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ARopski 05-15-2014 10:27 AM

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?


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