Commit ca547956 authored by David Hrbáč's avatar David Hrbáč

Cap correction

parent f06d45e5
# Resources Allocation Policy
## Job queue policies
## Job Queue Policies
The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and resources available to the Project. The fair-share at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the [Job scheduling](job-priority/) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:
......@@ -31,7 +31,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
!!! note
To access node with Xeon Phi co-processor user needs to specify that in [job submission select statement](job-submission-and-execution/).
## Queue notes
## Queue Notes
The job wall-clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be [set manually, see examples](job-submission-and-execution/).
......
......@@ -17,7 +17,7 @@ $ ml Clp
The module sets up environment variables required for linking and running applications using Clp. This particular command loads the default module Clp/1.16.10-intel-2017a, Intel module intel/2017a and other related modules.
## Compiling and linking
## Compiling and Linking
!!! note
Link with -lClp
......@@ -51,7 +51,7 @@ int main (int argc, const char *argv[])
}
```
### Load modules and compile:
### Load Modules and Compile:
```console
ml Clp
......
......@@ -28,7 +28,7 @@ SQLite/3.8.8.1
Python/2.7.9
```
## Running generic example
## Running Generic Example
LMGC90 software main API is a Python module. It comes with a pre-processor written in Python. There are several examples that you can copy from the `examples` directory which is in `/apps/all/LMGC90/2017.rc1-GCC-6.3.0-2.27` folder. Follow the next steps to run one of them.
......
# Resource Accounting Policy
## Wall-clock Core-Hours WCH
## Wall-Clock Core-Hours WCH
The wall-clock core-hours (WCH) are the basic metric of computer utilization time.
1 wall-clock core-hour is defined as 1 processor core allocated for 1 hour of wall-clock time. Allocating a full node (16 cores Anselm, 24 cores Salomon)
......
# Compilers
## Available compilers, including GNU, INTEL and UPC compilers
## Available Compilers, Including GNU, INTEL and UPC Compilers
There are several compilers for different programming languages available on the cluster:
......@@ -26,7 +26,7 @@ Commercial licenses:
For information about the usage of Intel Compilers and other Intel products, please read the [Intel Parallel studio](intel-suite/intel-compilers/) page.
## PGI Compilers (only on Salomon)
## PGI Compilers (Only on Salomon)
The Portland Group Cluster Development Kit (PGI CDK) is available on Salomon.
......
......@@ -413,7 +413,7 @@ Done
!!! note ""
Behavioral of automatic offload mode is controlled by functions called within the program or by environmental variables. Complete list of controls is listed [here](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
### Automatic offload example #2
### Automatic Offload Example #2
In this example, we will demonstrate automatic offload control via an environment vatiable MKL_MIC_ENABLE. The function DGEMM will be offloaded.
......@@ -922,7 +922,7 @@ $ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH \
: -host r25u26n711 -n 6 ~/mpi-test
```
### Symmetric model
### Symmetric Model
In a symmetric mode MPI programs are executed on both host computer(s) and MIC accelerator(s). Since MIC has a different
architecture and requires different binary file produced by the Intel compiler two different files has to be compiled before MPI program is executed.
......
......@@ -85,7 +85,7 @@ $ source activate anaconda2
The default is Python 3.6
### First usage Module Anaconda3
### First Usage Module Anaconda3
```console
$ ml Anaconda3/4.4.0
......
......@@ -24,7 +24,7 @@ $ which javac
Java applications may use MPI for inter-process communication, in conjunction with Open MPI. Read more on <http://www.open-mpi.org/faq/?category=java>. This functionality is currently not supported on Anselm cluster. In case you require the java interface to MPI, please contact [cluster support](https://support.it4i.cz/rt/).
## Java with OpenMPI
## Java With OpenMPI
Because there is an increasing interest in using Java for HPC. Also, MPI can benefit from Java because its widespread use makes it likely to find new uses beyond traditional HPC applications.
......
......@@ -55,7 +55,7 @@ $ ml av python/2
If you need software that is not listed, request it at support@it4i.cz.
```
### Used Module Python/2.X
### Used Module Python/2.x
```console
$ python --version
......@@ -65,7 +65,7 @@ $ python --version
Python 2.7.1
```
### Packages in Python/2.X
### Packages in Python/2.x
```console
$ pip list
......@@ -79,7 +79,7 @@ beautifulsoup4 (4.5.3)
...
