From 6495ea21107451a951ecaa3ede4d2a9da664efcc Mon Sep 17 00:00:00 2001
From: Lubomir Prda <lubomir.prda@vsb.cz>
Date: Fri, 3 Feb 2017 11:46:31 +0100
Subject: [PATCH] Finalized spell check
---
.spelling | 127 ++++++++++++++++++
README.md | 6 +-
.../software/intel-suite/intel-inspector.md | 6 +-
.../intel-trace-analyzer-and-collector.md | 2 +-
docs.it4i/salomon/software/mpi/mpi.md | 4 +-
.../software/numerical-languages/matlab.md | 4 +-
.../software/numerical-languages/octave.md | 2 +-
docs.it4i/salomon/storage.md | 14 +-
docs.it4i/software/orca.md | 2 +-
9 files changed, 148 insertions(+), 19 deletions(-)
diff --git a/.spelling b/.spelling
index 64de0b405..38106892a 100644
--- a/.spelling
+++ b/.spelling
@@ -254,6 +254,35 @@ 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
@@ -662,3 +691,101 @@ 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
diff --git a/README.md b/README.md
index cf8f9e087..a295a9d1d 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
# 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
diff --git a/docs.it4i/salomon/software/intel-suite/intel-inspector.md b/docs.it4i/salomon/software/intel-suite/intel-inspector.md
index 6231a6534..711611e20 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-inspector.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-inspector.md
@@ -1,6 +1,6 @@
# 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
@@ -28,9 +28,7 @@ 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.
-
-Results obtained from batch mode can be then viewed in the GUI by selecting File -> Open -> Result...
+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.
## References
diff --git a/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md b/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
index 5d4513d30..bb05bd837 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
@@ -1,6 +1,6 @@
# 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.
diff --git a/docs.it4i/salomon/software/mpi/mpi.md b/docs.it4i/salomon/software/mpi/mpi.md
index 411d54dda..09952b4d7 100644
--- a/docs.it4i/salomon/software/mpi/mpi.md
+++ b/docs.it4i/salomon/software/mpi/mpi.md
@@ -109,7 +109,7 @@ Compile the above example with
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.
@@ -124,7 +124,7 @@ 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
Important! Bind every OpenMP thread to a core!
diff --git a/docs.it4i/salomon/software/numerical-languages/matlab.md b/docs.it4i/salomon/software/numerical-languages/matlab.md
index aec28baae..58a660a8c 100644
--- a/docs.it4i/salomon/software/numerical-languages/matlab.md
+++ b/docs.it4i/salomon/software/numerical-languages/matlab.md
@@ -272,8 +272,8 @@ 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.
diff --git a/docs.it4i/salomon/software/numerical-languages/octave.md b/docs.it4i/salomon/software/numerical-languages/octave.md
index 6461bc4cc..7484d97a3 100644
--- a/docs.it4i/salomon/software/numerical-languages/octave.md
+++ b/docs.it4i/salomon/software/numerical-languages/octave.md
@@ -53,4 +53,4 @@ 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/).
diff --git a/docs.it4i/salomon/storage.md b/docs.it4i/salomon/storage.md
index d83dbc119..a3d47e408 100644
--- a/docs.it4i/salomon/storage.md
+++ b/docs.it4i/salomon/storage.md
@@ -360,7 +360,7 @@ 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/
@@ -392,16 +392,20 @@ Once done, please remember to unmount the storage
$ fusermount -u cesnet
```
-### Rsync Access
+### RSYNC Access
!!! 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.
+<<<<<<< HEAD
More about Rsync at [here](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>
+>>>>>>> Finalized spell check
Transfer large files to/from CESNET storage, assuming membership in the Storage VO
diff --git a/docs.it4i/software/orca.md b/docs.it4i/software/orca.md
index 8fcfd69bf..8215a9ead 100644
--- a/docs.it4i/software/orca.md
+++ b/docs.it4i/software/orca.md
@@ -1,6 +1,6 @@
# 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
--
GitLab