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esrf-bliss / Lima

Library for Image Acquisition
https://lima1.rtfd.io
GNU General Public License v3.0
39 stars 71 forks source link

install on CentOS6 : No such file or directory: '/home/det/Lima/build/third-party/Processlib/sip/processlib.sbf' #82

Closed PhilLAL closed 5 years ago

PhilLAL commented 5 years ago

Hi there, I tried to install Lima on CentOS6. Here are the steps I followed:

# LImA on Dectris PC

## Installation
mkdir ~/tmp
cd ~/tmp

### Getting Lima code
sudo yum install git 

### Lima build depedencies : cmake>=3.1
sudo yum install gcc cmake322 gsl gsl-devel

### Lima python dependencies (yum <= 4.18)
yum search sip
sudo yum install python numpy sip

### images format
sudo yum install libtiff zlib CBFlib hdf5 lz4 libconfig 

### libtango9
#### liblog4tango
wget -c http://pubrepo.maxiv.lu.se/rpm/el6/x86_64/liblog4tango5-5.0.1-7.el6.maxlab.x86_64.rpm
sudo rpm -i liblog4tango5-5.0.1-7.el6.maxlab.x86_64.rpm
#### zeromq4
sudo yum install libsodium
wget -c http://pubrepo.maxiv.lu.se/rpm/el6/x86_64/zeromq4-4.1.4-5.el6.x86_64.rpm
sudo rpm -i zeromq4-4.1.4-5.el6.x86_64.rpm
#wget -c http://pubrepo.maxiv.lu.se/rpm/el6/x86_64/zeromq4-devel-4.1.4-5.el6.x86_64.rpm
#sudo rpm -i zeromq4-devel-4.1.4-5.el6.x86_64.rpm
#wget -c http://pubrepo.maxiv.lu.se/rpm/el6/x86_64/cppzmq-devel-4.1.4-5.el6.x86_64.rpm
#sudo rpm -i cppzmq-devel-4.1.4-5.el6.x86_64.rpm
#### libtango9
wget -c http://pubrepo.maxiv.lu.se/rpm/el6/x86_64/libtango9-9.2.2-7.el6.maxlab.x86_64.rpm
sudo rpm -i libtango9-9.2.2-7.el6.maxlab.x86_64.rpm
#### libzmq
#### python-futures
sudo yum install python-futures

### PyTango
wget -c http://pubrepo.maxiv.lu.se/rpm/el6/x86_64/python-pytango-9.2.0-8.el6.maxlab.x86_64.rpm
sudo rpm -i python-pytango-9.2.0-8.el6.maxlab.x86_64.rpm
#### libtango
#### boost-python
sudo yum install boost-python
#### numpy
sudo yum install numpy
#### six
sudo yum install python-six
#### setuptools
sudo yum install python-setuptools
#### sphinx
sudo yum install python-sphinx
#### python-futures
#### gevent
sudo yum install python-gevent

cd ..

## Getting Lima code
git clone git://github.com/esrf-bliss/Lima.git
cd Lima

## Install.sh
sudo ln -s /usr/local/cmake/3.2.2/bin/cmake /usr/bin/cmake 
source /etc/bashrc
sudo ./install.sh --git --install-prefix=./install --install-python-prefix=./install/python pilatus python pytango-server

