feelpp/mso4sc

Guillaume Dollé

@gdolle

@prudhomm @lotfiAb try to recompile his app from docker

but it seems we "forget" the toolboxes headers (in the cmake install rule).

lotfiAb

@lotfiAb

Now I have an other error:

….
BOOST_NO_CXX11_SCOPED_ENUMS -D BOOST_NO_SCOPED_ENUMS -D BOOST_OPTIONAL_USE_OLD_DEFINITION_OF_NONE=1 -D BOOST_PARAMETER_MAX_ARITY=24 -D BOOST_PP_VARIADICS=0 -D BOOST_RESULT_OF_USE_TR1 -D BOOST_TEST_DYN_LINK -D BOOST_UBLAS_SHALLOW_ARRAY_ADAPTOR -D FEELPP_DIM=2 -D FEELPP_HAS_DLFCN_H -D FEELPP_HAS_DLOPEN -D FEELPP_HAS_GMSH=1 -D FEELPP_HAS_GMSH_ADAPT_H -D FEELPP_HAS_HPDDM -D FEELPP_HAS_JSONLAB -D FEELPP_HAS_METIS -D FEELPP_HAS_MPI=1 -D FEELPP_HAS_MPI_H=1 -D FEELPP_HAS_PARALUTION -D FEELPP_HAS_PETSC -D FEELPP_HAS_PETSC_H -D GMSH_EXECUTABLE=/usr/bin/gmsh -D HAVE_LIBDL -D IN_GINAC -D _FEELPP_HAS_GMSH_ -D vtkFiltersFlowPaths_AUTOINIT=1(vtkFiltersParallelFlowPaths) -D vtkIOExodus_AUTOINIT=1(vtkIOParallelExodus) -D vtkIOGeometry_AUTOINIT=1(vtkIOMPIParallel) -D vtkIOImage_AUTOINIT=1(vtkIOMPIImage) -D vtkIOParallel_AUTOINIT=1(vtkIOMPIParallel) -D vtkIOSQL_AUTOINIT=2(vtkIOMySQL,vtkIOPostgreSQL) -D vtkRenderingContext2D_AUTOINIT=1(vtkRenderingContextOpenGL) -D vtkRenderingCore_AUTOINIT=3(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingOpenGL) -D vtkRenderingFreeType_AUTOINIT=2(vtkRenderingFreeTypeFontConfig,vtkRenderingMatplotlib) -D vtkRenderingLIC_AUTOINIT=1(vtkRenderingParallelLIC) -D vtkRenderingVolume_AUTOINIT=1(vtkRenderingVolumeOpenclang: error: unable to execute command: Segmentation faultr/local/include/feel/ginac -I /usr/local/include/feel
clang: error: clang frontend command failed due to signal (use -v to see invocation)t -I /usr/lib/openmpi/include/openmp
clang version 3.9.0-1ubuntu1 (tags/RELEASE_390/final)r/lib/openmpi/include -I /usr/lib/openmpi/include/openmpi -I /usr/i
Target: x86_64-pc-linux-gnu/include/libxml2 -I /usr/include/python3.5m -I /usr/lib/petscdir/3.7.3/x86_64-linux-gnu-real/
Thread model: posixlude/suitesparse -I /usr/include/scotch -I /usr/lib/petsc/include -I /usr/lib/slepc/include -I /usr/i
InstalledDir: /usr/bin/include/freetype2 -I /usr/include/x86_64-linux-gnu/freetype2 -I /usr/include/python2.7 -I /usr/in
clang: note: diagnostic msg: PLEASE submit a bug report to http://llvm.org/bugs/ and include the crash backtrace, preprocessed source, and associated run script.sr/bin/../lib/gcc/x86_64-linux-gnu/6.2.0/../../../../include/c++/6.2.0 -interna
clang: note: diagnostic msg: /x86_64-linux-gnu/6.2.0/../../../../include/x86_64-linux-gnu/c++/6.2.0 -internal-isystem /u
********************6_64-linux-gnu/6.2.0/../../../../include/x86_64-linux-gnu/c++/6.2.0 -internal-isystem /usr/bin/../li
b/gcc/x86_64-linux-gnu/6.2.0/../../../../include/c++/6.2.0/backward -internal-isystem /usr/local/include -internal-isyst
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:-internal-externc-isystem /usr/include/x86_64-linux-gnu -internal-ex
Preprocessed source(s) and associated run script(s) are located at:c++14 -fdeprecated-macro -fdebug-compilation-dir /fee
clang: note: diagnostic msg: /tmp/fluid-a02dad.cppmessage-length 120 -fvisibility-inlines-hidden -pthread -fobjc-runtime
clang: note: diagnostic msg: /tmp/fluid-a02dad.shshow-option -fcolor-diagnostics -o CMakeFiles/feelpp_af_fluid.dir/fluid
clang: note: diagnostic msg: uid.cpp
1.
********************
CMakeFiles/feelpp_af_fluid.dir/build.make:62: recipe for target 'CMakeFiles/feelpp_af_fluid.dir/fluid.cpp.o' failed
make[2]: *** [CMakeFiles/feelpp_af_fluid.dir/fluid.cpp.o] Error 254
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/feelpp_af_fluid.dir/all' failed
make[1]: *** [CMakeFiles/feelpp_af_fluid.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
feelpp@e8ab23545b74:/feel/nfluid$

