Problem in installing steps

[cns-oist]

Problem in installing steps

[WeiliangChenOIST]

Hi Vinoth,
If you are using Ubuntu or similar system, please try to install pstec using the command below, then compile STEPS again.

sudo apt-get install petsc-dev

[Vinoth461996]

Thanks. I tried it. Still it is showing the same error

[WeiliangChenOIST]

Could you please provide the information about your system? I will see if I can reproduce the issue.

[tristan0x]

Hello @Vinoth461996
First let me thank you for your interests in STEPS.
Can you please follow the instructions to install the requirements in the Requirements section of the README, i.e:

sudo apt-get install g++ gcc cmake libopenblas-dev libmpich-dev python-numpy cython python-scipy

If you "just" want to try STEPS, and do not need to run MPI jobs in an HPC cluster, I suggest you to use the STEPS Docker image

[Vinoth461996]

Hello @Vinoth461996
First let me thank you for your interests in STEPS.
Can you please follow the instructions to install the requirements in the Requirements section of the README, i.e:

sudo apt-get install g++ gcc cmake libopenblas-dev libmpich-dev python-numpy cython python-scipy

If you "just" want to try STEPS, and do not need to run MPI jobs in an HPC cluster, I suggest you to use the STEPS Docker image

I am having problems in installing cmake only

[Vinoth461996]

Could you please provide the information about your system? I will see if I can reproduce the issue.

I am attaching the information about my sytem

[tristan0x]

Ubuntu dropped support of this distribution at the beginning of this month. Can you try with a more recent version of

Hello @Vinoth461996
First let me thank you for your interests in STEPS.
Can you please follow the instructions to install the requirements in the Requirements section of the README, i.e:

sudo apt-get install g++ gcc cmake libopenblas-dev libmpich-dev python-numpy cython python-scipy

If you "just" want to try STEPS, and do not need to run MPI jobs in an HPC cluster, I suggest you to use the STEPS Docker image

I am having problems in installing cmake only

Have you tried to install the packages I mentioned?

sudo apt-get install g++ gcc cmake libopenblas-dev libmpich-dev python-numpy cython python-scipy

[tristan0x]

Ubuntu 14.04 LTS reaches end of life this month
Can't you use a more recent distribution?

[Vinoth461996]

OK. Thanks a lot. I will update and try again

[WeiliangChenOIST]

just tested it on a 14.04 virtual machine but cannot reproduce the error.
Looks like for some reason it cannot find openblas.

@Vinoth461996 have you tried to install the required packages as suggested by @tristan0x and recompiled STEPS?

sudo apt-get install g++ gcc cmake libopenblas-dev libmpich-dev python-numpy cython python-scipy

If it still has problem, please copy the terminal output to us for analysis.

wchen@wchen-VirtualBox:~/STEPS/build$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 14.04.6 LTS
Release:	14.04
Codename:	trusty
wchen@wchen-VirtualBox:~/STEPS/build$ rm -rf *
wchen@wchen-VirtualBox:~/STEPS/build$ cmake ..
-- The C compiler identification is GNU 4.8.4
-- The CXX compiler identification is GNU 4.8.4
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Generating debug symbols: -ggdb3
-- Looking for strip utility
-- Looking for strip utility - found
-- Found PythonInterp: /usr/bin/python (found version "2.7.6") 
-- Found PythonInterpLibs: /usr/lib/python2.7/config-i386-linux-gnu/libpython2.7.so  
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found MPI_C: /usr/lib/i386-linux-gnu/libmpich.so;/usr/lib/i386-linux-gnu/libopa.so;/usr/lib/i386-linux-gnu/libmpl.so;/usr/lib/i386-linux-gnu/librt.so;/usr/lib/libcr.so;/usr/lib/i386-linux-gnu/libpthread.so  
-- Found MPI_CXX: /usr/lib/i386-linux-gnu/libmpichcxx.so;/usr/lib/i386-linux-gnu/libmpich.so;/usr/lib/i386-linux-gnu/libopa.so;/usr/lib/i386-linux-gnu/libmpl.so;/usr/lib/i386-linux-gnu/librt.so;/usr/lib/libcr.so;/usr/lib/i386-linux-gnu/libpthread.so  
-- Could NOT find PETSC (missing:  PETSC_LIBRARIES PETSC_INCLUDE_DIRS) 
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- A library with BLAS API found.
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- PYTHON packages being installed to /usr/lib/python2.7/dist-packages. To change use -DPYTHON_INSTALL_PREFIX=<dir>
-- Found Cython: /usr/bin/cython (found suitable version "0.29.6", minimum required is "0.25.1") 
-- Configuring done
-- Generating done
-- Build files have been written to: /home/wchen/STEPS/build

[Vinoth461996]

Hi,
I have updated my ubuntu. Now when i am trying with make command, this issue arises. Can you help with this?

[tristan0x]

1. Which version of ubuntu are you using. Can you print here the output of the command lsb_release -a?
2. it seems the python-dev package is missing. Can you please install it and try to rebuild?

[Vinoth461996]

python-dev is insatlled already. and I have attached image for my ubuntu version also.

[tristan0x]

Could you please send us the CMakeCache.txt file that should be in your CMake build directory?

[Vinoth461996]

CMakeCache.txt

[tristan0x]

From the PYTHON_EXECUTABLE CMake variable, it seems python 3 is used.
Can you please run the following commands?

cd build
cmake -DPYTHON_EXECUTABLE=/usr/bin/python2.7 .
make -j

[Vinoth461996]

Thanks , That helped me get through it. But , this error is showing up now. please help me rectify it.

[tristan0x]

THat's good news. Can you please share the full build output?

[Vinoth461996]

inoth@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: ''

[Vinoth461996]

Hi,
This is what i am getting when i am rebuilding using the command "cmake .."

-- Generating debug symbols: -ggdb3
-- Looking for strip utility
-- Looking for strip utility - found
-- Could NOT find PythonInterpLibs (missing: PYTHON_LIBRARIES)
-- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
-- Could NOT find MPI (missing: MPI_CXX_FOUND) (found version "3.1")
CMake Warning at CMakeLists.txt:126 (message):
Building without PETSC. If desired enable finding MPI libs as well!

-- A library with BLAS API found.
-- PYTHON packages being installed to . To change use -DPYTHON_INSTALL_PREFIX=

-- Configuring done
-- Generating done
-- Build files have been written to: /home/vinoth/STEPS/build

[WeiliangChenOIST]

@Vinoth461996 Sorry for the late reply. Looks like it has problem finding the install path. Can you provide the output of the following command please?

/usr/bin/python2.7 -c "import sys;print sys.path"

Also please try to make a full clean build start from cloning the repository as below, and send us the complete output texts. You can copy the text to a file and attach the file to the issue from the comment section.

git clone --recursive https://github.com/CNS-OIST/STEPS.git
cd STEPS
mkdir build
cd build
cmake -DPYTHON_EXECUTABLE=/usr/bin/python2.7 ..
make
sudo make install

[Vinoth461996]

Got it. Installed it. Thanks for the constant support