Problems to install larcv

[Gui1402]

Hi guys,

I am beginner in Linux and python so I have some problems with larcv installation.

I was trying to install larcv following this link :
My first attempt was using Linux Mint 19
Then I cloned the repository, used source configure.sh and make but did not work.

Error:
`
Building core...

Compiling Base...
make[1]: Entering directory '/home/guilherme/larcv2/larcv/core/Base'
<< checking dependencies>>
<< generating dict >>
In file included from input_line_12:6:
In file included from /home/guilherme/larcv2/larcv/core/Base/ConfigManager.h:18:
In file included from /home/guilherme/larcv2/larcv/core/Base/larcv_base.h:19:
In file included from /home/guilherme/larcv2/larcv/core/Base/larcv_logger.h:21:
In file included from /home/guilherme/larcv2/larcv/core/Base/LArCVTypes.h:22:
In file included from /home/guilherme/anaconda3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3/../../../../include/c++/4.8.3/climits:41:
In file included from /home/guilherme/anaconda3/include/limits.h:125:
In file included from /home/guilherme/anaconda3/etc/cling/lib/clang/3.7.0/include/limits.h:37:
/usr/include/limits.h:145:17: error: token is not a valid binary operator in a
preprocessor subexpression
#if __GLIBC_USE (IEC_60559_BFP_EXT)
~~~~~~~~~~~ ^
Error: rootcling: compilation failure (/home/guilherme/larcv2/build/lib/libLArCVBase784ddeac21_dictUmbrella.h)
/home/guilherme/larcv2/Makefile/GNUmakefile.CORE:41: recipe for target '/home/guilherme/larcv2/build/Base/BaseDict.cxx' failed
make[1]: *** [/home/guilherme/larcv2/build/Base/BaseDict.cxx] Error 1
make[1]: Leaving directory '/home/guilherme/larcv2/larcv/core/Base'
GNUmakefile:34: recipe for target 'obj' failed
make: *** [obj] Error 2
`

So my next attempt was to use Ubuntu 16.04 and did not have problems to install larcv but when I import larcv on Jupyter(or spyder) the kernel crashed.

Did someone have the same problem?

[drinkingkazu]

A few comments:

0. I am happy to help debugging. Shall we focus first on Ubuntu? Would you share the error message (which shows up on the terminal that runs jupyter notebook, not on notebook itself)?

1. Have you considered using our singularity image? We use singularity software container to address a few issues including reproducibility of analysis and distribution of a software. What's related to your issue is that a container is designed to deliver you a working larcv development (as well as analysis) environment without having you install dependent libraries.

I use singularity on my laptop, a GPU server, and even on a GPU cluster / cloud. If you are interested in but don't know what it is, here's introduction tutorial and our singularity recipe repository as well as built image repository.

[coreyjadams]

Do you need a custom build of larcv? Every if you do, singularity might be the answer. You can solve a lot of the dependancies that way pretty easily. Check out the larcv singularity builds and see if that works. The wiki page by Kazu gives great instructions.

…

On Mon, Oct 15, 2018, 6:11 PM Gui1402 ***@***.***> wrote: Hi guys, I am beginner in Linux and python so I have some problems with larcv installation. I was trying to install larcv following this link : <http://deeplearnphysics.org/Blog/tutorials/tutorial-01.html> My first attempt was using Linux Mint 19 Then I cloned the repository, used source configure.sh and make but did not work. Error: ` Building core... Compiling Base... make[1]: Entering directory '/home/guilherme/larcv2/larcv/core/Base' << checking dependencies>> << generating dict >> In file included from input_line_12:6: In file included from /home/guilherme/larcv2/larcv/core/Base/ConfigManager.h:18: In file included from /home/guilherme/larcv2/larcv/core/Base/larcv_base.h:19: In file included from /home/guilherme/larcv2/larcv/core/Base/larcv_logger.h:21: In file included from /home/guilherme/larcv2/larcv/core/Base/LArCVTypes.h:22: In file included from /home/guilherme/anaconda3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3/../../../../include/c++/4.8.3/climits:41: In file included from /home/guilherme/anaconda3/include/limits.h:125: In file included from /home/guilherme/anaconda3/etc/cling/lib/clang/3.7.0/include/limits.h:37: /usr/include/limits.h:145:17: error: token is not a valid binary operator in a preprocessor subexpression #if __GLIBC_USE (IEC_60559_BFP_EXT) ~~~~~~~~~~~ ^ Error: rootcling: compilation failure (/home/guilherme/larcv2/build/lib/libLArCVBase784ddeac21_dictUmbrella.h) /home/guilherme/larcv2/Makefile/GNUmakefile.CORE:41: recipe for target '/home/guilherme/larcv2/build/Base/BaseDict.cxx' failed make[1]: *** [/home/guilherme/larcv2/build/Base/BaseDict.cxx] Error 1 make[1]: Leaving directory '/home/guilherme/larcv2/larcv/core/Base' GNUmakefile:34: recipe for target 'obj' failed make: *** [obj] Error 2 ` So my next attempt was to use Ubuntu 16.04 and did not have problems to install larcv but when I import larcv on Jupyter(or spyder) the kernel crashed. Did someone have the same problem? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#30>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGUDOVnX6XggWCU9VoaZnlgDzdch1wlCks5ulRYmgaJpZM4XdTHP> .

[coreyjadams]

Yeah I echo Kazu. I use singularity on my ubuntu laptop to run an ubuntu image with root, tensorflow and larcv. It's just easier to make a nice consistent environment that I know will work elsewhere too.

…

On Mon, Oct 15, 2018, 6:34 PM Drinking Kazu ***@***.***> wrote: A few comments: 1. I am happy to help debugging. Shall we focus first on Ubuntu? Would you share the error message (which shows up on the terminal that runs jupyter notebook, not on notebook itself)? 2. Have you considered using our singularity image? We use singularity software container to address a few issues including reproducibility of analysis and distribution of a software. What's related to your issue is that a container is designed to deliver you a working karcv development (as well as analysis) environment without having you install dependent libraries. I use singularity on my laptop, a GPU server, and even on a GPU cluster / cloud. If you are interested in but don't know what it is, here's introduction tutorial <https://github.com/DeepLearnPhysics/playground-singularity/wiki> and our singularity recipe repository <https://github.com/DeepLearnPhysics/larcv2-singularity> as well as built image repository <https://singularity-hub.org/collections/459>. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#30 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGUDOSdl24GPVUCn33Ke-DNQ1apR91crks5ulRtygaJpZM4XdTHP> .

[Gui1402]

Thank you for reply guys

Really I never heard about singularity image, maybe it can help me because I would like to run this example:

http://deeplearnphysics.org/Blog/tutorials/tutorial-02.html

Do I need to install VirtualBox(or similar programs) to run a singularity image?

But when I after put from larcv import larcv on Jupyter notebook, the jupyter's terminal shows:
*** Break *** bus error [I 23:30:07.095 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports kernel 431c86fd-3727-43cb-8bd3-f3cabb344225 restarted

[coreyjadams]

You should check out the singularity site for information on how to run it: http://singularity.lbl.gov/docs-run

And, Kazu's wiki page for the larch singularity in detail:
https://github.com/DeepLearnPhysics/playground-singularity/wiki