Commit cb2411a1 authored by Lubomir Prda's avatar Lubomir Prda

Finalized spell check

parent 54b97784
......@@ -245,6 +245,35 @@ i.e.
pthreads
uninitialised
broadcasted
ITAC
hotspots
Bioinformatics
semiempirical
DFT
polyfill
ES6
HTML5Rocks
minifiers
CommonJS
PhantomJS
bundlers
Browserify
versioning
isflowing
ispaused
NPM
sublicense
Streams2
Streams3
blogpost
GPG
mississippi
Uint8Arrays
Uint8Array
endianness
styleguide
noop
MkDocs
- docs.it4i/anselm-cluster-documentation/environment-and-modules.md
MODULEPATH
bashrc
......@@ -653,3 +682,101 @@ EBROOTVALGRIND
O2
- docs.it4i/salomon/software/intel-suite/intel-compilers.md
UV1
- docs.it4i/salomon/software/numerical-languages/octave.md
octcode.m
mkoctfile
- docs.it4i/software/orca.md
pdf
- node_modules/es6-promise/README.md
rsvp.js
es6-promise
es6-promise-min
Node.js
testem
- node_modules/spawn-sync/lib/json-buffer/README.md
node.js
- node_modules/spawn-sync/node_modules/concat-stream/node_modules/readable-stream/doc/wg-meetings/2015-01-30.md
WG
domenic
mikeal
io.js
sam
calvin
whatwg
compat
mathias
isaac
chris
- node_modules/spawn-sync/node_modules/concat-stream/node_modules/readable-stream/node_modules/core-util-is/README.md
core-util-is
v0.12.
- node_modules/spawn-sync/node_modules/concat-stream/node_modules/readable-stream/node_modules/isarray/README.md
isarray
Gruber
julian
juliangruber.com
NONINFRINGEMENT
- node_modules/spawn-sync/node_modules/concat-stream/node_modules/readable-stream/node_modules/process-nextick-args/license.md
Metcalf
- node_modules/spawn-sync/node_modules/concat-stream/node_modules/readable-stream/node_modules/process-nextick-args/readme.md
process-nextick-args
process.nextTick
- node_modules/spawn-sync/node_modules/concat-stream/node_modules/readable-stream/node_modules/string_decoder/README.md
_decoder.js
Joyent
joyent
repo
- node_modules/spawn-sync/node_modules/concat-stream/node_modules/readable-stream/node_modules/util-deprecate/History.md
kumavis
jsdocs
- node_modules/spawn-sync/node_modules/concat-stream/node_modules/readable-stream/node_modules/util-deprecate/README.md
util-deprecate
Rajlich
- node_modules/spawn-sync/node_modules/concat-stream/node_modules/readable-stream/README.md
v7.0.0
userland
chrisdickinson
christopher.s.dickinson
gmail.com
9554F04D7259F04124DE6B476D5A82AC7E37093B
calvinmetcalf
calvin.metcalf
F3EF5F62A87FC27A22E643F714CE4FF5015AA242
Vagg
rvagg
vagg.org
DD8F2338BAE7501E3DD5AC78C273792F7D83545D
sonewman
newmansam
outlook.com
Buus
mafintosh
mathiasbuus
Denicola
domenic.me
Matteo
Collina
mcollina
matteo.collina
3ABC01543F22DD2239285CDD818674489FBC127E
- node_modules/spawn-sync/node_modules/concat-stream/readme.md
concat-stream
concat
cb
- node_modules/spawn-sync/node_modules/os-shim/README.md
0.10.x
os.tmpdir
os.endianness
os.EOL
os.platform
os.arch
0.4.x
Aparicio
Adesis
Netlife
S.L
- node_modules/spawn-sync/node_modules/try-thread-sleep/node_modules/thread-sleep/README.md
node-pre-gyp
npm
- node_modules/spawn-sync/README.md
iojs
# User documentation
This is project contain IT4Innovation user documentation source.
This is project contain IT4Innovations user documentation source.
## Environments
......@@ -26,11 +26,11 @@ CentOS
Mellanox
```
## Developemnt Environment
## Development Environment
### MkDocs
Documentation pages are build with [MkDocs](http://www.mkdocs.org/), [MkDocs at GitHub](https://github.com/mkdocs/mkdocs/). You need to install mkdocs loacally so that you can build the pages and run developement web server.
Documentation pages are build with [MkDocs](http://www.mkdocs.org/), [MkDocs at GitHub](https://github.com/mkdocs/mkdocs/). You need to install MkDocs locally so that you can build the pages and run development web server.
```bash
pip install mkdocs pygments pymdown-extensions
......
Intel Inspector
===============
Intel Inspector is a dynamic memory and threading error checking tool for C/C++/Fortran applications. It can detect issues such as memory leaks, invalid memory references, uninitalized variables, race conditions, deadlocks etc.
Intel Inspector is a dynamic memory and threading error checking tool for C/C++/Fortran applications. It can detect issues such as memory leaks, invalid memory references, uninitialized variables, race conditions, deadlocks etc.
Installed versions
------------------
......@@ -29,7 +29,7 @@ In the main pane, you can start a predefined analysis type or define your own. C
### Batch mode
Analysis can be also run from command line in batch mode. Batch mode analysis is run with command inspxe-cl. To obtain the required parameters, either consult the documentation or you can configure the analysis in the GUI and then click "Command Line" button in the lower right corner to the respective command line.
