Install ROOT6 in cluster locally error

ROOT
21

Hi,

What do you mean by saying: prefix PATH with /home/huangli/.linuxbrew/bin

I use:

export PATH="$HOME/.linuxbrew/bin:$PATH"

in my .bash_profile

Best,
Li

22

Yes (export PATH="$HOME/.linuxbrew/bin:$PATH") But I see that does not work.
I do not know exactly what kind of system you have but is very fishy. For example it finds lzma library in the system but is unusable

Found LZMA library at /usr/lib64/liblzma.so
/home/huangli/.linuxbrew/bin/ld: warning: liblzma.so.0, needed by ../lib/libCore.so, not found (try using -rpath or -rpath-link)
../lib/libCore.so: undefined reference to `lzma_stream_decoder'
../lib/libCore.so: undefined reference to `lzma_lzma_preset'
../lib/libCore.so: undefined reference to `lzma_code'
../lib/libCore.so: undefined reference to `lzma_end'
../lib/libCore.so: undefined reference to `lzma_stream_encoder'

What is pointing /usr/lib64/liblzma.so?

ls -la /usr/lib64/liblzma.so

You can build the builtin lzma library with ‘-Dbuiltin_lzma=ON’ as well as the pcre library ‘-Dbuiltin_pcre=ON’, but you will stumble into another problem.

Cheers,

Pere

23

Hi,

I think we make some progresses by using commands, lzma problem seems to be done.

(py2.7) (py2.7) [huangli@login2 root6]$ cmake -D "CMAKE_PREFIX_PATH=/home/huangli/.linuxbrew/;/home/huangli/.linuxbrew/bin/;/home/huangli/.linuxbrew/lib/;/home/huangli/.linuxbrew/lib64/;/home/huangli/bin/pyEV/py2.7/;/home/huangli/bin/pyEV/py2.7/bin/;/home/huangli/bin/pyEV/py2.7/lib" -Dx11=OFF ~/tools/root

But now there is a python problem, although I have installed python using virtualenv.

And the system information is:

(py2.7) (py2.7) [huangli@login2 python2.7]$ lsb_release -a
LSB Version:    :core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 6.2 (Santiago)
Release:        6.2
Codename:       Santiago
(py2.7) (py2.7) [huangli@login2 python2.7]$ uname -a
Linux login2 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux

Best,
Li
gcc5.txt (339 KB)

24

Hi,

After re install python, I solve the last problem, but there is another problem that I don’t understand,

The last few lines are:

[ 94%] Building CXX object tmva/tmva/CMakeFiles/TMVA.dir/src/VariableTransformBase.cxx.o
[ 94%] Building CXX object tmva/tmva/CMakeFiles/TMVA.dir/src/Volume.cxx.o
[ 94%] Building CXX object tmva/tmva/CMakeFiles/TMVA.dir/src/DNN/Architectures/Reference.cxx.o
[ 94%] Linking CXX shared library ../../lib/libRGL.so
CMakeFiles/RGL.dir/src/TGLFormat.cxx.o: In function `TGLFormat::InitAvailableSamples()':
/home/huangli/tools/root/graf3d/gl/src/TGLFormat.cxx:284: undefined reference to `XGetVisualInfo'
/home/huangli/tools/root/graf3d/gl/src/TGLFormat.cxx:293: undefined reference to `XFree'
CMakeFiles/RGL.dir/src/TGLWidget.cxx.o: In function `TGLWidget::CreateWindow(TGWindow const*, TGLFormat const&, unsigned int, unsigned int, std::pair<void*, void*>&)':
/home/huangli/tools/root/graf3d/gl/src/TGLWidget.cxx:521: undefined reference to `XCreateColormap'
/home/huangli/tools/root/graf3d/gl/src/TGLWidget.cxx:530: undefined reference to `XCreateWindow'
CMakeFiles/RGL.dir/src/TGLWidget.cxx.o: In function `TGLWidget::~TGLWidget()':
/home/huangli/tools/root/graf3d/gl/src/TGLWidget.cxx:166: undefined reference to `XFree'
CMakeFiles/RGL.dir/src/TX11GL.cxx.o: In function `TX11GLManager::DeleteGLContext(int)':
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:501: undefined reference to `XFreeGC'
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:503: undefined reference to `XFreeGC'
CMakeFiles/RGL.dir/src/TX11GL.cxx.o: In function `TX11GLManager::Flush(int)':
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:313: undefined reference to `XCopyArea'
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:305: undefined reference to `XCreateGC'
CMakeFiles/RGL.dir/src/TX11GL.cxx.o: In function `TX11GLManager::ReadGLBuffer(int)':
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:473: undefined reference to `XPutImage'
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:462: undefined reference to `XCreateGC'
CMakeFiles/RGL.dir/src/TX11GL.cxx.o: In function `TX11GLManager::InitGLWindow(unsigned long)':
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:218: undefined reference to `XGetGeometry'
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:221: undefined reference to `XCreateColormap'
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:234: undefined reference to `XCreateWindow'
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:237: undefined reference to `XMapWindow'
CMakeFiles/RGL.dir/src/TX11GL.cxx.o: In function `TX11GLManager::CreateGLPixmap(TX11GLManager::TGLContext_t&)':
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:325: undefined reference to `XCreatePixmap'
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:336: undefined reference to `XCreateImage'
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:347: undefined reference to `XInitImage'
CMakeFiles/RGL.dir/src/TX11GL.cxx.o: In function `~TX11PixGuard':
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:74: undefined reference to `XFreePixmap'
/home/huangli/tools/root/graf3d/gl/src/TX11GL.cxx:74: undefined reference to `XFreePixmap'
collect2: error: ld returned 1 exit status
[ 94%] Linking CXX shared library ../../lib/libTMVA.so
make[2]: *** [graf3d/gl/CMakeFiles/RGL.dir/build.make:2588: lib/libRGL.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:17961: graf3d/gl/CMakeFiles/RGL.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 94%] Built target TMVA
make: *** [Makefile:150: all] Error 2

Does anyone know what cause this problem?

Best,
Li

25

Hi,

Thanks for all. I finally find a way, using commands ( when I suddenly realize that the bad x11 and opengl packages in the cluster)

cmake -D "CMAKE_PREFIX_PATH=/home/huangli/.linuxbrew/;/home/huangli/.linuxbrew/bin/;/home/huangli/.linuxbrew/lib/;/home/huangli/.linuxbrew/lib64/" -Dx11=OFF -Dopengl=OFF ~/tools/root

And there is an confused thing that I can’t compile ROOT with python using virtualenv version, but the linuxbrew version is ok.

I guess the reason is that the virtualenv version lib file is something like “libpython.a” while linuxbrew one is “libpython.so”. I definitely sure that in both case, cmake find the right lib file. Maybe you guys know the deep reason.

There are still one more error in pyroot after installation. I will give a new ticket for that.

Best,
Li