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 d5056e45 authored by Ehsan Ullah's avatar Ehsan Ullah

Update README.md

parent d58842cc
......@@ -20,11 +20,11 @@ Starting from the folder where you downloaded run_GIGI
```cd GIGI-Quick/SPLIT/```
```g++ GIGISplit.cpp -o gigisplit```
```g++ -O2 GIGISplit.cpp -o gigisplit```
```cd ../MERGE/ ```
```g++ GIGIMerge.cpp -o gigimerge```
```g++ -O2 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)
......@@ -59,14 +59,14 @@ run_GIGI parameter_file -o [OUTPUT FOLDER] -n [RUN NAME] -t [THREADS] -m [MEMORY
Examples:
```bash
run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt #Output in the current folder with no run name identifying subfolder, threads and memory determined automatically
run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS -n test_run #Output in ./OUTPUTS/test_run
run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS -n test_run -v #Output in ./OUTPUTS/test_run, verbose mode (print more detailed information)
run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS -n test_run -l #Output in ./OUTPUTS/test_run for a parameter file 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 -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
./run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt #Output in the current folder with no run name identifying subfolder, threads and memory determined automatically
./run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS -n test_run #Output in ./OUTPUTS/test_run
./run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS -n test_run -v #Output in ./OUTPUTS/test_run, verbose mode (print more detailed information)
./run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS -n test_run -l #Output in ./OUTPUTS/test_run for a parameter file 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 -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.
......@@ -77,7 +77,7 @@ e.g. if the 2nd example failed, I would "rm -R ./OUTPUTS/test_run" before rerunn
With the addition of -v and cleanup of output, you may notice that even with -v you don't see the output of split, gigi, and merge any longer. These are now written to their own individual log files in the output directory/run subdirectory.
e.g. run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS -n test_run will have logs in ./OUTPUTS/test_run/LOGS
e.g. ./run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS -n test_run will have logs in ./OUTPUTS/test_run/LOGS
#### Memory and cgroups
......
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