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abyss-pe without openmpi

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 compiled abyss executable --without-mpi but still abyss-pe starts with mpirun. Any idea how to run it without having to use openmpi?

Thanks.

assembly abyss
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updated by benv benv • written by vinaykmittal • vinaykmittal

Can you provide how you installed/compiled abyss?

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written by st.ph.n st.ph.n 
./configure --prefix=/nv/hp16/downloads/abyss-1.3.4/abyss_bin --enable-maxk=96 --disable-popcnt --disable-openmp AM_CXXFLAGS=-Wall

make 
make install
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written by vinaykmittal • vinaykmittal

OpenMP and MPI are two different things. Take a look at this thread.

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written by st.ph.n st.ph.n

Thanks, st.ph.n. That clarifies a bit. Do you know if there was a way to run abyss-pe without mpirun?

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written by vinaykmittal • vinaykmittal

2 answers

Hi Vinay,

Sorry! Yesterday (in another thread) I suggested adding np=1 to your abyss-pe command. But looking at abyss-pe script, I see that won't work for running ABySS without MPI.

abyss-pe tries to detect the number of cores available based on the environment variables set by your job scheduler. And if it finds more than one core it tries to run the MPI version. I don't know which scheduler you are using, but try running this command immediately before abyss-pe in your job script:

unset NSLOTS LSB_DJOB_NUMPROC SLURM_NTASKS

If you like ABySS and are planning to continue using it, it is well worth downloading and building OpenMPI (you don't need administrative permissions -- you can install it in your home directory). It will make your ABySS jobs go a lot faster, even if you are only running the assemblies on a single machine.

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written by benv benv

install ABySS using Linuxbrew. See http://linuxbrew.sh Install Linuxbrew, and then

brew install homebrew/science/abyss
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written by Ron Ron

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