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

Raghav Kunnawalkam Elayavalli raghav.k.e at cern.ch
Wed Aug 3 12:42:59 BST 2016
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OK so when i removed that analysis path, the bootstrap-lcg works fine :) thanks!

now im trying to test it in the lxbatch system but something seems a miss, but i think i can follow that up with the batch people.

Im having a secondary issue this time around when i link to the fjcontrib location in the similar cvmfs directory. I my LD_LIBRARY_PATH pointing to that location so when build my analysis with that
/usr/bin/ld: /cvmfs/sft.cern.ch/lcg/releases/LCG_85/fjcontrib/1.022/x86_64-slc6-gcc49-opt/lib/libRecursiveTools.a<http://sft.cern.ch/lcg/releases/LCG_85/fjcontrib/1.022/x86_64-slc6-gcc49-opt/lib/libRecursiveTools.a>(RecursiveSymmetryCutBase.o): relocation R_X86_64_32S against `_ZTVSt9basic_iosIcSt11char_traitsIcEE' can not be used when making a shared object; recompile with -fPIC
/cvmfs/sft.cern.ch/lcg/releases/LCG_85/fjcontrib/1.022/x86_64-slc6-gcc49-opt/lib/libRecursiveTools.a:<http://sft.cern.ch/lcg/releases/LCG_85/fjcontrib/1.022/x86_64-slc6-gcc49-opt/lib/libRecursiveTools.a:> could not read symbols: Bad value
collect2: error: ld returned 1 exit status

I guess this is an error during the installation of fastjet itself or maybe rivet is not compiling with -fPIC (which i have no idea what it means) so this issue is totally out of my league. I have asked the fastjet authors as well but no response yet. Was just checking if anyone has any ideas.

Cheers
Raghav

On Aug 3, 2016, at 12:15 PM, Andy Buckley <a.g.buckley at gmail.com<mailto:a.g.buckley at gmail.com>> wrote:

What happens if you unset/don't set RIVET_ANALYSIS_PATH for now? If you've upgraded Rivet to a binary-incompatible version but not recompiled your private analyses, you could get segfaults.

In general an upgrade will require rebuilding private analyses -- we're not sophisticated enough to protect binary compatibility, do library-level version detection, etc. -- we'd need a lot more people to get that far down the priority list!

Andy


On 03/08/16 11:10, Raghav Kunnawalkam Elayavalli wrote:
Andy,
Ok something is very fishy here. this is my .bashrc

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# source scripts to run cmssw commands and eos directories
source /afs/cern.ch/cms/sw/cmsset_default.sh<http://cern.ch/cms/sw/cmsset_default.sh>
<http://cern.ch/cms/sw/cmsset_default.sh>
# the above doesnt do anything since it doesnt exist.
source /afs/cern.ch/project/eos/installation/user/etc/setup.sh<http://cern.ch/project/eos/installation/user/etc/setup.sh>
<http://cern.ch/project/eos/installation/user/etc/setup.sh>
#export EOS_MGM_URL=root://eos.cern.ch
export EOS_MGM_URL=root://eosuser.cern.ch
eosmount $HOME/eos

export
PATH=/afs/cern.ch/work/r/rkunnawa/JEWEL/jewel-2.1.0/local/bin:$PATH<http://cern.ch/work/r/rkunnawa/JEWEL/jewel-2.1.0/local/bin:$PATH>
<http://cern.ch/work/r/rkunnawa/JEWEL/jewel-2.1.0/local/bin:$PATH>
export
LD_LIBRARY_PATH=/afs/cern.ch/work/r/rkunnawa/JEWEL/jewel-2.1.0/local/lib:$LD_LIBRARY_PATH<http://cern.ch/work/r/rkunnawa/JEWEL/jewel-2.1.0/local/lib:$LD_LIBRARY_PATH>
<http://cern.ch/work/r/rkunnawa/JEWEL/jewel-2.1.0/local/lib:$LD_LIBRARY_PATH>

export
RIVET_ANALYSIS_PATH=/afs/cern.ch/work/r/rkunnawa/JEWEL/ANALYSIS/:$RIVET_ANALYSIS_PATH<http://cern.ch/work/r/rkunnawa/JEWEL/ANALYSIS/:$RIVET_ANALYSIS_PATH>
<http://cern.ch/work/r/rkunnawa/JEWEL/ANALYSIS/:$RIVET_ANALYSIS_PATH>
export
RIVET_ANALYSIS_PATH=/afs/cern.ch/work/r/rkunnawa/JEWEL/ANALYSIS/Validation/:$RIVET_ANALYSIS_PATH<http://cern.ch/work/r/rkunnawa/JEWEL/ANALYSIS/Validation/:$RIVET_ANALYSIS_PATH>
<http://cern.ch/work/r/rkunnawa/JEWEL/ANALYSIS/Validation/:$RIVET_ANALYSIS_PATH>
export
RIVET_ANALYSIS_PATH=/afs/cern.ch/work/r/rkunnawa/JEWEL/code:$RIVET_ANALYSIS_PATH<http://cern.ch/work/r/rkunnawa/JEWEL/code:$RIVET_ANALYSIS_PATH>
<http://cern.ch/work/r/rkunnawa/JEWEL/code:$RIVET_ANALYSIS_PATH>

and on top of this i just run the latest bootstrap_lcg and im still
getting the seg fault. I tested in a new lxplus machine with no python
path setup etc...

