Fixes to issue 129 #162
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Fixes to issue 129 #162
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This fixes the issue on large model but on my CaMKII model, it is causing seg-fault, Or, it is here |
dilawar
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Apr 26, 2017
…r very long time (#176) * Rallpack 3 takes 2 sec with moose. * Fixes #160 #159. * Fixes to #129 * Fixed to boost link error in previous pull request. * Updated. * Another update. * Fixes to issue #126 and #162 * Fixes recent travis build failure. If pygraphviz is not found, disable the function and let user know what needs to be done. python-pygraphviz is not an essential dependency of pymoose. * Doesn't resolve the bug. * Same add_definition for c++11 and cxx support in gnu compiler. * Lets test with this commit. * Another test casse; let see if error goes away. * This fixes the bug where mass conservation was not honored.
dilawar
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Jun 15, 2017
* Removing inject_ array transfer from device to host * CPU version of optimized pervasive matrix solver * Ported optimized pervasive solver to GPU * Fixes #21 and optimizes pervasive solver * fixes #23 Assumption that injectVarying is obsolete * Removed pervasive solver implementation based on algortihm in https://labnotes.ncbs.res.in/bhalla/cpu-algorithm-data-structure-pervasive-flow-matrix-solver * HinesMatrix.h/cpp cleaned and documented * fixes #24 * Less verbose ReadSwc and rdesigneur. Fix to SeqSynHandler * VERSION string is fixed to today's date if not given. * Updated default version in setup.py file. * Do not copy VERSION file for python. Lets find a better and more portable solution. * --std=c++11 is must now. Fixes BhallaLab/moose#214. * Cmake changes from chamcham branch. Build for launchpad. * Fixed revision issue. Conflicts: moose-core/CMakeLists.txt * Added missing Revision macro file from chamcham branch. * Added connectionList field to SparseMsg to allow direct control over connection matrix. Some sanity checks in SparseMatrix to go with this. * Local Documentation (#177) * adding local documentation.. * adding local documentation.. * Fixes to violation of mass-conservation when Dsolve and Gsolve run for very long time (#176) * Rallpack 3 takes 2 sec with moose. * Fixes #160 #159. * Fixes to #129 * Fixed to boost link error in previous pull request. * Updated. * Another update. * Fixes to issue #126 and #162 * Fixes recent travis build failure. If pygraphviz is not found, disable the function and let user know what needs to be done. python-pygraphviz is not an essential dependency of pymoose. * Doesn't resolve the bug. * Same add_definition for c++11 and cxx support in gnu compiler. * Lets test with this commit. * Another test casse; let see if error goes away. * This fixes the bug where mass conservation was not honored. * Bugfix for SparseMsg, corrects allocation of synapses when setting connectionList * color and textcolor inchanged for enzyme * reaction or enzyme name is empty then id is taken as name while reading files from SBML * Added in hack for rmoogli to display time * Fix for Table.vector bug (#179) * Updated setup.py for cygwin * Fixed bug in DestFinfo function call * Added NonlinearSystem.h from upstream to fork * Fixed the error in plot_tables utility. * More fixes to plot_utils * Added sequencePower term to SeqSynHandler to achieve greater specificity for sequences vs all inputs on at once. * Made ReadSwc less verbose. Fixed bug in SeqSynHandler in application of sequencePower. * added to ask User if merged model to be saved * python Counter function removed, just to give backward compatibility for Centos6 for python 2.6 * a warning message is sent out \n 1.if function is not connected to output and \n 2.yet to write back StimulusTable is to genesis. \n No more transformation with y axis as it has already taken care in kkit.py file * Added c++11 flag to nvcc compiler
dilawar
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Jun 20, 2017
* Removing inject_ array transfer from device to host * CPU version of optimized pervasive matrix solver * Ported optimized pervasive solver to GPU * Fixes #21 and optimizes pervasive solver * fixes #23 Assumption that injectVarying is obsolete * Removed pervasive solver implementation based on algortihm in https://labnotes.ncbs.res.in/bhalla/cpu-algorithm-data-structure-pervasive-flow-matrix-solver * HinesMatrix.h/cpp cleaned and documented * fixes #24 * Less verbose ReadSwc and rdesigneur. Fix to SeqSynHandler * VERSION string is fixed to today's date if not given. * Updated default version in setup.py file. * Do not copy VERSION file for python. Lets find a better and more portable solution. * --std=c++11 is must now. Fixes BhallaLab/moose#214. * Cmake changes from chamcham branch. Build for launchpad. * Fixed