I hope that now it goes.

Guillaume Dollé

@gdolle

I think you used CXX=clang instead of CXX=clang++

I just tried in docker, it seems to work for me adding toolboxes to include directory

lotfiAb

@lotfiAb

I use the following command:

cmake -DCMAKE_CXX_COMPILER=/usr/bin/clang++-3.9 -DCMAKE_C_COMPILER=/usr/bin/clang-3.9 .

in same directory than CMakeLists.txt

Guillaume Dollé

@gdolle

ok same for me

lotfiAb

@lotfiAb

The previous error occur when I use Docker under Widows system. But, when I run Docker under Linux system I have another type of error:

-- Generating done
-- Build files have been written to: /feel/nfluid
feelpp@5daa1b23148e:/feel/nfluid$ make
Scanning dependencies of target feelpp_mf_m-fluid_2d
[ 50%] Building CXX object CMakeFiles/feelpp_mf_m-fluid_2d.dir/fluid.o
[100%] Linking CXX executable feelpp_mf_m-fluid_2d
/usr/bin/ld: CMakeFiles/feelpp_mf_m-fluid_2d.dir/fluid.o: undefined reference to symbol '_ZNK4Feel10FeelModels9ModelBase9worldCommEv'
/usr/local/lib/libfeelpp_modelcore.so: error adding symbols: DSO missing from command line
clang: error: linker command failed with exit code 1 (use -v to see invocation)
CMakeFiles/feelpp_mf_m-fluid_2d.dir/build.make:444: recipe for target 'feelpp_mf_m-fluid_2d' failed
make[2]: *** [feelpp_mf_m-fluid_2d] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/feelpp_mf_m-fluid_2d.dir/all' failed
make[1]: *** [CMakeFiles/feelpp_mf_m-fluid_2d.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2
feelpp@5daa1b23148e:/feel/nfluid$

LA.

Guillaume Dollé

@gdolle

@lotfiAb I talk too fast yesterday, after retrying I can reproduce the same problem with missing symbol using docker while linking.

Guillaume Dollé

@gdolle

@/all just a tip for people using udocker on CESGA clusters. It can take some times (very very very long in fact on cesga) to create the feel++ container the first time with udocker. (pull is ok)
(A bit faster on atlas but still long). Running a container seems ok.

lotfiAb

@lotfiAb

Guillaume, I did not understand your last message.

Guillaume Dollé

@gdolle

Hi @lotfiAb, my last message was not related to thedocker error you mentionned. It is about udocker usage for users who do not have root access on their clusters.
However I confirm that there's a problem with symbols as you mentionned previously.

Guillaume Dollé

@gdolle

@prudhomm We'll have to ask more quota (currently 100000 per user) for cesga. In fact udocker extracts each images, then do a chroot. I got ~175000 files (5,5go) per feel++ containers with udocker on atlas after extraction. It explains also why it takes some times while creating the container.

