Just a heads up, we don't have a huge amount of space on this machine, ~750 GB for the git repos. We can include some data in the projects, but really big datasets will need to remain elsewhere. For anyone new to Git, this is a fairly good place to start: http://gitref.org/index.html Documentation for Gitlab is available here: http://doc.gitlab.com/

Commit d58842cc authored by Khalid Kunji's avatar Khalid Kunji

Merge branch 'master' of https://cse-git.qcri.org/Imputation/GIGI-Quick

Local and source got out of sync
parents df552090 e5f62a3c
......@@ -10,22 +10,30 @@ Somewhat modern version of g++ if you need to recompile the binaries, we haven't
##### With Git
git clone https://cse-git.qcri.org/Imputation/GIGI-Quick.git
##### With a browser
Go to this url: https://cse-git.qcri.org/Imputation/GIGI-Quick
Click on the icon with the down arrow just to the left of the "+" icon.
Go to this url: https://cse-git.qcri.org/Imputation/GIGI-Quick/tree/master
Click on the icon with the download arrow above the column "Last Update" on the right hand side.
There are several download options with different compressions, if you get run_GIGI this way, then you will need to decompress it before proceeding
#### Installation
Once you have the files, there are executables compiled on Red Hat, 64 bit Linux, if this is not your system, then you may need to recompile them:
Starting from the folder where you downloaded run_GIGI
cd GIGI-Quick/SPLIT/
g++ GIGISplit.cpp -o gigisplit
cd ../MERGE/
g++ GIGIMerge.cpp -o gigimerge
```cd GIGI-Quick/SPLIT/```
```g++ GIGISplit.cpp -o gigisplit```
```cd ../MERGE/ ```
```g++ GIGIMerge.cpp -o gigimerge```
That's it, GIGI-Quick is installed, they main file/command to run it is run_GIGI
If you like you can now add GIGI-Quick to your path, the examples assume that you have, you can do this by adding the folling to your .bashrc (located in your home folder)
export PATH=${PATH}:/path/to/folder/where/you/put/run_GIGI
```export PATH=${PATH}:/path/to/folder/where/you/put/run_GIGI```
Then source your .bashrc to apply the changes right away
```source ~/.bashrc```
#### Usage
......@@ -47,7 +55,7 @@ run_GIGI parameter_file -o [OUTPUT FOLDER] -n [RUN NAME] -t [THREADS] -m [MEMORY
[MEMORY IN MB] using an estimate of the amount of memory GIGI may need. If -m [MEMORY IN MB] wasn't given, then it will use the amount of memory available
as shown by 'free.' For older kernels this isn't shown and we use an estimate that is no longer accurate for modern systems (amount free + amount of buff/cache).
https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git/commit/?id=34e431b0ae398fc54ea69ff85ec700722c9da773 Also, -t is ignored when -q is given.
-e [MEMORY IN MB] : Not yet implemented, manual estimate of how much memory GIGI will need for queued mode in case the calculated estimate is too inaccurate
-e [MEMORY IN MB] : Manual estimate of how much memory GIGI will need for queued mode in case the calculated estimate is too inaccurate
Examples:
```bash
......
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