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,
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.
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
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 https://github.com/bayesiancook/pbmpi.git
module load intel/2018.2
module load openmpi/3.1.0rc4
I have installed it locally following your instructions. Thank you, jrosner.
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: libsharp_coll.so.4: cannot open shared object file: No such file or directory
And this is the script I am using:
#SBATCH –job-name 73×90.pb1
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,
I’m working on it now, I’ll let you know…
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/’
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.
that solved the problem.
Thanks a lot! Sergio
you bet, glad to hear it 🙂