[Rivet] seg fault in rivet-bootstrap-lcg in lxplus install

[Andy Buckley]

I see, I haven't tried on the batch system -- you mean lxbatch? I'll 
give that a try... I know that lxbatch annoyingly tries to be clever by 
setting some extra environment variables, maybe even depending on the 
user's unix group, which can screw up jobs in very mysterious ways. 
Maybe try submitting a job that just runs "env", to find what 
environment it is really giving you?

Andy


On 03/08/16 10:30, Raghav Kunnawalkam Elayavalli wrote:
> Hi Andy,
>
> So like i said, i currently have 2.4.1 working and able to submit batch
> jobs with it (only with the bootstrap and NOT with the bootstrap-lcg).
> If you are able to run  in a batch job rivet -a ANALYSIS test.hepmc with
> the latest installation of rivet, I will gladly use it. Ive been trying
> to do that and i keep getting the python unknown os or something like that.
> I also tried the installation of LCG_85 like i said with the same
> segfault issue. I will try with your latest bootstrap and see what it
> gives me.
>
> Maybe this is not for you guys but more for the fastjet team (i also
> sent them an email)
> Im getting another issue at the moment when i load a library from
> fjcontrib -lRecursiveTools  (which you may remember i was asking you
> guys in the past). So I have it working on my laptop but when i followed
> and did the same steps in lxplus i get the following error.
>
> [rkunnawa at lxplus017 ANALYSIS]$ rivet-buildplugin
> RivetJEWEL_JetGrooming.so JEWEL_JetGrooming.cc -lRecursiveTools
> $(root-config --cflags --libs)
> /usr/bin/g++ -o "RivetJEWEL_JetGrooming.so" -shared -fPIC
> -I/afs/cern.ch/work/r/rkunnawa/RIVET/local/include
> <http://cern.ch/work/r/rkunnawa/RIVET/local/include>
> -I/afs/cern.ch/work/r/rkunnawa/RIVET/local/include
> <http://cern.ch/work/r/rkunnawa/RIVET/local/include>
> -I/afs/cern.ch/work/r/rkunnawa/RIVET/local/include
> <http://cern.ch/work/r/rkunnawa/RIVET/local/include>
> -I/afs/cern.ch/work/r/rkunnawa/RIVET/local/include
> <http://cern.ch/work/r/rkunnawa/RIVET/local/include>
> -I/afs/cern.ch/work/r/rkunnawa/RIVET/local/include
> <http://cern.ch/work/r/rkunnawa/RIVET/local/include>
> -I/afs/cern.ch/work/r/rkunnawa/RIVET/local/include
> <http://cern.ch/work/r/rkunnawa/RIVET/local/include> -pedantic -ansi
> -Wall -Wno-long-long -Wno-format -Werror=uninitialized -O2
> -Wl,--no-as-needed -L/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib
> <http://cern.ch/work/r/rkunnawa/RIVET/local/lib>
> -L/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib
> <http://cern.ch/work/r/rkunnawa/RIVET/local/lib>
> -L/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib
> <http://cern.ch/work/r/rkunnawa/RIVET/local/lib>
> -Wl,-rpath,/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib
> <http://cern.ch/work/r/rkunnawa/RIVET/local/lib> -lm
> -L/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib
> <http://cern.ch/work/r/rkunnawa/RIVET/local/lib> -lfastjettools
> -lfastjet -lfastjetplugins -lsiscone_spherical -lsiscone
> JEWEL_JetGrooming.cc -lRecursiveTools -pthread -m64 -I/usr/include/root
> -L/usr/lib64/root -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d
> -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread
> -pthread -lm -ldl -rdynamic -lRivet
> JEWEL_JetGrooming.cc: In member function ‘std::pair<int, int>
