Run on XSEDE Comet
Follow the below steps to run HiCOPS on XSEDE Comet:
Important: The instructions in this document are ONLY for the XSEDE Comet system. For any other system, please use the instructions detailed here.
Setup
Complete the setup steps by following through the instructions in Getting Started document.
Run HiCOPS
Assuming that the HiCOPS has been installed at : $HICOPS_INSTALL.
o. If you are not working on XSEDE Comet system, then follow this link instead.
i. Ensure that the hicops-core library path has been added to LD_LIBRARY_PATH.
# append hicops-core lib path to LD_LIBRARY_PATH.
export LD_LIBRARY_PATH=$HICOPS_INSTALL/lib:$LD_LIBRARY_PATH
ii. Generate HiCOPS template runtime parameters file using the hicops_comet tool located at $HICOPS_INSTALL/bin/tools.
# run hicops_comet with -g
$ $HICOPS_INSTALL/bin/tools/hicops_comet -g
# generates: ./sampleparams.txt
iii. Edit the generated sampleparams.txt file and setup HiCOPS’ runtime parameters, database and data paths.
iv. Run HiCOPS through hicops_comet, however, this time providing the sampleparams.txt as argument to the tool.
# run hicops_comet with sampleparams.txt
$ $HICOPS_INSTALL/bin/tools/hicops_comet sampleparams.txt
v. Run HiCOPS with uparams.txt as input argument using SLURM with or without MPI depending on HiCOPS install options.
# run psm2excel using SLURM
$ srun --partition=compute --nodes=1 --ntasks-per-node=1 -t 00:15:00 \
--export=ALL $HICOPS_INSTALL/tools/psm2excel -i \
[/path/to/hicops/workspace/output]
vi. Repeat Steps iii to v when you modify parameters in the sampleparams.txt.
Precautions
Please read and understand the precautions mentioned here before running HiCOPS.