= JUMEL (JUROPA MEmory Logger) =

== General information ==
The JUROPA memory logger is intended for monitoring the memory usage of applications on NUMA architectures (especially JUROPA). It consists currently of two Python scripts:
  * `jumel` (JUROPA Memory Logger), the actual logger
  * `juman` (JUROPA Memory ANalyzer), a postprocessing tool

== Concept ==
The logger is started with `mpiexec` and subsequently starts the application to monitor. The monitoring is done per task and/or per node. In time steps information are gathered from files provided by the operating system or from commands that are issued by the logger itself. Currently, the following resources are used/monitored:

  * Monitoring by task:
    * file `/proc/<PID>/status` with keys
      * **`VmExe`**  (Memory of task marked as executable in kB)
      * **`VmSt`**   (Stack memory of task in kB)
      * **`VmData`** (Heap memory of task in kB)
      * **`VmSize`** (Total memory consumption of task in kB)
      * **`VmLck`**  (Memory locked by the kernel in kB)
      * **`VmLib`**  (Memory used as shared memory in kB)
      * **`VmRSS`**  (Resident Set Size of the task in kB)
  
  * Monitoring per node
    * command `vmstat` with keys
      * **`MFree`**  (Free memory of the node in kB)
      * **`TWait`**  (Number of waiting tasks on the node)
      * **`Idle`**   (CPU idling in %)
      * **`TDead`**  (Number of dead tasks on the node)
      * **`UsedUs`** (CPU used by user processes in %)
      * **`UsedKe`** (CPU used by Kernel in %)

When monitoring per task each task writes the value for each key to the file `.memlog/task<MPI-rank>.log` and waits for the next time step. When monitoring by node the process running on core 0 of each node writes the value for each key to the file `node<node-name>_task<MPI-task>.log`. Both (monitoring by task and monitoring by node) can be active at the same time.

The data produced by `jumel` can be analyzed by the `juman` script. It performs statistical analysis of the data (minimum, maximum and total sum of values) and generates corresponding graphs.

== Usage ==
In order to get an overview of the valid options please use

{{{
jumel -u
juman -u
}}}

Suppose the application to monitor is started usually as follows:

{{{
mpiexec -np 32 -e APP_ROOT app.x -i app.inp > my.out
}}}

To start the application with jumel use


{{{
mpiexec -np 32 -e PBS_ID,APP_ROOT jumel -n -a "app.x -i app.inp" > my.out
}}}

The variable `PBS_ID` needs not to be specified, however it will be displayed in the `jumel` logfiles and eases the tracking of the runs afterwards (e.g. when looking for the job in the system logfiles). Once the run is finished run `juman` in the same directory:

{{{
juman -s all -n -i
}}}

The -s option switches on the statistics and the `-i` option will start the graphical display of the results. Currently only a `gnuplot` interface is implemented and postscript or `xfig` files can be generated. An interface for visualization with Python is planned.

== Example: Namd ==
The following job script was used to monitor running the apoa1 benchmark with Namd:

{{{
#!/bin/bash 
#MSUB -l nodes=4:ppn=8
#MSUB -l walltime=00:15:00
#MSUB -v tpt=1 

module load namd/2.7

mpiexec -np 32 -e PBS_JOBID jumel -n -p -t -a "$NAMD_ROOT/bin/namd2 apoa1.namd"

}}}

The graphs were obtained afterwards on the login node with

{{{
juman -s all -n -t -i
}}}

== Results ==
Below the results for the Namd runs are shown for `VmSize` (default key). The values reported are in kB.[[BR]]
 
[[Image(source:/examples/Namd/task-statistics-VmSize.png,720px)]]
[[Image(source:/examples/Namd/task-statistics-minmax-VmSize.png,720px)]]
[[Image(source:/examples/Namd/task-statistics-total-VmSize.png,720px)]]
[[Image(source:/examples/Namd/node-statistics-MFree.png,720px)]]
[[Image(source:/examples/Namd/node-statistics-minmax-MFree.png,720px)]]
[[Image(source:/examples/Namd/node-statistics-total-MFree.png,720px)]]

== Example Mapt ==
{{{
#!/bin/bash 
#MSUB -l nodes=2:ppn=8
#MSUB -l walltime=00:05:00
#MSUB -v tpt=1 


mpiexec -np 16 jumel -d 2 -n -p -t -a "mapt.x" > mapt.out

}}}

The graphs were obtained afterwards on the login node with

{{{
juman -s all -i -n -t
}}}

== Results ==
Below the results for the Mapt runs are shown for `VmSize` (default key). The values reported are in kB.[[BR]]

[[Image(source:/examples/Mapt/task-statistics-VmSize.png,720px)]]
[[Image(source:/examples/Mapt/task-statistics-minmax-VmSize.png,720px)]]
[[Image(source:/examples/Mapt/task-statistics-total-VmSize.png,720px)]]
[[Image(source:/examples/Mapt/node-statistics-MFree.png,720px)]]
[[Image(source:/examples/Mapt/node-statistics-minmax-MFree.png,720px)]]
[[Image(source:/examples/Mapt/node-statistics-total-MFree.png,720px)]]


== SVN Access ==
{{{
svn list https://svn.version.fz-juelich.de/jumel
}}}