FORUMPhyloBayes MPI on Niagara
Sergio asked 11 months ago

  • Hello,
    I was wondering whether PhyloBayes MPI can be installed in Niagara. I tried to do it follow the manual instructions below but it didn’t work. It might be that some requirements for its compilation are missing in Niagara.
    Thank you very much for your help,

    3 Answers
    jrosner Staff answered 11 months ago

  • Hi Sergio,
    No problem, we’ll install this for you on the Compute Canada software stack.
    Once it’s ready, you’ll be able to access the software using the ‘module load’ command.
    I’ll notify you when it’s good to go.

    jrosner Staff replied 11 months ago

    Hi again, phylobayes-mpi is now installed on our software stack.
    It’s available now on Cedar and Graham systems, but might take a bit longer to reach Niagara.
    you can check availability using:

    module spider phylobayes-mpi

    jrosner Staff answered 11 months ago

  • also, if it’s taking too long for your liking, and you’d like to try installing again locally, give this a shot:
    git clone
    cd pbmpi/sources/
    module load intel/2018.2
    module load openmpi/3.1.0rc4

    Sergio replied 10 months ago

    I have installed it locally following your instructions. Thank you, jrosner.

    Sergio replied 10 months ago

    I am getting the following error when I tried to run the locally installed PhyloBayes MPI:

    /scratch/r/roger/sr773767/pbmpi-master/data/pb_mpi: error while loading shared libraries: cannot open shared object file: No such file or directory

    And this is the script I am using:

    #SBATCH –nodes=2
    #SBATCH –ntasks=64
    #SBATCH –time=12:00:00
    #SBATCH –job-name 73×90.pb1
    #SBATCH –output=73×90.pb1.out

    cd /directory/

    module load intel/2018.2
    module load openmpi/3.1.0rc3

    mpirun /scratch/r/roger/sr773767/pbmpi-master/data/pb_mpi -d 73×90.phy -dgam 4 -gtr -cat 73×90.pb1

    Thank you for your help,

    jrosner Staff replied 10 months ago

    Hi Sergio,

    I’m working on it now, I’ll let you know…


    jrosner Staff answered 10 months ago

  • Hi Sergio,

    I think i’ve found the problem… try the following:

    1. login to niagara
    2. go to your pbmpi/source/ directory and run: ‘make clean’
    3. now do ‘module load intel/2018.2’
    4. and ‘module load openmpi/3.1.0rc4’
    5. ‘cd ../sources/’
    6. ‘make’

    now, in your script, make the following changes:
    1. above the ‘module load intel/2018.2’ add the line ‘module load NiaEnv/2018a’
    2. change the openmpi line to read ‘module load openmpi/3.1.0rc4’

    this should fix the missing library issue
    1. it seems the rc3 version is not setup properly, using rc4 fixes this
    2. on the compute node, you need to load the default library ‘NiaEnv’ first (not sure why it’s set up like this).

    so, if you make these changes, it should be able to find the missing libraries.

    also, this is unrelated to the shared library issue, but you might want to have a look at the ‘cd /directory/’ line of your code… not sure that this is correct.

    hope this helps, let me know how if this works for you.

    Sergio replied 10 months ago

    Hi Jamie,
    that solved the problem.
    Thanks a lot! Sergio

    jrosner Staff replied 10 months ago

    you bet, glad to hear it 🙂