> Rivet::JEWEL_JetGrooming::FindCandidateBin(double, double)’:
> JEWEL_JetGrooming.cc:76: warning: comparison between signed and unsigned
> integer expressions
> JEWEL_JetGrooming.cc:77: warning: comparison between signed and unsigned
> integer expressions
> JEWEL_JetGrooming.cc: In member function ‘virtual void
> Rivet::JEWEL_JetGrooming::analyze(const Rivet::Event&)’:
> JEWEL_JetGrooming.cc:342: warning: unused variable ‘FS’
> /usr/bin/ld:
> /afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/libRecursiveTools.a
> <http://cern.ch/work/r/rkunnawa/RIVET/local/lib/libRecursiveTools.a>(SoftDrop.o):
> relocation R_X86_64_32 against `.bss' can not be used when making a
> shared object; recompile with -fPIC
> /afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/libRecursiveTools.a:
> <http://cern.ch/work/r/rkunnawa/RIVET/local/lib/libRecursiveTools.a:>
> could not read symbols: Bad value
> collect2: ld returned 1 exit status
> [rkunnawa at lxplus017 ANALYSIS]$
>
> Any ideas?
>
> Cheers
> Raghav Kunnawalkam Elayavalli
> PhD Candiate
> Rutgers University
> http://physics.rutgers.edu/~raghav/
> <http://www.google.com/url?q=http%3A%2F%2Fphysics.rutgers.edu%2F~raghav%2F&sa=D&sntz=1&usg=AFQjCNENvwedEL22DMATPxyb0WMvVEm9Bw>
>
>> On Aug 3, 2016, at 11:23 AM, Andy Buckley <a.g.buckley at gmail.com
>> <mailto:a.g.buckley at gmail.com>> wrote:
>>
>> Hi Raghav,
>>
>> This is very strange. I just tried the 2.5.0 version of
>> rivet-bootstrap-lcg and it worked fine, giving me a functioning setup.
>> At least it could list analyses without segfaulting.
>>
>> It's possible that I've got something set by default in my shell
>> environment that helps me, but by default on lxplus I get the same gcc
>> 4.4 and Python 2.6 as you do. Maybe someone else could try to
>> reproduce your problem.
>>
>> I've just updated the LCG bootstrap script to use LCG_85, a newer GCC
>> and FastJet, etc. This also works for me. Maybe you'd have more luck
>> with that?
>>
>> To use the normal bootstrap on lxplus and other SL6 systems with an
>> old system compiler you need to set up your environment to use a newer
>> compiler and a version of Python compiled with the same. The LCG
>> bootstrap does this automatically and puts the relevant lines into the
>> env.sh script. From my updated LCG_85 build, the relevant lines are these:
>>
>> source
>> /cvmfs/sft.cern.ch/lcg/releases/LCG_85/gcc/4.9.3/x86_64-slc6/setup.sh
>> <http://sft.cern.ch/lcg/releases/LCG_85/gcc/4.9.3/x86_64-slc6/setup.sh>
>> source
>> /cvmfs/sft.cern.ch/lcg/releases/LCG_85/Python/2.7.10/x86_64-slc6-gcc49-opt/Python-env.sh
>> <http://sft.cern.ch/lcg/releases/LCG_85/Python/2.7.10/x86_64-slc6-gcc49-opt/Python-env.sh>
>>
>> There are other, fancier ways to do it, but hopefully this will help.
>> It's definitely a good idea to use a newer release than 2.4.1 -- at
>> least 2.4.3, please! We will soon be releasing 2.5.1.
>>
>> Andy
>>
>>
>>
>> On 02/08/16 16:23, Raghav Kunnawalkam Elayavalli wrote:
>>> Hi Rivet Experts,
>>>
>>> I tried a fresh install of the rivet-bootstrap-lcg out of the box in an
>>> lxplus machine and after i did
>>> $ ./rivet-bootstrap-lcg
>>> [rkunnawa at lxplus016 RIVET]$ source
>>> /afs/cern.ch/work/r/rkunnawa/RIVET/local/env.sh
>>> <http://cern.ch/work/r/rkunnawa/RIVET/local/env.sh>
>>> <http://cern.ch/work/r/rkunnawa/RIVET/local/env.sh>
>>> [rkunnawa at lxplus016 RIVET]$ which rivet
>>> /afs/cern.ch/work/r/rkunnawa/RIVET/local/bin/rivet
>>> <http://cern.ch/work/r/rkunnawa/RIVET/local/bin/rivet>
>>> <http://cern.ch/work/r/rkunnawa/RIVET/local/bin/rivet>
>>> [rkunnawa at lxplus016 RIVET]$ which python
>>> /cvmfs/sft.cern.ch/lcg/releases/LCG_82/Python/2.7.10/x86_64-slc6-gcc48-opt/bin/python
>>> <http://sft.cern.ch/lcg/releases/LCG_82/Python/2.7.10/x86_64-slc6-gcc48-opt/bin/python>
>>> <http://sft.cern.ch/lcg/releases/LCG_82/Python/2.7.10/x86_64-slc6-gcc48-opt/bin/python>
>>> [rkunnawa at lxplus016 RIVET]$ echo $PYTHONPATH
>>> /afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/cvmfs/sft.cern.ch/lcg/releases/LCG_82/Python/2.7.10/x86_64-slc6-gcc48-opt/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/cvmfs/sft.cern.ch/lcg/releases/LCG_85/Python/2.7.10/x86_64-slc6-gcc49-opt/lib/python2.7/site-packages:
>>> <http://cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/cvmfs/sft.cern.ch/lcg/releases/LCG_82/Python/2.7.10/x86_64-slc6-gcc48-opt/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/cvmfs/sft.cern.ch/lcg/releases/LCG_85/Python/2.7.10/x86_64-slc6-gcc49-opt/lib/python2.7/site-packages:>
>>> <http://cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/cvmfs/sft.cern.ch/lcg/releases/LCG_82/Python/2.7.10/x86_64-slc6-gcc48-opt/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/afs/cern.ch/work/r/rkunnawa/RIVET/local/lib/python2.7/site-packages:/cvmfs/sft.cern.ch/lcg/releases/LCG_85/Python/2.7.10/x86_64-slc6-gcc49-opt/lib/python2.7/site-packages:>
>>> [rkunnawa at lxplus016 RIVET]$ rivet --list-analyses
>>> Segmentation fault
>>> [rkunnawa at lxplus016 RIVET]$
>>>
>>> I tried this with LCG_82 and LCG_85 (with appropriately changing the
>>> other locations) and i get the same issues. any ideas whats happening?
>>>
>>> I also tried to install rivet with the normal bootstrap and i got an
>>> issue with yoda installation since the default gcc in lxplus is 4.4 and
>>> it doesnt support C++11. so any ideas how i can over come that issue? I
>>> would really like to use something like the herwig bootstrap which
>>> installs all the necessary items.
>>>
>>> In the meanwhile should i try to install an older version of rivet? one
>>> that doesnt need c++11?
>>> Again, the whole reason why im using this is so that i can run my rivet
>>> analysis on the lxplus batch system since at the moment (my earlier lcg
>>> installation) doesnt work and gives me weird python errors which even
>>> the cern service desk is having a hard time with.
>>>
>>> Cheers
>>> Raghav Kunnawalkam Elayavalli
>>> PhD Candiate
>>> Rutgers University
>>> http://physics.rutgers.edu/~raghav/
>>> <http://www.google.com/url?q=http%3A%2F%2Fphysics.rutgers.edu%2F~raghav%2F&sa=D&sntz=1&usg=AFQjCNENvwedEL22DMATPxyb0WMvVEm9Bw>
>>>
>>>
>>>
>>> _______________________________________________
>>> Rivet mailing list
>>> Rivet at projects.hepforge.org <mailto:Rivet at projects.hepforge.org>
>>> https://www.hepforge.org/lists/listinfo/rivet
>>>
>>
>>
>> --
>> Dr Andy Buckley, Lecturer / Royal Society University Research Fellow
>> Particle Physics Expt Group, University of Glasgow
>


-- 
Dr Andy Buckley, Lecturer / Royal Society University Research Fellow
Particle Physics Expt Group, University of Glasgow