Difference between revisions of "Haphpipe"
(Created page with "Category:SoftwareCategory:PhylogeneticsCategory:Biology {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|haphpipe}} |{{#vardefine:url|https://gwcbi.github.io/hap...") |
|||
| Line 31: | Line 31: | ||
|}} | |}} | ||
<!--Run--> | <!--Run--> | ||
| − | {{#if: {{#var: exe}}|==Additional Information== | + | {{#if: {{#var: exe}}1|==Additional Information== |
| − | + | For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default. To enable it, please set the environment variable <code>OMPI_MCA_opal_cuda_support=true</code> before launching your MPI processes. Equivalently, you can set the MCA parameter in the command line: <code>mpiexec --mca opal_cuda_support 1 ...</code> | |
| + | In addition, the UCX support is also built but disabled by default. To enable it, set the environment variables <code>OMPI_MCA_pml="ucx"</code> <code>OMPI_MCA_osc="ucx"</code> before launching your MPI processes. Equivalently, you can set the MCA parameters in the command line: <code>mpiexec --mca pml ucx --mca osc ucx ...</code> | ||
| + | Note that you might also need to set <code>UCX_MEMTYPE_CACHE=n</code> for CUDA awareness via UCX. Please consult UCX's documentation for detail. | ||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
Latest revision as of 16:40, 14 March 2023
Description
HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.
Environment Modules
Run module spider haphpipe to find out what environment modules are available for this application.
System Variables
- HPC_HAPHPIPE_DIR - installation directory
- HPC_HAPHPIPE_BIN - executable directory
Additional Information
For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default. To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before launching your MPI processes. Equivalently, you can set the MCA parameter in the command line: mpiexec --mca opal_cuda_support 1 ...
In addition, the UCX support is also built but disabled by default. To enable it, set the environment variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes. Equivalently, you can set the MCA parameters in the command line: mpiexec --mca pml ucx --mca osc ucx ...
Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX. Please consult UCX's documentation for detail.
Citation
If you publish research that uses haphpipe you have to cite it as follows:
When using HAPHPIPE, please cite their article when it is available. For now, reference the GitHub website: https://github.com/gwcbi/haphpipe and the validation paper.