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https://github.com/billsioros/mpisuite
Using bash to automate the compilation, scheduling and profiling of MPI / OpenMP applications
https://github.com/billsioros/mpisuite
automated automated-build automated-deployment automated-testing automated-tests automation-framework bash bash-script bash-scripting openmp openmp-parallelization openmp-support openmpi openmpi-cpu-clusters
Last synced: about 1 month ago
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Using bash to automate the compilation, scheduling and profiling of MPI / OpenMP applications
- Host: GitHub
- URL: https://github.com/billsioros/mpisuite
- Owner: billsioros
- License: mit
- Created: 2019-11-20T21:15:27.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2023-12-15T17:42:32.000Z (about 1 year ago)
- Last Synced: 2023-12-15T18:54:11.445Z (about 1 year ago)
- Topics: automated, automated-build, automated-deployment, automated-testing, automated-tests, automation-framework, bash, bash-script, bash-scripting, openmp, openmp-parallelization, openmp-support, openmpi, openmpi-cpu-clusters
- Language: Shell
- Homepage: http://www.di.uoa.gr/eng/node/1451
- Size: 635 KB
- Stars: 7
- Watchers: 2
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
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README
# **MPIsuite** - MPI / OpenMP Task Automation
[](https://opensource.org/licenses/MIT)
_Important Notice: This project is in early development. Features are sparse and bugs may arise._
## **The Suite**
[mpis-compile](./MPIs/mpis-compile) is responsible for compiling the supplied MPI, OpenMP or Hybrid source file.
It is expecting at least one arguement, which should be the source file. Any other arguements are grouped and form pairs of keys and values. Each pair represents a macro, named **key** with a value of **value**, that is going to be defined at compile time.
[mpis-schedule](./MPIs/mpis-schedule) is responsible for generating a job and submitting it to the PBS queue.
It is expecting exactly two arguements, the executable and the number of processes that should be created.
[mpis-profile](./MPIs/mpis-profile) is responsible for compiling our program with various (key, value) macro pairs, running it with different numbers of processes and collecting our measurements.
It is expecting exactly two arguements, the source file and a [profiling description](#profiling-descriptions).
## **Installation**
chmod +x setup.sh
./setup.sh
Uninstalling **MPIs** can be achieved simply by running
./setup.sh --uninstall
## **Configuration**
* **MPIS_OUTPUT_ROOT** indicates the directory, under which the files and directories generated by our scheduler and profiler are going to be saved.
* **MPIS_USER_ID** is being used when querying the job queue to check if a job is done running.
* **MPIS_EDITOR** and **MPIS_EDITOR_ARGS** are optional and are used by the profiler to open files in your favorite editor.
You are more than welcome to check _~/.mpisrc_ out, for additional configuration settings.
## **Profiling Descriptions**
[mpis-profile](./MPIs/mpis-profile) is expecting a profiling description, which **must** define:
* a regular expression named **TIME_PATTERN**, which indicates the format of our timer's output.
* a string named **MACRO**, containing the name of the macro that should be defined by [mpis-compile](./MPIs/mpis-compile).
* an array named **VALUES**, containing the values that macro **MACRO** should receive in different runs.
You can optionally define **MPIS_ENABLE_PROFILING** and/or **MPIS_LINK_OPENMP**,
in order to bypass confirmation on the corresponding compilation step. These can be globally defined, as well, in _~/.mpisrc_.
## **Example**
Let' s assume we would like to estimate the integral from a to b of an equation f(x) using the trapezoidal rule.
Let' s also assume that we have already developed an **MPI** program, named **mpi_trap1.c** to do so and this program defines a macro named **nTraps**, which corresponds to the **number of trapezoids** that are going to be used in the calculation of the integral.
### **Compiling**
We now need to compile our source file using [mpis-compile](./MPIs/mpis-compile) as follows
mpis-compile mpi_trap1.c nTraps 512
[mpis-compile] enable profiling: y
[mpis-compile] link OpenMP: n
This results in the creation of an executable file named **mpi_trap1.x**, inside which the macro **nTraps** has been assigned the value **512**.
**ATTENTION:** If your source code contains a _#define_ statement corresponding to the macro provided, the supplied value will be **overriden**. Remove the _#define_ statement or surround it with a _#ifndef MACRO ... #endif_ preprocessor block to resolve this issue.
Executing [mpis-compile](./MPIs/mpis-compile) with the _--clean_ option deletes the executable.
### **Scheduling**
Scheduling the executable can be achieved like so
mpis-schedule mpi_trap1.x 16
[mpis-schedule] name='mpi_trap1_16_argo059_job', id='14524.argo', ps=16, ns=2, ppn=8
Job id Name User Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
12507.argo myJob argo081 0 Q workq
14524.argo mpi_trap1_16_ar argo059 00:00:00 R workq
* **ps** stands for the **number of processes**
* **ns** stands for the **number of nodes**
* **ppn** stands for the **number of processes per node**
The following files and directories are generated
find ./out
./out/
./out/16
./out/16/21_11_2019
./out/16/21_11_2019/15_06_30
./out/16/21_11_2019/15_06_30/mpi_trap1_16_argo059_job.stderr
./out/16/21_11_2019/15_06_30/mpi_trap1_16_argo059_job.stdout
Executing [mpis-schedule](./MPIs/mpis-schedule) with the _--clean_ option removes any mpiP and job associated files and removes any **MPIS_USER_ID** associated job from the queue.
### **Profiling**
We firstly need to define a [profiling description](#profiling-descriptions) like so
```bash
#!/bin/bash
export MPIS_ENABLE_PROFILING=true
export MPIS_LINK_OPENMP=false
TIME_PATTERN="Elapsed time: \K([0-9]+\.[0-9]+)"
MACRO="nTraps"
VALUES=()
for ((power = 20; power <= 28; power += 2))
do
VALUES+=( "$(( 2 << ($power - 1) ))" )
done
```
We can compile the source file with different numbers of trapezoids defined and schedule it with different numbers of processes in a single command as follows
mpis-profile ./mpi_trap1.c ./description.sh
The following files and directories are generated
find ./out
./out/
./out/21_11_2019
./out/21_11_2019/15_13_08
./out/21_11_2019/15_13_08/67108864
./out/21_11_2019/15_13_08/67108864/4
./out/21_11_2019/15_13_08/67108864/4/mpi_trap1_4_argo059_job.stderr
./out/21_11_2019/15_13_08/67108864/4/mpi_trap1_4_argo059_job.stdout
...
./out/21_11_2019/15_13_08/268435456/32
./out/21_11_2019/15_13_08/268435456/32/mpi_trap1_32_argo059_job.stderr
./out/21_11_2019/15_13_08/268435456/32/mpi_trap1_32_argo059_job.stdout
./out/21_11_2019/15_13_08/268435456/16
./out/21_11_2019/15_13_08/268435456/16/mpi_trap1_16_argo059_job.stderr
./out/21_11_2019/15_13_08/268435456/16/mpi_trap1_16_argo059_job.stdout
./out/21_11_2019/15_13_08/results.csv
Here is how our measurements look like
head -5 ./out/21_11_2019/15_13_08/results.csv
nTraps , Processes, Time , Speed Up , Εfficiency
1048576 , 1 , 0.000925, 1.0 , 1.0
1048576 , 2 , 0.00082 , 1.12804878049 , 0.564024390245
1048576 , 4 , 0.000841, 1.09988109394 , 0.274970273485
1048576 , 8 , 0.001022, 0.905088062622 , 0.113136007828
## **Licence**
This project is licensed under the [MIT License](./LICENCE).