Analysis can be also run from command line in batch mode. Batch mode analysis is run with command `inspxe-cl`. To obtain the required parameters, either consult the documentation or you can configure the analysis in the GUI and then click "Command Line" button in the lower right corner to the respective command line.
Results obtained from batch mode can be then viewed in the GUI by selecting File -> Open -> Result...
......
Intel Trace Analyzer and Collector
==================================
Intel Trace Analyzer and Collector (ITAC) is a tool to collect and graphicaly analyze behaviour of MPI applications. It helps you to analyze communication patterns of your application, identify hotspots, perform correctnes checking (identify deadlocks, data corruption etc), simulate how your application would run on a different interconnect.
Intel Trace Analyzer and Collector (ITAC) is a tool to collect and graphically analyze behavior of MPI applications. It helps you to analyze communication patterns of your application, identify hotspots, perform correctness checking (identify deadlocks, data corruption etc), simulate how your application would run on a different interconnect.
ITAC is a offline analysis tool - first you run your application to collect a trace file, then you can open the trace in a GUI analyzer to view it.
......
......@@ -112,7 +112,7 @@ Running MPI Programs
The MPI program executable must be compatible with the loaded MPI module.
Always compile and execute using the very same MPI module.
It is strongly discouraged to mix mpi implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors.
It is strongly discouraged to mix MPI implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors.
The MPI program executable must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem. You need to preload the executable, if running on the local scratch /lscratch filesystem.
......@@ -127,7 +127,7 @@ Consider these ways to run an MPI program:
**One MPI** process per node, using 24 threads, is most useful for memory demanding applications, that make good use of processor cache memory and are not memory bound. This is also a preferred way for communication intensive applications as one process per node enjoys full bandwidth access to the network interface.
**Two MPI** processes per node, using 12 threads each, bound to processor socket is most useful for memory bandwidth bound applications such as BLAS1 or FFT, with scalable memory demand. However, note that the two processes will share access to the network interface. The 12 threads and socket binding should ensure maximum memory access bandwidth and minimize communication, migration and numa effect overheads.
**Two MPI** processes per node, using 12 threads each, bound to processor socket is most useful for memory bandwidth bound applications such as BLAS1 or FFT, with scalable memory demand. However, note that the two processes will share access to the network interface. The 12 threads and socket binding should ensure maximum memory access bandwidth and minimize communication, migration and NUMA effect overheads.
!!! Note "Note"
Important! Bind every OpenMP thread to a core!
......
......@@ -271,8 +271,8 @@ You can use MATLAB on UV2000 in two parallel modes:
### Threaded mode
Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set maxNumCompThreads accordingly and certain operations, such as fft, , eig, svd, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.
Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set maxNumCompThreads accordingly and certain operations, such as `fft`, `eig`, `svd`, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.
### Local cluster mode
You can also use Parallel Toolbox on UV2000. Use l[ocal cluster mode](matlab/#parallel-matlab-batch-job-in-local-mode), "SalomonPBSPro" profile will not work.
You can also use Parallel Toolbox on UV2000. Use [local cluster mode](matlab/#parallel-matlab-batch-job-in-local-mode), "SalomonPBSPro" profile will not work.
......@@ -54,4 +54,4 @@ The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c c
$ mkoctfile -v
```
Octave may use MPI for interprocess communication This functionality is currently not supported on the cluster cluster. In case you require the octave interface to MPI, please contact our [cluster support](https://support.it4i.cz/rt/).
Octave may use MPI for inter-process communication This functionality is currently not supported on the cluster cluster. In case you require the octave interface to MPI, please contact our [cluster support](https://support.it4i.cz/rt/).
......@@ -366,7 +366,7 @@ First, create the mount point
$ mkdir cesnet
```
Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz (Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno) Mount tier1_home **(only 5120M !)**:
Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz (Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno) Mount tier1_home **(only 5120 MB !)**:
```bash
$ sshfs username@ssh.du1.cesnet.cz:. cesnet/
......@@ -398,16 +398,16 @@ Once done, please remember to unmount the storage
$ fusermount -u cesnet
```
### Rsync access
### RSYNC access
!!! Note "Note"
Rsync provides delta transfer for best performance, can resume interrupted transfers
RSYNC provides delta transfer for best performance, can resume interrupted transfers
Rsync is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. Rsync is widely used for backups and mirroring and as an improved copy command for everyday use.
RSYNC is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. RSYNC is widely used for backups and mirroring and as an improved copy command for everyday use.
Rsync finds files that need to be transferred using a "quick check" algorithm (by default) that looks for files that have changed in size or in last-modified time. Any changes in the other preserved attributes (as requested by options) are made on the destination file directly when the quick check indicates that the file's data does not need to be updated.
RSYNC finds files that need to be transferred using a "quick check" algorithm (by default) that looks for files that have changed in size or in last-modified time. Any changes in the other preserved attributes (as requested by options) are made on the destination file directly when the quick check indicates that the file's data does not need to be updated.
More about Rsync at <https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele>
More about RSYNC at <https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele>
Transfer large files to/from CESNET storage, assuming membership in the Storage VO
......
ORCA
====
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multi-reference correlated ab initio methods. It can also treat environmental and relativistic effects.
Making orca available
---------------------
......
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