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 017e7aeb authored by Khalid Kunji's avatar Khalid Kunji

Update README.md

parent fd785bf1
......@@ -23,22 +23,31 @@ 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
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
#### Usage
Note: The parameter file is the same as you would use for GIGI normally, but if you are using the long format, then pass the "-l" option
The examples in shown below use the file "param-v1_06.txt" because it is included in the repository and can be run by simply cutting and pasting the example line.
Note: Memory constraints are not yet implemented, use your own judgement, we have not yet seen an example that won't fit in 6GB comfortably.
run_GIGI parameter_file -o [OUTPUT FOLDER] -n [RUN NAME] -t [THREADS] -m [MEMORY IN MB] [-l] [-v]
run_GIGI parameter_file -o [OUTPUT FOLDER] -n [RUN NAME] -t [THREADS] -m [MEMORY IN MB] [-l] [-v] -q [THREADS] -r [START] [END] [-V] [-h]
-o [OUTPUT FOLDER] : This is the path to use for the outputs from the run_GIGI scripts, including temporary files.
-n [RUN NAME] : This is a path relative to the [OUTPUT FOLDER] to use to keep the outputs from more than one run of run_GIGI separated.
-t [THREADS] : The number of threads to use for run_GIGI, and also the number of chunks to split the input into.
-m [MEMORY IN MB] : The amount of RAM that run_GIGI will restrict its use to, not yet implemented
-l : Specifies that the input is in the long format.
-v : Verbose mode, output from run_GIGI is much quiter now, you can see much more of what it is doing and what variables are set to at various stages with -v.
-V : Verbose mode, output from run_GIGI is much quiter now, you can see much more of what it is doing and what variables are set to at various stages with -v.
-v : Display the version of GIGI-Quick and exit.
-h : Display this help text.
-r [START] [END] : Run on only a selected region, starting at start and ending at end, this region will be selected before any further splitting.
-q [THREADS] : Run in queued mode, this mode will run up to THREADS instances of GIGI at a time and will attempt to keep the total amount of memory being used less than
[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
Examples:
```bash
......@@ -49,7 +58,7 @@ Examples:
run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -t 2 #Limit to only 2 threads (and hence two chunks)
run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -m 1000 #Limit memory use to 1 GB, please read the section on memory and cgroups
run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -lmt 1000 2 #Limit memory use to 1 GB, please read the section on memory and cgroups, and threads to 2 with input in the long format, do not cut and paste this one because the included param-v1_06.txt is NOT in the long format
run_GIGI INPUTS/Sample_Input/param-v1_06.txt -o RUN_FOLDER/ -n test_run -m 20 -q 3 -V -r 3 70 #Output in ./RUN_FOLDER/test_run, limit memory to 20 MB, use the queued mode with up to 3 threads at a time, and run on only the region from 3 to 70, note: the memory estimated as needed in queued mode does not account for the restricted region
```
If there is a problem that makes GIGI stop before completion, then the output files are left as they are in order to allow users to rerun only failed portions as needed.
......
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