From 5cb5b05606c69c32fc305bffe2b83f5565d8b62c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Benno=20Pu=CC=88tz?= Date: Wed, 23 Mar 2016 02:48:08 +0100 Subject: [PATCH] getting closer ... --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index ec79fc6..475e9a7 100644 --- a/README.md +++ b/README.md @@ -28,14 +28,14 @@ which is a small script to create the needed filesystem structure and compile us ## 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 @@ -88,15 +88,15 @@ Results will be processed in the background by the CPU while the GPU creates new 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: