cns-oist/steps

Public release repository for STochastic Engine of Pathway Simulation (STEPS)

steps's Issues

GPL2 vs. GPL3 license issues

Based on LICENSE.md, it appears that the overall license of STEPS is intended to be GPL-2.0-only.

However, the metadata for the Python packages (wrongly?) indicates a license of GPL-3.0-only:

STEPS/pysteps/setup.py

Line 63 in a910839

'license' : 'GNU General Public License Version 3.0',

STEPS/pysteps/cmake_setup.py.in

Line 37 in a910839

'license' : 'GNU General Public License Version 3.0',

A number of source files within pysteps explicitly contradict this, e.g:

STEPS/pysteps/steps/__init__.py

Lines 12 to 14 in a910839

	# STEPS is free software: you can redistribute it and/or modify
	# it under the terms of the GNU General Public License version 2,
	# as published by the Free Software Foundation.

Furthermore, a few source files really are marked with a license of GPL-3.0-or-later:

STEPS/src/steps/geom/sdiffboundary.hpp

Lines 10 to 13 in a910839

	// STEPS is free software: you can redistribute it and/or modify
	// it under the terms of the GNU General Public License as published by
	// the Free Software Foundation, either version 3 of the License, or
	// (at your option) any later version.

STEPS/src/steps/solver/sdiffboundarydef.hpp

Lines 10 to 13 in a910839

	// STEPS is free software: you can redistribute it and/or modify
	// it under the terms of the GNU General Public License as published by
	// the Free Software Foundation, either version 3 of the License, or
	// (at your option) any later version.

STEPS/src/steps/mpi/tetopsplit/sdiffboundary.hpp

Lines 10 to 13 in a910839

	// STEPS is free software: you can redistribute it and/or modify
	// it under the terms of the GNU General Public License as published by
	// the Free Software Foundation, either version 3 of the License, or
	// (at your option) any later version.

STEPS/src/steps/mpi/tetopsplit/sdiffboundary.cpp

Lines 10 to 13 in a910839

	// STEPS is free software: you can redistribute it and/or modify
	// it under the terms of the GNU General Public License as published by
	// the Free Software Foundation, either version 3 of the License, or
	// (at your option) any later version.

This is problematic because GPLv2 and GPLv3 are not compatible.

error: 'CV_FUNCTIONAL' was not declared in this scope

Hi all.

Please, could you make STEPS-3.6.0 compatible with recent Sundials-5.7.0 (if possible)?:

[ 20%] Building CXX object src/CMakeFiles/libsteps-obj.dir/steps/solver/api_main.cpp.o
cd /builddir/build/BUILD/STEPS-3.6.0/build-mpich/src && /usr/lib64/mpich/bin/mpicxx -DELPP_DISABLE_DEFAULT_CRASH_HANDLING=1 -DELPP_NO_DEFAULT_LOG_FILE=1 -DELPP_STL_LOGGING=1 -DENABLE_ASSERTLOG=1 -DGNU_FORCE_INLINE=[[gnu::always_inline]] -DUSE_MPI -I/builddir/build/BUILD/STEPS-3.6.0/src/. -isystem /builddir/build/BUILD/STEPS-3.6.0/src/third_party/easyloggingpp/src -isystem /builddir/build/BUILD/STEPS-3.6.0/src/third_party/cvode-2.6.0/src -isystem /builddir/build/BUILD/STEPS-3.6.0/src/third_party/cvode-2.6.0/include -std=c++11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -lpthread -lgtest -lgtest_main -march=native -fopenmp  -DNDEBUG -fPIC -MD -MT src/CMakeFiles/libsteps-obj.dir/steps/solver/api_main.cpp.o -MF CMakeFiles/libsteps-obj.dir/steps/solver/api_main.cpp.o.d -o CMakeFiles/libsteps-obj.dir/steps/solver/api_main.cpp.o -c /builddir/build/BUILD/STEPS-3.6.0/src/steps/solver/api_main.cpp
/builddir/build/BUILD/STEPS-3.6.0/src/steps/tetode/tetode.cpp: In constructor 'steps::tetode::CVodeState::CVodeState(uint, uint, realtype, realtype)':
/builddir/build/BUILD/STEPS-3.6.0/src/steps/tetode/tetode.cpp:205:45: error: 'CV_FUNCTIONAL' was not declared in this scope
  205 |     cvode_mem_cvode = CVodeCreate(CV_ADAMS, CV_FUNCTIONAL) ;
      |                                             ^~~~~~~~~~~~~

Regards.

Problem in installing steps

Hi,
I tried installing STEPS through source code. the first command "cd STEPS" is itself, and then i assumed "STEPS-master" is the folder mentioned. Then, while entering "cmake..", it is showing two errors, for which i have attached the screenshot also.

Please help me resolve it.

Problem installing on Ubuntu

Hi,

I am trying to install STEPS on Ubuntu-16.04-Cuda.

after using cmake -DBLAS_LIBRARIES=/home/cloud-user/amber/miniconda/lib/ -DLAPACK_LIBRARIES=/home/cloud-user/amber/miniconda/lib/ ..

I get the following, I was wondering if you know where the issue is.

-- Generating debug symbols: -ggdb3
-- Looking for strip utility
-- Looking for strip utility - found
-- A library with BLAS API found.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp=libomp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp=libomp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
-- PYTHON packages being installed to /usr/lib/python2.7/dist-packages. To change use -DPYTHON_INSTALL_PREFIX=

-- Configuring done
WARNING: Target "cysteps" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "cysteps" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "libsteps" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "libsteps" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_membership" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_petscsystem" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_tetmesh" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_point3d" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_checkid" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_rng" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_sample" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_bbox" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_small_binomial" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "test_bdsystem" requests linking to directory "/home/cloud-user/amber/miniconda/lib/". Targets may link only to libraries. CMake is dropping the item.
-- Generating done
-- Build files have been written to: /home/cloud-user/STEPS/build

Thank you.

libgomp: Invalid value for environment variable OMP_DYNAMIC

This is a resolved issue.

OS: CentOS 6.5 (Old. many softwares are updated including gcc)
Python: 2.7.13 （Anaconda）

Python 2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:09:15) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import steps

libgomp: Invalid value for environment variable OMP_DYNAMIC
>>> 

Solution:
add export OMP_DYNAMIC=FALSE to environment profile.

Unbundling various libraries

Hello,

I am working on making STEPS available in NeuroFedora. While auditing the source, I see that a couple of libraries are bundled. Is this necessary? Would it be possible to remove these bundles or provide a mechanism that permis the use of system installations of these libraries?

• easyloggingpp: single header library so relatively easy to unbundle, can be down downstream
• Random123: not developed any more but still easy to unbundle and can also be done downstream. Please note that Random123 does not support all architectures, and therefore using it also implies that STEPS does not support all architectures. (Neuron, which also uses Random123 has similar constraints)
• cvode: outdated version of SUNDIALS, as the current version is 3.2.x. One needs to check if STEPS compile with the newer version, so unbundling this is potentially a more involved task.
• superLU_dist: outdated version of SuperLU_dist as the current version is 5.2.x. Here too, one needs to check if STEPS will compile with the newer version, and that makes this a more involved task also.

I can help with testing with the newer libraries, since they are available in Fedora. However, it would be nice if STEPS did not bundle older versions of software, or if it did it bundled newer versions that contain fixes and enhancements. If a mechanism to enable the use of system versions of libraries can be included in the CMake files, that would be awesome.

STEPS Manual link is not available

Hi STEPS developers,

Apologies for the stream of issues :-) I just tried reading the STEPS manual as per link in the main page[1] but I get a 404[2]:

An error has been encountered in accessing this page.

1. Server: steps.sourceforge.net 
2. URL path: /manual_3.0.0/manual_index.html 
3. Error notes: NONE 
4. Error type: 404 
5. Request method: GET 
6. Request query string: NONE 
7. Time: 2017-03-10 10:21:20 UTC (1489141280)

Thanks for your time

Marco

[1] http://steps.sourceforge.net/STEPS/documentation.php
[2] http://steps.sourceforge.net/manual_3.0.0/manual_index.html

problem in installing STEPS

vinoth@Vinoth:~/STEPS/build$ sudo make install
[sudo] password for vinoth:
[ 81%] Built target libsteps-obj
[ 82%] Built target libsteps
[ 83%] Built target libsteps_static
[ 84%] Built target cysteps
[ 84%] Built target steps_package_pure_py
[ 86%] Built target gtest
[ 87%] Built target gtest_main
[ 89%] Built target test_rng
[ 91%] Built target test_tetmesh
[ 92%] Built target test_membership
[ 93%] Built target test_point3d
[ 95%] Built target test_bbox
[ 96%] Built target test_checkid
[ 98%] Built target test_bdsystem
[ 99%] Built target test_sample
[100%] Built target test_small_binomial
Install the project...
-- Install configuration: "Release"
-- Up-to-date: /steps/cysteps.so
running build
running build_py
running install
running install_lib
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/visual/init.py -> steps/visual
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/visual/SimDisplay.py -> steps/visual
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/visual/Plotting.py -> steps/visual
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/visual/StaticComponent.py -> steps/visual
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/visual/DynamicComponent.py -> steps/visual
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/visual/Control.py -> steps/visual
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/visual/Colors.py -> steps/visual
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/visual/PartitionViewer.py -> steps/visual
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/init.py -> steps
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/model.py -> steps
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/rng.py -> steps
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/quiet.py -> steps
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/morph_support.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/init.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/geom_decompose.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/steps_cubit.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/matlab_support/init.py -> steps/utilities/matlab_support
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/matlab_support/simulate.py -> steps/utilities/matlab_support
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/matlab_support/matlab_parser.py -> steps/utilities/matlab_support
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/matlab_support/event_parser.py -> steps/utilities/matlab_support
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/meshio.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/meshctrl.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/sbml.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/steps_shadow.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/metis_support.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/utilities/cubit_support.py -> steps/utilities
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/geom.py -> steps
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/mpi/init.py -> steps/mpi
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/mpi/solver.py -> steps/mpi
copying /home/vinoth/STEPS/build/lib.linux-x86_64-2.7/steps/solver.py -> steps
byte-compiling steps/visual/init.py to init.pyc
byte-compiling steps/visual/SimDisplay.py to SimDisplay.pyc
byte-compiling steps/visual/Plotting.py to Plotting.pyc
byte-compiling steps/visual/StaticComponent.py to StaticComponent.pyc
byte-compiling steps/visual/DynamicComponent.py to DynamicComponent.pyc
byte-compiling steps/visual/Control.py to Control.pyc
byte-compiling steps/visual/Colors.py to Colors.pyc
byte-compiling steps/visual/PartitionViewer.py to PartitionViewer.pyc
byte-compiling steps/init.py to init.pyc
byte-compiling steps/model.py to model.pyc
byte-compiling steps/rng.py to rng.pyc
byte-compiling steps/quiet.py to quiet.pyc
byte-compiling steps/utilities/morph_support.py to morph_support.pyc
byte-compiling steps/utilities/init.py to init.pyc
byte-compiling steps/utilities/geom_decompose.py to geom_decompose.pyc
byte-compiling steps/utilities/steps_cubit.py to steps_cubit.pyc
byte-compiling steps/utilities/matlab_support/init.py to init.pyc
byte-compiling steps/utilities/matlab_support/simulate.py to simulate.pyc
byte-compiling steps/utilities/matlab_support/matlab_parser.py to matlab_parser.pyc
byte-compiling steps/utilities/matlab_support/event_parser.py to event_parser.pyc
byte-compiling steps/utilities/meshio.py to meshio.pyc
byte-compiling steps/utilities/meshctrl.py to meshctrl.pyc
byte-compiling steps/utilities/sbml.py to sbml.pyc
byte-compiling steps/utilities/steps_shadow.py to steps_shadow.pyc
byte-compiling steps/utilities/metis_support.py to metis_support.pyc
byte-compiling steps/utilities/cubit_support.py to cubit_support.pyc
byte-compiling steps/geom.py to geom.pyc
byte-compiling steps/mpi/init.py to init.pyc
byte-compiling steps/mpi/solver.py to solver.pyc
byte-compiling steps/solver.py to solver.pyc
running install_egg_info
Creating
error: [Errno 2] No such file or directory: ''

Consider renaming repository, removing postfix "_Release"

Hi STEPS developers,

I think the "_Release" postfix is a bit confusing. Presumably the name of the product is STEPS right? i.e. what's the difference between STEPS and STEPS_Release? Presumably you want to make some kind of separation between your internal repository with full version history and a "release" repository? Even so I'd consider not calling the GitHub repository STEPS_Release, since all the forks will also be called STEPS_Release and so on.

Cheers

Marco

incompatibility with Anaconda

@FrancescoCasalegno @adevress

One user has reported an issue importing STEPS with Ubuntu 16.04 and Anaconda, as follows:

urakubo-h@knv00:~/SOFTWARES/STEPS-master/build$ python
Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
import steps
Unable to import STEPS with NumPy support, try to import without NumPy...
Unable to import STEPS.
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/home/urakubo-h/anaconda/lib/python2.7/site-packages/steps/__init__.py", line 46, in <module>
   _steps_swig.init()
NameError: name '_steps_swig' is not defined

The installation log seems fine.

steps_install2.txt

I've reproduced the issue with this docker image anaconda_steps.

Interestingly, replacing Anaconda with Miniconda resolves the issue, as shown in this docker image miniconda_steps, so I assume the issue comes from Anaconda. Any idea what could cause this issue?

CMake does not halt when SWIG is missing

Hi STEPS developers,

I just noticed a minor bug on your build system: even though SWIG is marked as required, CMake still goes ahead and generates all the makefiles:

<snip>
-- Looking for strip utility
-- Looking for strip utility - found
-- Could NOT find SWIG (missing:  SWIG_EXECUTABLE SWIG_DIR) 
-- Found PythonInterp: /usr/bin/python (found version "2.7.13") 
-- Found PythonInterpLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so  
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so  
<snip>
-- Build files have been written to: /home/marco/Development/phd/STEPS_Release/output

The normal CMake behaviour is to bomb out when a required dependency is missing. I am investigating as to why this is not working correctly, your CMake files look fine at first glance.

Can we install STEPS on a local machine (Desktop computer) ?

Hi @mesimulator, I create a new issue for you and will answer your question here.

Dear STEPS Support,

I am just starting to use STEPS for my research. I question is :
Can we install STEPS on a local machine (Desktop computer) ? I mean will it take
a lot of space / slow down my desktop ?

In that case, I should install it on computing clusters ?

Please let me know your suggestions on this.

Thanks in anticipation,

Yes, you can install and use STEPS on a desktop. In fact, this is our recommendation for new users. The installation itself shouldn't take much of time and storage. The CPU/memory/storage consumption of the simulation depends on your model, but a desktop should be able to handle common pathway models.
The parallel solver is mainly designed for modeling large scale spatial systems with a great number of tetrahedrons (~10e6 and above). For that, you will need to deploy STEPS on a cluster.