When I launched this last instruction, I get this output

~/Lima> sudo ./install.sh --git --install-prefix=./install --install-python-prefix=./install/python pilatus python pytango-server
Executing:git submodule init camera/pilatus
Submodule 'camera/pilatus' (git://github.com/esrf-bliss/Lima-camera-pilatus) registered for path 'camera/pilatus'
Executing:git submodule update camera/pilatus
Cloning into 'camera/pilatus'...
remote: Enumerating objects: 900, done.
remote: Total 900 (delta 0), reused 0 (delta 0), pack-reused 900
Receiving objects: 100% (900/900), 224.41 KiB | 0 bytes/s, done.
Resolving deltas: 100% (472/472), done.
Submodule path 'camera/pilatus': checked out '0a26b61f31d41c60a6b45385279f889f7791d2d4'
Executing:git submodule init
Executing:git submodule init applications/tango/python
Submodule 'applications/tango/python' (git://github.com/esrf-bliss/Lima-tango-python) registered for path 'applications/tango/python'
Executing:git submodule update applications/tango/python
Cloning into 'applications/tango/python'...
remote: Enumerating objects: 1547, done.
remote: Total 1547 (delta 0), reused 0 (delta 0), pack-reused 1547
Receiving objects: 100% (1547/1547), 470.60 KiB | 0 bytes/s, done.
Resolving deltas: 100% (1069/1069), done.
Submodule path 'applications/tango/python': checked out 'df3bf14910abd2576147891046d155e4f4661338'
Executing:git submodule init
Executing:git submodule init third-party/Processlib
Submodule 'third-party/Processlib' (git://github.com/esrf-bliss/Processlib) registered for path 'third-party/Processlib'
Executing:git submodule update third-party/Processlib
Cloning into 'third-party/Processlib'...
remote: Enumerating objects: 2223, done.
remote: Total 2223 (delta 0), reused 0 (delta 0), pack-reused 2223
Receiving objects: 100% (2223/2223), 821.11 KiB | 0 bytes/s, done.
Resolving deltas: 100% (1043/1043), done.
Submodule path 'third-party/Processlib': checked out 'f56b83502ddab7e70874a4665b76e0fed0019446'
Executing:git submodule init
Executing:cmake /home/det/Lima -G"Unix Makefiles" -DLIMACAMERA_SIMULATOR=1 -DLIMACAMERA_PILATUS=1 -DLIMA_ENABLE_PYTHON=1 -DLIMA_ENABLE_PYTANGO_SERVER=1 -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=./install -DPYTHON_SITE_PACKAGES_DIR=./install/python
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- 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
-- 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 PythonInterp: /usr/bin/python (found version "2.6.6") 
-- Found PythonLibs: /usr/lib64/libpython2.6.so (found version "2.6.6") 
-- Found SIP version: 4.9.3
-- Found GSL: /usr/lib64/libgsl.so  
Traceback (most recent call last):
  File "/home/det/Lima/cmake/readsipsbf.py", line 9, in <module>
    for l in open(sbf_fname):
IOError: [Errno 2] No such file or directory: '/home/det/Lima/build/third-party/Processlib/sip/processlib.sbf'
CMake Error at cmake/SIPMacros.cmake:136 (add_custom_command):
  add_custom_command Wrong syntax.  A TARGET or OUTPUT must be specified.
Call Stack (most recent call first):
  third-party/Processlib/CMakeLists.txt:244 (add_sip_python_module)

CMake Error at third-party/Processlib/CMakeLists.txt:245 (target_include_directories):
  Cannot specify include directories for target "python_module_processlib"
  which is not built by this project.

CMake Error at third-party/Processlib/CMakeLists.txt:246 (target_link_libraries):
  Cannot specify link libraries for target "python_module_processlib" which
  is not built by this project.

-- Configuring incomplete, errors occurred!
See also "/home/det/Lima/build/CMakeFiles/CMakeOutput.log".
See also "/home/det/Lima/build/CMakeFiles/CMakeError.log".
Problem building/installing Lima: Something is wrong in CMake environment. Make sure your configuration is good. [cmake /home/det/Lima -G"Unix Makefiles" -DLIMACAMERA_SIMULATOR=1 -DLIMACAMERA_PILATUS=1 -DLIMA_ENABLE_PYTHON=1 -DLIMA_ENABLE_PYTANGO_SERVER=1 -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=./install -DPYTHON_SITE_PACKAGES_DIR=./install/python]

I will try to use cmake, but perhaps there is something wrong with the script install.sh If you understand what's wrong...

Regards

PhilLAL commented 5 years ago

For information, I encountered the same issue with cmake:

~/Lima> mkdir -p build install/python && cd build && cmake .. -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=../install/ -DPYTHON_SITE_PACKAGES_DIR=../install/python -DLIMACAMERA_PILATUS=true -DLIMA_ENABLE_PYTANGO_SERVER=true -DLIMA_ENABLE_PYTHON=true
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- 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
-- 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 PythonInterp: /usr/bin/python (found version "2.6.6") 
-- Found PythonLibs: /usr/lib64/libpython2.6.so (found version "2.6.6") 
-- Found SIP version: 4.9.3
-- Found GSL: /usr/lib64/libgsl.so  
Traceback (most recent call last):
  File "/home/det/Lima/cmake/readsipsbf.py", line 9, in <module>
    for l in open(sbf_fname):
IOError: [Errno 2] No such file or directory: '/home/det/Lima/build/third-party/Processlib/sip/processlib.sbf'
CMake Error at cmake/SIPMacros.cmake:136 (add_custom_command):
  add_custom_command Wrong syntax.  A TARGET or OUTPUT must be specified.
Call Stack (most recent call first):
  third-party/Processlib/CMakeLists.txt:244 (add_sip_python_module)

CMake Error at third-party/Processlib/CMakeLists.txt:245 (target_include_directories):
  Cannot specify include directories for target "python_module_processlib"
  which is not built by this project.

CMake Error at third-party/Processlib/CMakeLists.txt:246 (target_link_libraries):
  Cannot specify link libraries for target "python_module_processlib" which
  is not built by this project.

-- Configuring incomplete, errors occurred!
See also "/home/det/Lima/build/CMakeFiles/CMakeOutput.log".
See also "/home/det/Lima/build/CMakeFiles/CMakeError.log".

Here is the CMakeError.log:

Determining if the pthread_create exist failed with the following output:
Change Dir: /home/det/Lima/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTryCompileExec1846950021/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1846950021.dir/build.make CMakeFile
s/cmTryCompileExec1846950021.dir/build
gmake[1]: entrant dans le répertoire « /home/det/Lima/build/CMakeFiles/CMakeTmp 
»
/usr/local/cmake/3.2.2/bin/cmake -E cmake_progress_report /home/det/Lima/build/C
MakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1846950021.dir/CheckSymbolExists.c.
o
/usr/bin/cc    -o CMakeFiles/cmTryCompileExec1846950021.dir/CheckSymbolExists.c.
o   -c /home/det/Lima/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTryCompileExec1846950021
/usr/local/cmake/3.2.2/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExe
c1846950021.dir/link.txt --verbose=1
/usr/bin/cc       CMakeFiles/cmTryCompileExec1846950021.dir/CheckSymbolExists.c.
o  -o cmTryCompileExec1846950021 -rdynamic 
CMakeFiles/cmTryCompileExec1846950021.dir/CheckSymbolExists.c.o: In function `main':
CheckSymbolExists.c:(.text+0xc): undefined reference to `pthread_create'
collect2: ld a retourné 1 code d'état d'exécution
gmake[1]: *** [cmTryCompileExec1846950021] Erreur 1
gmake[1]: quittant le répertoire « /home/det/Lima/build/CMakeFiles/CMakeTmp »
gmake: *** [cmTryCompileExec1846950021/fast] Erreur 2

File /home/det/Lima/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include <pthread.h>

int main(int argc, char** argv)
{
  (void)argv;
#ifndef pthread_create
  return ((int*)(&pthread_create))[argc];
#else
  (void)argc;
  return 0;
#endif
}

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/det/Lima/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTryCompileExec2221387823/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2221387823.dir/build.make CMakeFiles/cmTryCompileExec2221387823.dir/build
gmake[1]: entrant dans le répertoire « /home/det/Lima/build/CMakeFiles/CMakeTmp »
/usr/local/cmake/3.2.2/bin/cmake -E cmake_progress_report /home/det/Lima/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec2221387823.dir/CheckFunctionExists.c.o
/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTryCompileExec2221387823.dir/CheckFunctionExists.c.o   -c /usr/local/cmake/3.2.2/share/cmake/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2221387823
/usr/local/cmake/3.2.2/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2221387823.dir/link.txt --verbose=1
/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create    CMakeFiles/cmTryCompileExec2221387823.dir/CheckFunctionExists.c.o  -o cmTryCompileExec2221387823 -rdynamic -lpthreads 
/usr/bin/ld: cannot find -lpthreads
collect2: ld a retourné 1 code d'état d'exécution
gmake[1]: *** [cmTryCompileExec2221387823] Erreur 1
gmake[1]: quittant le répertoire « /home/det/Lima/build/CMakeFiles/CMakeTmp »
gmake: *** [cmTryCompileExec2221387823/fast] Erreur 2

and the CMakeOutput:

The system is: Linux - 2.6.32-431.el6.x86_64 - x86_64
Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
Compiler: /usr/bin/cc 
Build flags: 
Id flags: 

The output was:
0

Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"

The C compiler identification is GNU, found in "/home/det/Lima/build/CMakeFiles/3.2.2/CompilerIdC/a.out"

Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded.
Compiler: /usr/bin/c++ 
Build flags: 
Id flags: 

The output was:
0

Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"

The CXX compiler identification is GNU, found in "/home/det/Lima/build/CMakeFiles/3.2.2/CompilerIdCXX/a.out"

Determining if the C compiler works passed with the following output:
Change Dir: /home/det/Lima/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTryCompileExec3834998194/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec3834998194.dir/build.make CMakeFiles/cmTryCompileExec3834998194.dir/build
gmake[1]: entrant dans le répertoire « /home/det/Lima/build/CMakeFiles/CMakeTmp »
/usr/local/cmake/3.2.2/bin/cmake -E cmake_progress_report /home/det/Lima/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec3834998194.dir/testCCompiler.c.o
/usr/bin/cc    -o CMakeFiles/cmTryCompileExec3834998194.dir/testCCompiler.c.o   -c /home/det/Lima/build/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTryCompileExec3834998194
/usr/local/cmake/3.2.2/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3834998194.dir/link.txt --verbose=1
/usr/bin/cc       CMakeFiles/cmTryCompileExec3834998194.dir/testCCompiler.c.o  -o cmTryCompileExec3834998194 -rdynamic 
gmake[1]: quittant le répertoire « /home/det/Lima/build/CMakeFiles/CMakeTmp »

Detecting C compiler ABI info compiled with the following output:
Change Dir: /home/det/Lima/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTryCompileExec483332461/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec483332461.dir/build.make CMakeFiles/cmTryCompileExec483332461.dir/build
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It's a bit late and I don't really see where is the issue, if you have any tip, I'll take it.

laurent-claustre commented 5 years ago

Hi, Your sip version is pretty old, 4.9 is not working with Lima. you need 4.10 minimum. You should download sip 4.18 and compile/install after having uninstall sip-4.9 with yum.

sdebionne commented 5 years ago

Hi PhilLAL, While it is true that we currently support SIP 4.18, it looks like the build system of Processlib and Lima are out of sync on Github. If you look at cmake/SIPMacros.cmake in both projects, one is using the .sbf file (to get the list of cpp files to compile), the other one uses the "parts" feature of sip. This won't work and needs to be fixed -probably a question of syncing our Gitlab instance and Github.

laurent-claustre commented 5 years ago

Hi Phil, Vincent Michel told me you will be at ESRF tomorrow? We can meet if you want. I would like to propose you to test installing Conda packages on your system. Regards,

Laurent

stufisher commented 5 years ago

Any news on this? I'm on centos7 (sip 4.14) and seeing the same thing trying to build the hexitec driver with: ./install.sh --git --install-prefix=/home/dir/hexitec/install hexitec python pytango-server

sdebionne commented 5 years ago

I am confused because I have just try to compile the simulator from Github master branch and it builds successfully. I use conda because I have multiple development environments but it should not make any difference. My environment has python 2.7, SIP 4.18, GSL 2.4. Here are the steps I followed:

conda create -n test-github python=2.7
conda activate test-github
conda install cmake gsl sip=4.18
git clone https://github.com/esrf-bliss/Lima.git lima-github && cd lima-github
git submodule update --init third-party/Processlib/
mkdir build && cd build
cmake -DLIMA_ENABLE_PYTHON=1 -DCMAKE_FIND_ROOT_PATH=$CONDA_PREFIX -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY ..
make -j8
...
[100%] Built target python_module_limacore

I am using SIP 4.18 since this is the version we support. If your package manager does not have this version, you can easily recompile SIP from source with python setup.py install.

laurent-claustre commented 5 years ago

Hi Stufisher, sorry but github.com/esf-bliss/lima is in bad shape. We will upgrade it soon, Could you re-clone the LIMA from our gitlab repo at gitlab.esrf.fr/limagroup/lima ? The new documentation is available here: http://lima-doc.readthedocs.io/

stufisher commented 5 years ago

Sorry @laurent-claustre @sdebionne, you are right, its the sip version thats causing the issue. Manually installed SIP==4.18 and we are in business. Thanks for your speedy replies!