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

[Andy Buckley]

Seems to work on lxplus for me. I submitted this script to the test and 
8nm queues on lxbatch, and got the expected output:

---
#! /usr/bin/env bash

. $HOME/tmp/rivetbootstraplcgtest/local/env.sh
rivet --list-analyses
---

Weird. This is with the LCG_85 build from the latest version of the 
2.5.0 bootstrap, by the way.

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