::BeagleGPUImpl<double>::updateTransitionMatrices(int, int
const*, int const*, int const*, double const*, int)+0xed
#
# Failed to write core dump. Core dumps have been disabled. To enable
core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/atila/applications/BEASTv1.7.pre/examples/Benchmarks/
hs_err_pid23711.log
#
# If you would like to submit a bug report, please visit:
# http://bugreport.sun.com/bugreport/crash.jsp

I tried to use open-jdk and the error only changes to

CUDA error: "Invalid value" from file <GPUInterfaceCUDA.cpp>, line
485.

and then:

# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f5871d38b50, pid=23950,
tid=140018069825280
#
# JRE version: 6.0_23-b23
# Java VM: OpenJDK 64-Bit Server VM (20.0-b11 mixed mode linux-amd64
compressed oops)
# Derivative: IcedTea6 1.11pre
# Distribution: Ubuntu 11.10, package 6b23~pre11-0ubuntu1.11.10.2
# Problematic frame:
# C [libhmsbeagle-cuda.so.1+0x11b50]
beagle::gpu::BeagleGPUImpl<float>::removeScaleFactors(int const*, int,
int)+0x30

Is this a problem from BEAST ou beagle-lib?

Thank you,
Atila Iamarino

[Andrew Rambaut]

Dear Atila,

To answer your last question, it looks like it is a problem in BEAGLE. Firstly, does it work if you use -beagle_cpu or -beagle_sse? If so, it may be an issue with CUDA. Have you installed the latest CUDA drivers? If you run the 'nvidia-smi' utility does it recognize your GPU?

Andrew

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[Atila Iamarino]

Dear Rambaut,

Yes, it works with -beagle_cpu and -beagle_sse. Also, my GPU is recognized, but I checked BEAGLE installation and it fails the tests. I haev forwarded the error message to beagle-dev group.

Thank you,

Atila

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[Guy Baele]

I was a bit surprised to see that the problem occurs when running beagle_GPU. I've loaded benchmark2.xml using beagle_GPU and it works fine by the way, although I can't run it in double precision due to my graphics card. But lately we've been having some problems with the beagle_CPU version for the updateTransitionMatrices method, but not for the beagle_GPU version:

# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fce4b8ce674, pid=18034,
tid=140524083943168 #
# JRE version: 6.0_26-b03
# Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode
linux-amd64 compressed oops) # Problematic frame:
# C  [libhmsbeagle-cpu.so.1+0xf674]
beagle::cpu::EigenDecompositionCube<double,1>::updateTransitionMatrices(int,int
const*, int const*, int const*, 1>double const*, double
const*,double**, int)+0x2a4 #

This doesn't occur with the benchmark2.xml, but with some custom xml files that we made. So maybe there are some problems with the updateTransitionMatrices methods ...

Cheers,

Guy

Op dinsdag 13 maart 2012 16:09:46 UTC+1 schreef Atila Iamarino het volgende:

[Andrew Rambaut]

Dear Atila,

This sounds like one of two things - either an issue with the CUDA driver you have installed or a physical problem with your GPU board. If you have installed CUDA tools, try running 'nvidia-smi -q' to get a detailed probe of your GPU board.

Andrew

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___________________________________________________________________
Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624

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[Andrew Rambaut]

I have created a BEAGLE user group which it may be better to use to discuss technical BEAGLE issues:

http://groups.google.com/group/beagle-user

A.

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[Atila Iamarino]

I posted the results at beagle-user group:

https://groups.google.com/forum/?fromgroups#!topic/beagle-user/TFzdZkPF5gY

Best,

Atila

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