```
### How to Install New Package to Python/2.X?
### How to Install New Package to Python/2.x?
```console
$ ml Python/2.7.13
......@@ -92,7 +92,7 @@ Installing collected packages: wheel
Successfully installed wheel-0.30.0
```
### How to Update Package in Python/2.X?
### How to Update Package in Python/2.x?
```console
$ ml Python/2.7.13
......@@ -124,7 +124,7 @@ $ ml av python/3
```
### Used Module Python/3.X
### Used Module Python/3.x
```console
$ python --version
......@@ -134,7 +134,7 @@ $ python --version
Python 3.6.2
```
### Packages in Python/3.X
### Packages in Python/3.x
```console
$ pip3 list
......@@ -143,7 +143,7 @@ pip (8.0.2)
setuptools (20.1.1)
```
### How to Install New Package to Python/3.X
### How to Install New Package to Python/3.x
```console
$ ml Python/3.6.2-base
......@@ -173,7 +173,7 @@ Installing collected packages: six, python-dateutil, pytz, numpy, pandas
Successfully installed numpy-1.13.1 pandas-0.20.3 python-dateutil-2.6.1 pytz-2017.2 six-1.11.0
```
### How to Update Package in Python/3.X?
### How to Update Package in Python/3.x?
```console
$ pip3 install scipy --upgrade --user
......
......@@ -7,7 +7,7 @@ For searching available modules type:
$ ml av Tensorflow
```
## Anselm modules
## Anselm Modules
Anselm provides beside others these three different TensorFlow modules:
......@@ -25,7 +25,7 @@ Anselm provides beside others these three different TensorFlow modules:
* CUDA/8.0.44
* cuDNN/5.1-CUDA-8.0.44
## Salomon modules
## Salomon Modules
Salomon provides beside others these three different TensorFlow modules:
......@@ -42,7 +42,7 @@ Salomon provides beside others these three different TensorFlow modules:
* Python/3.6.1
* protobuf/3.2.0-GCC-7.1.0-2.28-Python-3.6.1
## TensorFlow application example
## TensorFlow Application Example
After loading one of the available TensorFlow modules, you can check the functionality running the following python script.
......
......@@ -108,7 +108,7 @@ $ mpiexec -bycore -bind-to-core python hello_world.py
In this example, we run MPI4Py enabled code on 4 nodes, 16 cores per node (total of 64 processes), each python process is bound to a different core. More examples and documentation can be found on [MPI for Python webpage](https://pypi.python.org/pypi/mpi4py).
### Adding numbers
### Adding Numbers
Task: count sum of numbers from 1 to 1 000 000. (There is an easy formula to count the sum of arithmetic sequence, but we are showing the MPI solution with adding numbers one by one).
......
......@@ -29,7 +29,7 @@ end program hello_world
* num_images() - returns the number of all images
* this_image() - returns the image index - numbered from 1 to num_images()
### Co-dimension Variables Declaration
### Co-Dimension Variables Declaration
Coarray variables can be declared with the **codimension[*]** attribute or by adding trailing index **[*]** after the variable name.
Notice, the ***** character always has to be in the square brackets.
......
......@@ -83,7 +83,7 @@ Options:
## Build Software Using Provided EasyConfig File
### Search For Available Easyconfig
### Search for Available Easyconfig
Searching for available easyconfig files can be done using the **--search** (long output) and **-S** (short output) command line options. All easyconfig files available in the robot search path are considered and searching is done case-insensitive.
......
......@@ -29,7 +29,7 @@ Singularity.centos:latest> cat /etc/redhat-release
CentOS Linux release 7.3.1611 (Core)
```
## Creating Own Image from Docker Image
## Creating Own Image From Docker Image
```console
hrb33@hrb33-toshiba:/$ cd /tmp/
......
......@@ -20,7 +20,7 @@ $ ml av Spack
!!! note
Spack/default is rule for setting up local installation
## First Usage Module Spack/default
## First Usage Module Spack/Default
The Spack will be installed into `~/Spack` folder. You can set the configuration by modifying ~/.spack/configure.yml.
......@@ -61,7 +61,7 @@ $ spack --version
0.10.0
```
## Usage Module Spack/default
## Usage Module Spack/Default
```console
$ ml Spack
......@@ -102,7 +102,7 @@ apr font-ibm-type1 libmesh op
...
```
#### Specify Software Version (for package)
#### Specify Software Version (For Package)
To see more available versions of a package, run `spack versions`.
......@@ -114,7 +114,7 @@ $ spack versions git
Found no versions for git
```
## Graph For Software Package
## Graph for Software Package
Spack provides `spack graph` command to display dependency graph. The command by default generates an ASCII rendering of a spec’s dependency graph.
......@@ -317,7 +317,7 @@ $ spack load git
source ~/.local/easybuild/software/Spack/0.10.0/share/spack/setup-env.csh
```
### First usage
### First Usage
```console
$ . ~/.local/easybuild/software/Spack/0.10.0/share/spack/setup-env.sh
......
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