Christophe Prud'homme

@prudhomm

@gdolle OK I will mention that this morning in our meeting

@lotfiAb what do you think about spending some time in Strasbourg working with us?

Say a few days, a week to start with

lotfiAb

@lotfiAb

For me, it’s OK!

Christophe Prud'homme

@prudhomm

Ok then let's discuss with Zoltan. Would the first second or third be OK? L

First week second week or third week

lotfiAb

@lotfiAb

First I need the permission of Zoli. Secondly problem of finance - my stays in strasboug ...
May be third week…
à plus tard

Christophe Prud'homme

@prudhomm

@gdolle @Trophime is feel++ working on finis terrae working now ?

Trophime

@Trophime

As for me I haven't worked on porting Feelpp on Finis Terrae II.

Still working on Salome (preparing dockerfile with custom installation for Ubuntu 16.10) and HiFiMagnet (preparing a dockerfile)

Christophe Prud'homme

@prudhomm

@lotfiAb we may have to have your stay in Strasbourg earlier in March because we will probably have a techboard meeting later in march

Christophe Prud'homme

@prudhomm

@/all I have added the project MSO4SC to get an overview of some of the task to be done here

@gdolle it is quite urgent to have feelpp/feelpp#852 running :)

Guillaume Dollé

@gdolle

yes actually I still don't have the quota for udocker

193.144.35.12:/Store_uni
                1602088  102400000 104857600              86  100000  101000        
193.144.35.13:/Home_SVG
                   5544  10240000 11264000              20  100000  101000        
193.144.35.12:/Home_FT2
                   1016  10240000 11264000              18  100000  101000

Guillaume Dollé

@gdolle

@prudhomm I'm currently using their VPN to connect the cluster, but maybe we should ask to add atlas IP, it'd be more convenient for everyone.

Guillaume Dollé

@gdolle

@prudhomm ok on $LUSTRE we are now at 200000 files, it should be ok :+1:

peoples should configure the bashrc

export UDOCKER_DIR=$LUSTRE/udocker  # dir where containers are installed. (faster // file system + 200000 quota)
export FEELPP_WORKDIR=$LUSTRE/feel

on ft2.

Christophe Prud'homme

@prudhomm

, @gdolle can you gather this info in a adoc file?

Guillaume Dollé

@gdolle

Yep I'll create a adoc doc

I looked about current modules for compiling feel++, there will be some work..

because some softwares are present on FT2 and not SVG (and inverse).

and most soft are not compiled with the same compilers (meaning we can't load them together :/ )

I'll also put that in the adoc so we have a clear view on what is missing.

Christophe Prud'homme

@prudhomm

:+1:

Christophe Prud'homme

@prudhomm

@/all this room will be closed and we move to this room

Trophime

@Trophime

@gdolle Once you have be bitten by quota on on FT2 how do you manage to remove files? udocker.py ps gives me an error...

Christophe Prud'homme

@prudhomm

@Trophime use this room now ;)

victorsndvg

@victorsndvg

Hello all, I'm Víctor Sande. A new member of the CESGA team

I'm going to read the chat to try to understand the current status of the issue

Christophe Prud'homme

@prudhomm

@victorsndvg thx for jumping in. as you can see above we have some issues on ft2 with udocker. @Trophime and @gdolle are working on this. First there is the quota issue because udocker create a chroot environment and copies all the files. Only lustre seems to handle this in terms of number of files

oops @victorsndvg it is actually here

Christophe Prud'homme

@prudhomm

@lsala @gdolle @Trophime we can discuss here during the talks ;)

@lsala did you put your presentation in google drive MSO4SC

Guillaume Dollé

@gdolle

@prudhomm :+1:

lsala

@lsala

yes I have, the link is here:
https://docs.google.com/presentation/d/1xNZdsPhkO0pCesXJd2yXziXw0O4UnWoUmjwk_JZ866E/edit#slide=id.g2243b577b8_0_0

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