revision issue. Conflicts: moose-core/CMakeLists.txt * Added missing Revision macro file from chamcham branch. * Added connectionList field to SparseMsg to allow direct control over connection matrix. Some sanity checks in SparseMatrix to go with this. * Local Documentation (#177) * adding local documentation.. * adding local documentation.. * Fixes to violation of mass-conservation when Dsolve and Gsolve run for very long time (#176) * Rallpack 3 takes 2 sec with moose. * Fixes #160 #159. * Fixes to #129 * Fixed to boost link error in previous pull request. * Updated. * Another update. * Fixes to issue #126 and #162 * Fixes recent travis build failure. If pygraphviz is not found, disable the function and let user know what needs to be done. python-pygraphviz is not an essential dependency of pymoose. * Doesn't resolve the bug. * Same add_definition for c++11 and cxx support in gnu compiler. * Lets test with this commit. * Another test casse; let see if error goes away. * This fixes the bug where mass conservation was not honored. * Bugfix for SparseMsg, corrects allocation of synapses when setting connectionList * color and textcolor inchanged for enzyme * reaction or enzyme name is empty then id is taken as name while reading files from SBML * Added in hack for rmoogli to display time * Fix for Table.vector bug (#179) * Updated setup.py for cygwin * Fixed bug in DestFinfo function call * Added NonlinearSystem.h from upstream to fork * Fixed the error in plot_tables utility. * More fixes to plot_utils * Added sequencePower term to SeqSynHandler to achieve greater specificity for sequences vs all inputs on at once. * Made ReadSwc less verbose. Fixed bug in SeqSynHandler in application of sequencePower. * added to ask User if merged model to be saved * python Counter function removed, just to give backward compatibility for Centos6 for python 2.6 * a warning message is sent out \n 1.if function is not connected to output and \n 2.yet to write back StimulusTable is to genesis. \n No more transformation with y axis as it has already taken care in kkit.py file * Added c++11 flag to nvcc compiler * Cleaned up stale benchmarks * Modified files to remove conflicts with master branch of remote * Error handling. fixes #31 * Removed dump comments
dilawar
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Jun 21, 2017
7c9fe23 Fixes to issue #167. (#168) 3f077c1 Resolved merge conflict with Table.h 9b175c8 Major bugfix for Table and derived class Streamer, to fix error introduced by duplicating the 'name' field which is already defined for Neutral. Minor bugfix for melement.cpp f0d4c02 Update INSTALL.md 2737220 Fixes to issue165 (#166) a934676 Update .travis.yml 601d06a Fixes to PYTHON3 build failure on travis. 9d9d925 Tested locally for linux. The scripts seems to be fine on openSUSE-42.2 93bbd4f By default travis pick up /opt/bin/python when `which python` is used. Do not use this construct in script. Moved travis related scripts to a hidden folder .travis. c0d3871 If python3 exists (installed on travis), then check for the compatibility otherwise don't. 65a85da Almost there. Calling script from top of directory. 0db2016 Make trusty default build environment. python3-matplotlib is not available by default. d8c1c6a setuid to root for linux script. 4c90f04 Some more fixes in travis script. 429420b Cleanup, osx related travis macros. e287118 Disable OSX build here on master brach. Created issue #165 to build and test for MacOSX. 87aeb1a Travis build scripts for macosx and linux are in ./scripts folder. 24643bc Some more fixes to travis build failure on OSX. a05826e Fixing brew taps and build dependencies. ea0ede1 This commit is just to test the OSX build on travis. Unfortunately there is no way to test it offline. 1b6f42a Fixes to travis scripts. b0baaab Excluded linux and osx build from config file. 626fd30 Testing with OsX support on travis. xcode-8.1. Most likely to break ab933ad Fixes to recent travis build failure. make all python files python3 compatible in addition to #164. 72afc02 Enabled macosx build on travis. Though allowing failure for now. bedb51e Fixes for issue #164. Also hotfix for branch chamcham. e821a9d Fixes due to API change in SBML support. bb8c850 Fixes to #164. 806605d Fixed the prog -> position. Hotfix for release. 2cba78a Merge branch '3.1.1' of github.com:BhallaLab/moose-core into 3.1.1 82c3024 Fixes to #163. 598433e Related to BhallaLab/moose#204. 48c5535 formating 0cec9d2 spell correction 6d66bc1 function to add and delete solvers to Chemical solver eefafa9 filename changed c9208a9 added mooseWriteKkit, moosedeleteChemSolver,mooseaddChemSolver and cleaned up write/ReadSBML as mooseWriteSBML, mooseReadSBML for consistency in moose.py d462c7e Removed saveModel which doesn't exists anymore 8c5af82 Fixes to issue 129 (#162) eee822b Fixes to recent build failure on travis. bdc1436 Alternative implementation of moose.Streamer (#161) 94444f9 Notify user if python-libsbml is not found. db41ad5 Merge pull request #157 from dilawar/master c11cb03 Added recently added C++ files in synapses folder. 