abyss-pe without openmpi

Question: abyss-pe without openmpi

3.8 years ago by

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.

abyss assembly • 1.7k views

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modified 3.8 years ago by benv • 720 • written 3.8 years ago by vinaykmittal • 10

Can you provide how you installed/compiled abyss?

ADD REPLY • link written 3.8 years ago by st.ph.n • 2.5k

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

make 
make install

ADD REPLY • link written 3.8 years ago by vinaykmittal • 10

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

ADD REPLY • link written 3.8 years ago by st.ph.n • 2.5k

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

ADD REPLY • link written 3.8 years ago by vinaykmittal • 10

3.8 years ago by

benv • 720

Canada

benv • 720 wrote:

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.

ADD COMMENT • link written 3.8 years ago by benv • 720

3.8 years ago by

Ron • 1.0k

United States

Ron • 1.0k wrote:

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

brew install homebrew/science/abyss

ADD COMMENT • link written 3.8 years ago by Ron • 1.0k

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