Warning
Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.
BLESS: Bloom-filter-based Error Correction Solution for High-throughput Sequencing Reads
BLESS uses MPI and we currently have no interactive MPI environments available. As such, it is not possible to run BLESS interactively on Iceberg.
The latest version of bless (currently 1.02) is made available with the command
module load apps/gcc/4.9.2/bless/1.02
The module create the environment variable BLESS_PATH which points to the BLESS installation directory. It also loads the dependent modules
compilers/gcc/4.9.2
mpi/gcc/openmpi/1.8.3
Here is an example batch submission script that makes use of two example input files we have included in our installation of BLESS:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | #!/bin/bash
# Next line is memory per slot
#$ -l rmem=5G
# Ask for 4 slots in an OpenMP/MPI Hybrid queue
# These 4 slots will all be on the same node
#$ -pe openmpi-hybrid-4 4
# load the module
module load apps/gcc/4.9.2/bless/1.02
# Output information about nodes where code is running
cat $PE_HOSTFILE > nodes
data_folder=$BLESS_PATH/test_data
file1=test_small_1.fq
file2=test_small_2.fq
# Number of cores per node we are going to use.
cores=4
export OMP_NUM_THREADS=$cores
# Run BLESS
mpirun $BLESS_PATH/bless -kmerlength 21 -smpthread $cores -prefix test_bless -read1 $data_folder/$file1 -read2 $data_folder/$file2
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BLESS makes use of both MPI and OpenMP parallelisation frameworks. As such, it is necessary to use a Hybrid MPI/SMP Parallel environment. The current build of BLESS does not work on more than one node. This will limit you to the maximum number of cores available on one node.
For example, to use all 16 cores on a 16 core node you would request the following parallel environment
#$ -pe openmpi-hybrid-16 16
Remember that memory is allocated on a per-slot basis. You should ensure that you do not request more memory than is available on a single node or your job will be permanently stuck in a queue-waiting (qw) status.
Various issues were encountered while attempting to install BLESS. It was necessary to install gcc 4.9.2 in order to build BLESS. No other compiler worked!
Here are the install steps
tar -xvzf ./bless.v1p02.tgz
mkdir -p /usr/local/modulefiles/apps/gcc/4.9.2/bless/
cd v1p02/
Load Modules
module load compilers/gcc/4.9.2
module load mpi/gcc/openmpi/1.8.3
Modify the Makefile. Change the line
cd zlib; ./compile
to
cd zlib;
Manually compile zlib
cd zlib/
./compile
Finish the compilation
cd ..
make
Copy the bless folder to the central location
cd ..
cp -r ./v1p02/ /usr/local/packages6/apps/gcc/4.9.2/bless/
No test suite was found.