SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
Ray: a NEW MPI-based 100% parallel genome assembler seb567 Bioinformatics 278 12-10-2015 05:25 AM
New Ray crash krobison Bioinformatics 2 06-05-2012 10:32 AM
novalign MPI jgSoton Bioinformatics 4 01-02-2012 05:50 AM
ClustalW MPI arkal Bioinformatics 2 07-03-2011 08:55 AM

Reply
 
Thread Tools
Old 05-15-2014, 10:27 AM   #1
ARopski
Junior Member
 
Location: Chicago

Join Date: Feb 2013
Posts: 2
Default Using Ray assembler in an MPI script

I'm running a set of samples through a short pipeline, ultimately ending with de novo assembly using Ray. However, the application does not execute, seemingly because the worker nodes are trying to call mpiexec. My c script uses MPI to send the sample name (Fec2 in this example shown below) to each worker. The pipeline works okay unzipping, converting formats, and has been working prior to the addition of the assembler for sample sets in the dozens.

Initially, I didn't notice the second mpiexec call made for Ray, so I removed the mpiexec (as shown below) which runs fine in the command line, but never in the c script.

Code:
Ray p Fec2_R1_filtered.fastq Fec2_R2_filtered.fastq -o Fec2
Within the c script I have:

Code:
snprintf(buffer, sizeof(buffer), "Ray -k21 p %s%s %s%s -o %s", myjob, "_filtered.fastq", myjob2, "_filtered.fastq", myjob);
system(buffer);
Is there some restriction with using Ray with a worker node being fed via MPI?
ARopski 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 01:57 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO