mpi error abyss-pe

[Vinay Mittal]

Hi,

I am sure this must have been covered earlier but I am having hard time finding it.

I am assembling paired-end RNA-Seq data. Running abyss-pe as follows:

~/downloads/abyss-1.3.4/bin/abyss-pe E=0 n=4 q=10 v=-v k=64 j=12 name=my_lib_name -C my_out_dirr in="<fq1> <fq2>" OVERLAP_OPTIONS='--no-scaffold' SIMPLEGRAPH_OPTIONS='--no-scaffold' MERGEPATHS_OPTIONS='--greedy' mp=''

Running this gives me following error:

which: no mpirun in (<system PATH>)

/bin/bash: mpirun: command not found

make: *** [<my lib>-1.fa] Error 127

I am sure I configured abyss without mpi but it's still looking for MPI. Not sure how to proceed.

Thanks.

[Ben Vandervalk]

Hi Vinay,

Try adding `np=1` to your `abyss-pe` arguments.  That should force it to run the non-MPI version.

- Ben

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[Vinay Mittal]

Hi Ben,

Thanks for the prompt response. I am still getting the same error. Interestingly, it only fails (exits with error) when I submit it as a job using PBS. But it runs fine (after giving the mpirun error) if I run abyss-pe directly on terminal (without using PBS). Any idea what might be going on?

Thanks.

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[Ka Ming Nip]

Hi Vinay,

abyss-pe would attempt to run the assembly with mpirun when one of the follow environment variables is defined:

NSLOTS
LSB_DJOB_NUMPROC
SLURM_NTASKS

You can unset them before running abyss-pe, eg.

unset NSLOTS
abyss-pe E=0 n=4 q=10 v=-v k=64 j=12 name=my_lib_name ...

Hope that helps!

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Vinay Mittal [vinayk...@gmail.com]
Sent: March 22, 2017 10:30 PM
To: Trans-ABySS
Subject: Re: mpi error abyss-pe

Hi Ben,
Thanks for the prompt response. I am still getting the same error. Interestingly, it only fails (exits with error) when I submit it as a job using PBS. But it runs fine (after giving the mpirun error) if I run abyss-pe directly on terminal (without using PBS). Any idea what might be going on?

Thanks.


On Wednesday, March 22, 2017 at 12:24:23 PM UTC-4, Ben Vandervalk wrote:
Hi Vinay,

Try adding `np=1` to your `abyss-pe` arguments. That should force it to run the non-MPI version.

- Ben

On Tue, Mar 21, 2017 at 9:26 PM, Vinay Mittal <vinayk...@gmail.com<javascript:>> wrote:

Hi,
I am sure this must have been covered earlier but I am having hard time finding it.
I am assembling paired-end RNA-Seq data. Running abyss-pe as follows:


~/downloads/abyss-1.3.4/bin/abyss-pe E=0 n=4 q=10 v=-v k=64 j=12 name=my_lib_name -C my_out_dirr in="<fq1> <fq2>" OVERLAP_OPTIONS='--no-scaffold' SIMPLEGRAPH_OPTIONS='--no-scaffold' MERGEPATHS_OPTIONS='--greedy' mp=''


Running this gives me following error:

which: no mpirun in (<system PATH>)

/bin/bash: mpirun: command not found
make: *** [<my lib>-1.fa] Error 127

I am sure I configured abyss without mpi but it's still looking for MPI. Not sure how to proceed.

Thanks.


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[Vinay Mittal]

Thanks Ka Ming.

This is really helpful.

Interestingly our servers got updated a while ago and they moved all the packages to a new location. Adjusting the path variable and re-installing openmpi helped and I was able to run it properly.