search

beagle-dev / beagle-lib

general purpose library for evaluating the likelihood of sequence evolution on trees
MIT License
130 stars 57 forks source link

Instal fail on supercomputer #140

Closed LTBroda closed 5 years ago

LTBroda commented 5 years ago

Hi guys,

I'm experiencing install error of Beagle lib. v 3.1.2 on computing node with slurm 17.02.9 and Scientific Linux release 6.10 (Carbon). With basic parameters installation goes smoothly, but it wan't run with MrBayes 3.2.7a on more than one node. I assume that I require '--enable-openmp' flag so it works with openmpi. Unfortunately with that flag make fails with Error code 2 ([install-am]) and 1 ([install-libLTLIBRARIES] and [install-recursive]). make check indicates fail with tinytest.

Do you have any experience with installation of Beagle on supercomputers or have any idea how to solve this problem?

Best regards, Łukasz

koadman commented 5 years ago

Hi Łukasz, OpenMP and OpenMPI are two different things. OpenMP supports multiple threads on a single system image (e.g. a single node in your 'supercomputer'), OpenMPI supports communication among different system images/nodes. In your case it is probably enough to just use OpenMPI, so you can build without the --enable-openmp flag. If you want to get OpenMP working we'll probably need more details from the build log. The error numbers don't tell us much.

LTBroda commented 5 years ago

Thank you koadman for your response. What you suggest I did at the beginning, but got error so in my desperation I tried different things...

MrBayes Error:

Running benchmarks to automatically select fastest BEAGLE resource... Unable to load CPU plugin! Please check for proper libhmsbeagle installation. Failed to start BEAGLE instance

  Running benchmarks to automatically select fastest BEAGLE resource...       Failed to start BEAGLE instance
  Using standard FMA likelihood calculator
LTBroda commented 5 years ago

OK, I solved this. MrBayes needs some local variables to locate beagle. export LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH solved my problem. Sorry for wasting your time and gave a great day!