Skip to content
Snippets Groups Projects
Commit 1680bac6 authored by Dilawar Singh's avatar Dilawar Singh
Browse files

Squashed 'moose-core/' changes from 6a6bcc1..bd86fb5

bd86fb5 Update INSTALL.md
3602353 Update README.md
f96dbda Merge pull request #155 from dilawar/master
50d720b Merge branch 'master' into master
b408e36 Instead of simple sin/cos use fmod and divide method. Sin/cosine functions gets value of 1 or many points near the maxima when simulation time is large (T for sin/cos). This changes fixes that.

git-subtree-dir: moose-core
git-subtree-split: bd86fb53a865dce7d482e21f959513e5621b1062
parent d0a6060b
No related branches found
No related tags found
No related merge requests found
...@@ -2,14 +2,13 @@ ...@@ -2,14 +2,13 @@
Use our repositories hosted at [Open Build Service](http://build.opensuse.org). Use our repositories hosted at [Open Build Service](http://build.opensuse.org).
We have packages for Debian, Ubuntu, CentOS, Fedora, OpenSUSE/SUSE, RHEL, We have packages for Debian, Ubuntu, CentOS, Fedora, OpenSUSE/SUSE, RHEL,
Scientific Linux. Visit the following page and follow the instructions there. Scientific Linux. Visit the following page for instructions.
https://software.opensuse.org/download.html?project=home:moose&package=moose https://software.opensuse.org/download.html?project=home:moose&package=moose
# Building MOOSE from source # Building MOOSE from source
If you really want to build `MOOSE` from source, you can either use `cmake` (recommended) To build `MOOSE` from source, you can either use `cmake` (recommended) or GNU `make` based flow.
or GNU `make` based flow.
Download the latest source code of moose from github or sourceforge. Download the latest source code of moose from github or sourceforge.
...@@ -21,21 +20,9 @@ For moose-core: ...@@ -21,21 +20,9 @@ For moose-core:
- gsl-1.16 or higher. - gsl-1.16 or higher.
- libhdf5-dev (optional) - libhdf5-dev (optional)
- libsbml-dev (5.9.0, optional)
- python-dev - python-dev
- python-numpy - python-numpy
__Note on libsbml__
Make sure that `libsml` is installed with `zlib` and `lxml` support. Following instructions
are known to work.
- wget http://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/libSBML-5.9.0-core-src.tar.gz
- tar -xzvf libSBML-5.9.0-core-src.tar.gz
- cd libsbml-5.9.0
- ./configure --prefix=/usr --with-zlib --with-bzip2 --with-libxml
- make
- sudo make install
On Ubuntu-12.04 or higher, these can be installed with: On Ubuntu-12.04 or higher, these can be installed with:
sudo apt-get install python-dev python-numpy libhdf5-dev cmake libgsl0-dev g++ sudo apt-get install python-dev python-numpy libhdf5-dev cmake libgsl0-dev g++
...@@ -81,17 +68,17 @@ calling make: ...@@ -81,17 +68,17 @@ calling make:
export LDFLAGS= -L/opt/libsbml/lib export LDFLAGS= -L/opt/libsbml/lib
## Release build: ### Release build:
cd moose cd moose
make BUILD=release make BUILD=release
## Debug build: ### Debug build:
cd moose cd moose
make BUILD=debug make BUILD=debug
## Python 3K ### Python 3K
By default, MOOSE is built for Python 2. In case you want to build MOOSE for By default, MOOSE is built for Python 2. In case you want to build MOOSE for
Python 3K, you need to pass the additional flag: Python 3K, you need to pass the additional flag:
......
[![Build Status - master](https://travis-ci.org/BhallaLab/moose-core.svg?branch=master)](https://travis-ci.org/BhallaLab/moose-core) [![Build Status - master](https://travis-ci.org/BhallaLab/moose-core.svg?branch=master)](https://travis-ci.org/BhallaLab/moose-core)
This is the core computational engine of [MOOSE simulator](https://github.com/BhallaLab/moose). This repository contains This is the core computational engine of [MOOSE simulator](https://github.com/BhallaLab/moose). This repository contains
C++ codebase and its python interface. For more details about MOOSE simulation, see https://github.com/BhallaLab/moose/blob/master/README.md C++ codebase and python interface. For more details about MOOSE simulator, see https://github.com/BhallaLab/moose/blob/master/README.md
This repository is sufficient for using MOOSE as python module. If you want to build `moose-python` using this repository, follow instructions given here at https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md . This repository is sufficient for using MOOSE as a python module. If you just want to build moose python module, follow instructions given here at https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md .
...@@ -733,23 +733,17 @@ void Clock::handleStep( const Eref& e, unsigned long numSteps ) ...@@ -733,23 +733,17 @@ void Clock::handleStep( const Eref& e, unsigned long numSteps )
++k; ++k;
} }
// Don't write too much. When 10% of simulation is over, write to // When 10% of simulation is over, notify user when notify_ is set to
// the file. We need 10 points. We just use a sine function // true.
// which cross 0 ten time in this time interval.
// NOTE: Dont use == 0.0 since we may never get a sample for
// which sine is 0.0. Hoever, getting 1.0 or -1.0 is very likely
// since sin function is relatively flat when its value is near
// 1.0/-1.0.
// NOTE: Use cosine instead of sin to sample 0%, 10% etc.
if( notify_ ) if( notify_ )
{ {
if( cos(20 * M_PI * currentTime_ / runTime_) == 1.0) if( fmod(100 * currentTime_ / runTime_ , 10.0) == 0.0 )
{ {
time( &rawtime ); time( &rawtime );
timeinfo = localtime( &rawtime ); timeinfo = localtime( &rawtime );
strftime(now, 80, "%c", timeinfo); strftime(now, 80, "%c", timeinfo);
cout << "@ " << now << ": " << 100 * currentTime_ / runTime_ cout << "@ " << now << ": " << 100 * currentTime_ / runTime_
<< "% of total " << runTime_ << " is over." << endl; << "% of total " << runTime_ << " seconds is over." << endl;
} }
} }
} }
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment