2016/12/13 PacBio GenomicConsensus and multiple prerequisites/components
quiver,ccs,blasr,bax2bam,bam2bax,pbbams,samtools are installed on trestles. Use
module load gcc/4.9.1 mkl/16.0.1 python/2.7.3 pitchfork/5.3.
2016/12/06 hpcwiki article learning_resources (credit and non-credit classes and reference material) installed.
2/016/09/22 IBM Platform MPI Community Edition 9.1.2 (formerly HP MPI) installed on razor. Use
module platform_mpi/9.1.2. Either
platform_mpi may be used with
ansys. Platform MPI, like Intel MPI, is not tied to a compiler.
2016/09/19 Update: razor frontend file system problems fixed. (updated from: Frontend razor-l3 has unmounted file systems and is causing login problems on razor. If it hangs on login, ctrl-c and try login again to randomly get another frontend. Rebooting it soon.)
2016/09/15 matlab R2016b installed on Razor. Use
module matlab/r2016b and, for mex,
2016/09/15 perl 5.24.0 installed on Razor. Use
module perl/5.24.0 and, for compiling or C links,
BioPerl and dependencies are installed as modules. We will be installing new module requests on 5.24.0 as default 5.10.1 has some issues. After testing 5.24.0 will be copied to Trestles.
$ module load gcc/4.7.2 mkl/16.0.1 mvapich2/2.1 cuda/7.5 python/2.7.11 $ export THEANO_FLAGS='cuda.root=/share/apps/cuda/cuda-7.5,device=gpu,floatX=float32' $ python
$ module load intel/14.0.3 mkl/14.0.3 openmpi/1.8.8 qbox/1.63.5 $ mpirun -np $NP -machinefile $PBS_NODEFILE -x LD_LIBRARY_PATH qb file.i
2016/08/21 Microsoft R Open installed on Razor. Use
module R/MR3.3.1. Supposedly “enhanced” but we don't see any advantage over open source
R/3.3.1 in limited testing.