diff --git a/INSTALL.md b/INSTALL.md index 581e1a8708cc18caf066b2dfb7649a4975152fb6..0bc6e631d502e55efd4ac623f3f1464e82ffe2b5 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -2,14 +2,13 @@ Use our repositories hosted at [Open Build Service](http://build.opensuse.org). 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 # Building MOOSE from source -If you really want to build `MOOSE` from source, you can either use `cmake` (recommended) -or GNU `make` based flow. +To build `MOOSE` from source, you can either use `cmake` (recommended) or GNU `make` based flow. Download the latest source code of moose from github or sourceforge. @@ -21,21 +20,9 @@ For moose-core: - gsl-1.16 or higher. - libhdf5-dev (optional) -- libsbml-dev (5.9.0, optional) - python-dev - 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: sudo apt-get install python-dev python-numpy libhdf5-dev cmake libgsl0-dev g++ @@ -81,17 +68,17 @@ calling make: export LDFLAGS= -L/opt/libsbml/lib -## Release build: +### Release build: cd moose make BUILD=release -## Debug build: +### Debug build: cd moose make BUILD=debug -## Python 3K +### Python 3K 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: diff --git a/README.md b/README.md index bc315faa3019c539e5ac98600582dd8273745e83..3c8c144804e5485969288f1dcf6b32c6ef7652fe 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ [](https://travis-ci.org/BhallaLab/moose-core) 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 . diff --git a/scheduling/Clock.cpp b/scheduling/Clock.cpp index 433e52e05f3bf690861c4377991c03266f8bbe6c..e48b6a343506df5110c2dfc9320e7b5c5847dd99 100644 --- a/scheduling/Clock.cpp +++ b/scheduling/Clock.cpp @@ -733,23 +733,17 @@ void Clock::handleStep( const Eref& e, unsigned long numSteps ) ++k; } - // Don't write too much. When 10% of simulation is over, write to - // the file. We need 10 points. We just use a sine function - // 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. + // When 10% of simulation is over, notify user when notify_ is set to + // true. if( notify_ ) { - if( cos(20 * M_PI * currentTime_ / runTime_) == 1.0) + if( fmod(100 * currentTime_ / runTime_ , 10.0) == 0.0 ) { time( &rawtime ); timeinfo = localtime( &rawtime ); strftime(now, 80, "%c", timeinfo); cout << "@ " << now << ": " << 100 * currentTime_ / runTime_ - << "% of total " << runTime_ << " is over." << endl; + << "% of total " << runTime_ << " seconds is over." << endl; } } }