SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Can't get Ray working lednakashim De novo discovery 7 07-23-2012 05:52 AM
New Ray crash krobison Bioinformatics 2 06-05-2012 10:32 AM
Ray crash: how to debug? krobison De novo discovery 3 06-05-2012 09:50 AM
v3: Effect of high cluster densities on cluster PF and %Q30 pmiguel Illumina/Solexa 3 10-05-2011 05:36 AM
RE: Geeting from Ray L RayLangley Introductions 2 06-20-2011 08:56 AM

Reply
 
Thread Tools
Old 03-14-2013, 09:56 AM   #1
yaximik
Senior Member
 
Location: Oregon

Join Date: Apr 2011
Posts: 205
Default Help is needed with openmpi and Ray on cluster

Hi,

I run a small Ray job on a cluster to check openmpi and Ray. The current versions on the cluster are openmpi-1.6.4 and Ray is 2.1.

When compiled on my server with openmpi-1.4, Ray2.1 works just fine with large metazoan dataset (about 30 GB) completing assembly in about 20 hours on machine with 2 quad core E5620 (16 threads) and 96GB memory

On the cluster Ray2.1 compiled fine as well, and then I tried to run it with one of datasets (about 36 MB) from the above pile that assembled fine on my server. It failed, generating ouput, which I am not quite understand and would appreciate help in interpretation and fixing the problem. Here is Ray.job file:

Code:
#$ -S /bin/bash
#$ -cwd
#
#$ -N RayTest
#$ -pe openmpi 32
#$ -l h_rt=00:10:00,s_rt=00:08:00,h_vmem=3G
#$ -j y
#
#$ -M yaximik@gmail.com
#$ -m eas
#
# Load the appropriate module files
# Should be loaded already
#$ -V

mpiexec -n $NSLOTS ~/bin/Ray ~/jobs/Ray/Ray.conf
Here is Ray.conf file:

Code:
# configuration file
-k 31 # k-mer=31

# default autocalc averageOuterDistance standardDeviation
# all reads trimmed, Q30, FGMGPGIGVA

-s <TestFile.fasta>                    # single read file

-o ~/jobs/Ray/RayOutput         # outputDirectory

-one-color-per-file                # Sets one color per file instead of one per sequence
-amos                           # writes the AMOS file called RayOutput/AMOS.afg
#-show-memory-usage              # Shows memory usage
# -show-memory-allocations        # Shows memory allocation events
#-write-checkpoints ~/SC/Ray/Checkpoints   # Write checkpoint files
The ouput file is a bit loger, so it is attached.
Attached Files
File Type: doc RayTest.o9017964.doc (6.1 KB, 17 views)
yaximik is offline   Reply With Quote
Old 03-14-2013, 11:42 AM   #2
severin
Genome Informatics Facility
 
Location: Iowa @isugif

Join Date: Sep 2009
Posts: 105
Default make options

Did you specify your MPICXX during compile?

make PREFIX=`pwd` MAXKMERLENGTH=99 MPICXX='/shared/openmpi/intel/bin/mpicxx'

also I use mpirun -np numberofcpu
severin is offline   Reply With Quote
Old 03-14-2013, 11:56 AM   #3
yaximik
Senior Member
 
Location: Oregon

Join Date: Apr 2011
Posts: 205
Default [SOLVED] Help is needed with openmpi and Ray on cluster

The cluster guys quickly pointed my error - I compiled Ray with an earlier existing version of openmpi before the latest version was installed on the cluster. I recompuiled it and all works fine now. Thanks to everyone who read my post and responded or was going to respond!
yaximik is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:22 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO