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CNS-OIST / STEPS

Public release repository for STochastic Engine of Pathway Simulation (STEPS)
http://steps.sourceforge.net
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Problem in installing steps #17

Closed Vinoth461996 closed 5 years ago

Vinoth461996 commented 5 years ago

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.

Screenshot from 2019-04-03 10:17:01

WeiliangChenOIST commented 5 years ago

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 commented 5 years ago

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

WeiliangChenOIST commented 5 years ago

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

tristan0x commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 Screenshot from 2019-04-03 11:25:22

tristan0x commented 5 years ago

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 commented 5 years ago

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

Vinoth461996 commented 5 years ago

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

WeiliangChenOIST commented 5 years ago

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 commented 5 years ago

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

tristan0x commented 5 years ago
  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 commented 5 years ago

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

tristan0x commented 5 years ago

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

Vinoth461996 commented 5 years ago

CMakeCache.txt

tristan0x commented 5 years ago

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 commented 5 years ago

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

tristan0x commented 5 years ago

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

Vinoth461996 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

@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 commented 5 years ago

Got it. Installed it. Thanks for the constant support