5868a2f Added libsbml test. Runs only when python2 is used. 716305c Fixes to boost build failure on travis. 4355f02 Various fixes to libsbml related part. acf46ff Fixes to lintian errors [ skip ci ] 75c8f34 Similar fixes to writeSBML file. 54f127e Cleanup and fixed pylint error power( ) -> pow( ) Instead of try catch, check for libsbml at the begining and warn user. d24b389 Fixes to test_sbml scripts. The basic functions are working. 0430732 #156 . Created writeSBML and readBSML functions in moose.py c56b347 #156 . Removed deprecated sbml functions. 0e09e0b VERSION is a temp file. 29190b6 Merge branch 'master' of github.com:BhallaLab/moose-core 2c8156a Changed the environement variable which cmake uses to search for GSL. ee4ae8a Merge branch 'master' of github.com:dilawar/moose-core da93767 Fixes to recent travis failure. All files are now compile with python2 and python3. 0ec89d2 Added test to make sure each python script compiles with python2 as well. 98d6c31 Merge branch 'master' of github.com:BhallaLab/moose-core 3bc4e6c Update .travis.yml c1f4c84 Adding pre-commit hooks. BhallaLab/moose#189 . 8847b26 Update .travis.yml 6b2fa39 Disabling libsbml on travis. It does not build with clang. 12a72da python-libsbml doesn't build with clang. Allowing failure for clang compiler on travis (test commit). be83da8 Fixed import statement in genesis. Related to python3 import. ac29a99 Enable QUIET_MODE for Release. No information is printed onto console when moosemodule is loaded. 6e871fa Changes : 0. Mixed tabs and spaces are turned into 4 spaces. 1. Python code is python3 compatible. 2. Removed libmumbl from source tree. Not in active development. 5916f7f Fixed a typo in travis. 246bc58 Merge commit '04170cb4d5a69b48041a12229181d7e4d2bf5afd' 0390d6a Updated. 993f8f7 Fixed, python2 incompatible print function use. 030aea3 Some updates to fix static hdf5 libraries. 4255ecf This project build pymoose, gui and its examples. TODO: ctest must check each example as well. c92e761 Builds whole moose project. d40fbe6 Added some sanity tests for both moose and moogli. 29fd242 Even when format is set, stream! f96fe68 One test failing on nargis (centos-6). Try it locally. eb61ab7 ctest script setups its environment. No need to have set environment for each tests. 1b43dc7 This fixes python3 linking problem on openSUSE-Leap. Not sure about travis. ec15bd2 Linking error with boost-filesystem. 0847eb2 This might or might now work with python3. Taking a shot. e7a87b8 Some changes in Makefile. Protected some boost related code with USE_BOOST macros. git-subtree-dir: moose-core git-subtree-split: 7c9fe23
dilawar
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Jan 2, 2018
* Rallpack 3 takes 2 sec with moose. * Fixes #160 #159. * Fixes to #129 * Fixed to boost link error in previous pull request. * Updated. * Another update. * Fixes to issue #126 and #162 * Fixes recent travis build failure. If pygraphviz is not found, disable the function and let user know what needs to be done. python-pygraphviz is not an essential dependency of pymoose. * Doesn't resolve the bug. * Same add_definition for c++11 and cxx support in gnu compiler. * Lets test with this commit. * Another test casse; let see if error goes away. * This fixes the bug where mass conservation was not honored. * For build purpose, we have added WITH_BOOST and DEBUG options set to ON. * Working script. * Fixes to plot functions. * Fixed CMake for cuda compilation and MOOSE_VERSION is moved to pymoose. * Test branch. * Added the ksolve test script description! * I changed Nothing * Just Testing * Just correcting things * OpenMP changes * Got cmake changes from multithreaded branch. * Discarded hsolve gpu changes. Now only using openmp. * Builds, compiles and parallelize. * Fixed makefile and added time-taken to run script info. * Compile and test run. * Test. * Test script and chemical system with with 1000 reactions. * C++ speedup using std::async. * Fixed one seg-fault. Caused another. * Remove bin file. * Removed temp files. * Adding a new openmp version * Adding a new openmp parallelised code * Parallelised the Clock::handleStep * No change as such * Added using MPI method in OpenMP * The value of currentStep_ is being updated just once * Seg-faults in ctest -V as well. The seg-faults are the same. python/free combination is causing them. #1. * This fixed the issue. * This fixed the issue. #1. * Removed _build folder. And fix to #1. * Checking the dt_ value * removed temporary files * Missing ksolve changes. * Some parallelism using std::async. * With openmp but not getting speedup. * Added build macros for CUDA. * Build passes for CUDA. * Test skeleton