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puetz committed Mar 23, 2016
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## Changes you may need to make in the _Makefile_

Please customize your Makefile as you need. You may want to change
(friendly reminder: in sh shells there must not be any whitespace between VARIABLE=VALUE)
(friendly reminder: in sh shells there must not be any whitespace in `VARIABLE=VALUE`)


- the location of your CUDA compiler nvcc (line 5)
- change the compute capability according to your device (e.g. m_35 to sm_20, line 5)
- the location of your CUDA library (line 6)
- add debugging flags "-g -G" to OPT (line 7)
- and anything you want to change, as long as you know what you are doing.
- add debugging flags `-g -G` to OPT (line 7)
- and anything else you want to change, as long as you know what you are doing.

## What should my data look like?
In order to perform brute-force statistical 3-way interaction tests on SNP data with kleEpistasis you will have to provide your genotype data in PLINK binary format and a phenotype in PLINK alternate phenotype format. Please see
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Depending on your CPU und Graphics Card, the GPU has to wait for the CPU to finish before copying the next results.
To resolve this the task is split into chunks and processed by one thread each.
We used an Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz combined with a NVIDIA Tesla K40 and 8 threads (`-threads 8`) without encountering wait time.
This program will altogether create n+2 threads with n as the number passed via the `-threads` flag.
The program will altogether create `n+2` threads when `n` is the number passed via the `-threads` flag.


## General

#### Memory:
Doing a run on 5k SNPs and 1k Individuals, you need at least 20GB of RAM
For a run on 5000 SNPs and 1000 Individuals, you need at least 20GB of RAM
#### Execution time:
We were able to perform a run on 5k SNPs and 1k Individuals, on an Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz combined with a NVIDIA Tesla K40 in approx. 2 hours
We were able to perform a run on 5000 SNPs and 1000 Individuals, on an Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz combined with a NVIDIA Tesla K40 in approx. 2 hours


### Result file:
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