📦 coop-computing-tools

A

• allpairs_master(1)executes All-Pairs workflow in parallel on distributed systems✨
• allpairs_multicore(1)executes All-Pairs workflow in parallel on a multicore machine✨

C

• catalog_query(1)query records from the catalog server✨
• catalog_server(1)start a catalog server✨
• catalog_update(1)send update to catalog server✨
• chirp(1)command line tool providing explicit control of a Chirp server.✨
• chirp_audit_cluster(1)share resources in a heterogeneous, and unreliable computing environment✨
• chirp_benchmark(1)do micro-performance tests on a Chirp server✨
• chirp_distribute(1)copy a directory from one Chirp server to one or more Chirp server(s).✨
• chirp_fuse(1)create a FUSE mount point with virtual access to remote chirp servers✨
• chirp_get(1)get a single file from a Chirp server to local machine✨
• chirp_md5sum(1)share resources in a heterogeneous, and unreliable computing environment✨
• chirp_put(1)copy a single file from local machine to a Chirp server✨
• chirp_server(1)create a Chirp user-level filesystem✨
• chirp_server_hdfs(1)run a chirp server with HDFS client setup✨
• chirp_status(1)get current status of a one or more Chirp server(s)✨
• chirp_stream_files(1)move data to/from chirp servers in parallel✨
• chroot_package_run(1)repeat a program within the package with the help of chroot✨
• condor_submit_makeflow(1)submit workflow to HTCondor batch system✨
• condor_submit_workers(1)submit work_queue_worker to the Condor grid.✨
• confuga(1)An active storage cluster file system.✨
• confuga_adm(1)Administrating the Confuga cluster.✨
• coop-computing-tools(1)share resources in a heterogeneous, and unreliable computing environment✨

D

• deltadb_query(1)query historical data stored by the catalog server.✨
• disk_allocator(1)tool for creating and deleting loop device allocations of a given size.✨

J

• jx_repl(1)interactive command line tool to explore the JX language.✨

M

• make_growfs(1)generate directory listings for the GROW filesystem✨
• makeflow(1)workflow engine for executing distributed workflows✨
• makeflow_amazon_batch_cleanup(1)clean up Amazon services after running Makeflow✨
• makeflow_amazon_batch_setup(1)set up Amazon services for running Makeflow✨
• makeflow_analyze(1)analysis of Makeflow workflows✨
• makeflow_blast(1)Generate a Makeflow to parallelize and distribute blastall jobs✨
• makeflow_ec2_cleanup(1)clean up Amazon services after running Makeflow✨
• makeflow_ec2_setup(1)set up Amazon services for running Makeflow✨
• makeflow_graph_log(1)convert a makeflow log into a graph✨
• makeflow_linker(1)automatic dependency location for workflows✨
• makeflow_log_parser(1)share resources in a heterogeneous, and unreliable computing environment✨
• makeflow_monitor(1)Makeflow log monitor✨
• makeflow_mpi_starter(1)mpi wrapper program for makeflow and workqueue✨
• makeflow_status(1)command line tool retrieving the status of makeflow programs.✨
• makeflow_viz(1)visualization of Makeflow workflows✨
• maker_wq(1)Run the Maker genome annotation tool using Work Queue to harness heterogenous resources✨
• mpi_queue_worker(1)share resources in a heterogeneous, and unreliable computing environment✨

P

• parrot_cp(1)a replacement for cp that provides higher performance when dealing with remote files via parrot_run.✨
• parrot_getacl(1)get ACL information for Parrot filesystem✨
• parrot_identity_box(1)share resources in a heterogeneous, and unreliable computing environment✨
• parrot_locate(1)provides the true location of the data stored in a named file.✨
• parrot_lsalloc(1)list current status of a space allocation✨
• parrot_md5(1)returns the MD5 checksum of a file, generated on the remote system if possible.✨
• parrot_mkalloc(1)create a directory with a space allocation✨
• parrot_mount(1)mount new directories inside of a Parrot instance.✨
• parrot_namespace(1)run a command in a modified namespace.✨
• parrot_package_create(1)generate a package based on the accessed files and the preserved environment variables✨
• parrot_package_run(1)repeat a program within the package with the help of parrot_run✨
• parrot_run(1)run a program in the Parrot virtual file system✨
• parrot_setacl(1)set ACL information for Parrot filesystem✨
• parrot_timeout(1)changes or resets the main timeout for the current parrot session✨
• parrot_whoami(1)returns the user's credentials (id and authentication method) from the perspective of the system being accessed.✨
• pbs_submit_workers(1)submit work_queue_worker to a PBS cluster.✨
• poncho_package_analyze(1)command-line utility for analyzing Python script for library and interpreter dependencies✨
• poncho_package_create(1)command-line utility for creating a Conda virtual environment given a Python dependencies file✨
• poncho_package_run(1)wrapper script that executes Python script within an isolated Conda environment✨

R

• replica_exchange(1)Work Queue application for running replica exchange simulations using ProtoMol✨
• resource_monitor(1)monitors the cpu, memory, io, and disk usage of a tree of processes.✨
• resource_monitor_histograms(1)create HTML pages and graphs of resource monitor data✨
• resource_monitor_visualizer(1)create HTML pages and graphs of resource monitor data✨

S

• sand_align_kernel(1)align candidate sequences sequentially✨
• sand_align_master(1)align candidate sequences in parallel✨
• sand_compress_reads(1)compress sequence data✨
• sand_filter_kernel(1)filter read sequences sequentially✨
• sand_filter_master(1)filter sequences for alignment in parallel✨
• sand_runCA(1)share resources in a heterogeneous, and unreliable computing environment✨
• sand_runCA_5.4(1)share resources in a heterogeneous, and unreliable computing environment✨
• sand_runCA_6.1(1)share resources in a heterogeneous, and unreliable computing environment✨
• sand_runCA_7.0(1)share resources in a heterogeneous, and unreliable computing environment✨
• sand_uncompress_reads(1)uncompress sequence data✨
• sge_submit_workers(1)submit work_queue_worker to a SUN Grid Engine (SGE).✨
• slurm_submit_workers(1)submit work_queue_worker to a SLURM cluster.✨
• split_fasta(1)Split a fasta file according to sequence and character counts✨
• starch(1)STandalone application ARCHiver✨
• starch.bin(1)share resources in a heterogeneous, and unreliable computing environment✨

T

• torque_submit_workers(1)submit work_queue_worker to a Torque cluster.✨

U

• uge_submit_workers(1)submit work_queue_worker to a Univa Grid Engine (UGE) cluster.✨

V

• vine_factory(1)maintain a pool of TaskVine workers on a batch system.✨
• vine_graph_log(1)plots TaskVine performance logs.✨
• vine_status(1)display status of currently running TaskVine applications.✨
• vine_submit_workers(1)submit vine_worker to the Condor, Slurm, or UGE batch systems.✨
• vine_worker(1)worker process for executing tasks dispatched through TaskVine✨

W

• wavefront(1)share resources in a heterogeneous, and unreliable computing environment✨
• wavefront_master(1)executes Wavefront workflow in parallel on distributed systems✨
• weaver(1)workflow engine for executing distributed workflows✨
• work_queue_factory(1)maintain a pool of Work Queue workers on a batch system.✨
• work_queue_graph_log(1)plots Work Queue statistics logs.✨
• work_queue_graph_workers(1)visualize Work Queue transaction logs✨
• work_queue_pool(1)maintain a pool of Work Queue workers on a batch system.✨
• work_queue_status(1)display status of currently running Work Queue applications.✨
• work_queue_worker(1)worker process for executing tasks dispatched through Work Queue✨