of kernel. * Added another skeleton. * Added benchmark cuda code * Added Benchmark Script Cuda * Minor changes to test script: Dont wait till test is over to print which test is being executed. * Refactoring in cmake file. * Fixes to debian related python install. When --prefix=/usr is given, its installs in site-packages rather than dist-pacakges. * Parallel ksolve. * Fast Ksolve with 2 default threads. * Removed the debug message. Lets check it now. By default it should be not slower than the default version. * Optimized GSolve with default 2 threads. * Added skeleton function for cuda ksolve. * Added data transfer lines cpu to gpu and then gpu to cpu * Added checkCudaErrors * Added include paths to external/cuda folder. * We can now find the ksolve using wildcard. Now access its VoxelPools and build the data-structure for cuda. * Changed _buiild to _build * Commented out things using #if0 and #endif * removed VERSION file coming in the way. * Added both CUDA file and normal file. * Commented out lines using #if 0 and #endif * Added various #include statement due to - Access Ksolve and VoxelPool in Clock.cu - These import are only relevant if CUDA is used. * We can access VoxelPools* now from ksolve object. * If for some reason matplotlib is not imported successfully, disable kkit import. * Writing data to the voxelpools * Added tests in cuda folder. Skeletpm seems to be working. * Added CudaKsolve to scheduling folder. Needs a better place for this Modified build flow to use these changes. * Fixes to debian related python install. When --prefix=/usr is given, its installs in site-packages rather than dist-pacakges. * Better formatted output on running tests. These tests are moose-examples scripts which are known to pass. * Can access VoxelPools state vector. * can access the boost system. * Force --install-layout=deb when on debian/ubuntu. * moose.test( ) is added not cmake but not enabled. Enable them once all scripts are fixed in moose-examples. * Commented out code appropriately. * Time to test the Gsolve performance when threads are enabled. * Some changes to Ksolve. Still seg-faults. * Rdesigneur has python3 default import : absolute_import. * This is good but do parallelism at Clock.cpp * Added MACRO to integrate serial and parallel version. * Equivalent serial code which can easily be called from std::async now. * Implemented first parallel version. * asyncing clock is not producing great results. * Async version is slower (80sec vs 70 sec). * Slower version but results are same. * Added note on what to do. * All tests are passing and new code is protected by appropriate macros. * Added pre-commit pip install pre-commit --user to activate it. * Using version v0.8 now. * Fixes by pre-commit hooks. - Removed trailing whitespaces automatically. - insert * coding - utf8 * line on top of each python script automatically. * Test docqs agains gsl version/python2 moose-core. * Fix to travis-ci/travis-ci#6307. * Only test doqcs on LinuxOS, not on MacOSX. * Don't use timeout in script. So that we can run on macosx as well. Removed timeout command from script. Now it can run on OSX as well. * Hopefully this will fix issue on travis-osx build failure. Related to travis-ci/travis-ci#6522. * Lets see if is a workaround fixes the OSX bug. * Lets see if this is a good workaround travis issue travis-ci/travis-ci#6522. * Install moose on osx as well. Prerequisite to test DOQCS. * The bug on travis is still not bypassed. If this does not work, disable DOQCS tests on OSX. * Cherry-pick "Added connectionList field to SparseMsg to allow direct control over connection matrix. Some sanity checks in SparseMatrix to go with this" * Removed trailing spaces from code by pre-commit hook utility. * Fixes to missing function declaration, post cherry-pick. * Added RK4 Method * Corrected Data Transfer * Renamed some files to avoid confusion with Ksolve. * Merged master branch from BhallaLab and intergrated CUDA based ODE solver. * Now debug statements has been removed. * Changed the values of the matrix size used in rk4 * Uncommented the lines in order to know the location of the seg fault * Added cuda code which passes the cudacheckerror but fails aat cudachecklasterror(which i think is okay) * Added Some Details About Data Extraction * Update AdvanceChannel.cu * Update AdvanceChannel.cu * Update AdvanceChannel.cu * Update AdvanceChannel.cu * Added the lines which are there on GPU branch * CudaGlobal.h * Update AdvanceChannel.cu * Update HSolveActive.h * Update HSolveActiveSetup.cpp * Update HSolvePassive.h * Update RateLookup.h * Update StorageFormats.h * Update SparseMsg.cpp * Update SparseMsg.h * Update moose.py * Update chemConnectUtil.py * Update chemConnectUtil.py * Update chemConnectUtil.py * Update CMakeLists.txt * Update chemConnectUtil.py
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Fixes to issue #129