Holger,
hmm i did the diff, but i dont see anything obviously different. maybe
im not looking at the right lines.

Cheers
Raghav
On Aug 3, 2016, at 11:55 AM, Holger Schulz <holger.schulz at durham.ac.uk<mailto:holger.schulz at durham.ac.uk>
<mailto:holger.schulz at durham.ac.uk>> wrote:

Weird.

For me it works. I dumped my environment (after he source commands) here:

https://users.hepforge.org/~holsch/Temp/env.dump

Could you please run a diff against your env?

Holger


On 03/08/16 10:34, Raghav Kunnawalkam Elayavalli wrote:
just to make clear, i didnt have any PYTHONPATH set before i did this
and the only other LD_LIBRARY_PATH was pointing to my MC generator
path.

Cheers
Raghav
On Aug 3, 2016, at 11:32 AM, Raghav Kunnawalkam Elayavalli
<raghav.k.e at cern.ch <mailto:raghav.k.e at cern.ch>> wrote:

Hi Holger,

I also tried this morning with the same seg fault

kunnawa:~ raghav$ cern
Password:
Last login: Tue Jun 21 08:56:17 2016 from kunnawa.dyndns.cern.ch
<http://kunnawa.dyndns.cern.ch/>
* ********************************************************************
* Welcome to lxplus105.cern.ch <http://lxplus105.cern.ch/>, SLC, 6.8
* Archive of news is available in /etc/motd-archive
* Reminder: You have agreed to comply with the CERN computing rules
* https://cern.ch/ComputingRules
* Puppet environment: production, Roger state: production
* Foreman hostgroup: bi/inter/plus/login
* LXPLUS Public Login Service
* ********************************************************************
-bash: /afs/cern.ch/cms/sw/cmsset_default.sh:
<http://cern.ch/cms/sw/cmsset_default.sh:> No such file or directory
OK
===> Mountpoint   : /afs/cern.ch/user/r/rkunnawa/eos
<http://cern.ch/user/r/rkunnawa/eos>
===> Fuse-Options :
kernel_cache,attr_timeout=30,entry_timeout=30,max_readahead=131072,max_write=4194304,fsname=eosuser.cern.ch
<http://eosuser.cern.ch/> root://eosuser.cern.ch//eos/
===> xrootd ra             : 131072
===> xrootd cache          : 393216
===> fuse debug            : 0
===> fuse write-cache      : 1
===> fuse write-cache-size : 100000000
[rkunnawa at lxplus105 ~]$ work
[rkunnawa at lxplus105 rkunnawa]$ mkdir RIVET_test
[rkunnawa at lxplus105 rkunnawa]$ cd RIVET_test/
[rkunnawa at lxplus105 RIVET_test]$ ls
[rkunnawa at lxplus105 RIVET_test]$ source
/afs/cern.ch/sw/lcg/releases/LCG_84/Python/2.7.10/x86_64-slc6-gcc48-opt/Python-env.sh
<http://cern.ch/sw/lcg/releases/LCG_84/Python/2.7.10/x86_64-slc6-gcc48-opt/Python-env.sh>
[rkunnawa at lxplus105 RIVET_test]$ source
/afs/cern.ch/sw/lcg/releases/LCG_84/MCGenerators/rivet/2.5.0/x86_64-slc6-gcc48-opt/rivetenv.sh
<http://cern.ch/sw/lcg/releases/LCG_84/MCGenerators/rivet/2.5.0/x86_64-slc6-gcc48-opt/rivetenv.sh>
[rkunnawa at lxplus105 RIVET_test]$ which rivet
/afs/cern.ch/sw/lcg/releases/MCGenerators/rivet/2.5.0-1aa46/x86_64-slc6-gcc48-opt/bin/rivet
<http://cern.ch/sw/lcg/releases/MCGenerators/rivet/2.5.0-1aa46/x86_64-slc6-gcc48-opt/bin/rivet>
[rkunnawa at lxplus105 RIVET_test]$ rivet --list-analyses
Segmentation fault

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%7Eraghav%2F&sa=D&sntz=1&usg=AFQjCNENvwedEL22DMATPxyb0WMvVEm9Bw>

On Aug 3, 2016, at 11:30 AM, Holger Schulz
<holger.schulz at durham.ac.uk <mailto:holger.schulz at durham.ac.uk>> wrote:

Hi Raghav,

we recently held a Rivet tutorial at CERN using prebuilt rivet2.5
from LCG:

source
/afs/cern.ch/sw/lcg/releases/LCG_84/Python/2.7.10/x86_64-slc6-gcc48-opt/Python-env.sh
<http://cern.ch/sw/lcg/releases/LCG_84/Python/2.7.10/x86_64-slc6-gcc48-opt/Python-env.sh>
source
/afs/cern.ch/sw/lcg/releases/LCG_84/MCGenerators/rivet/2.5.0/x86_64-slc6-gcc48-opt/rivetenv.sh
<http://cern.ch/sw/lcg/releases/LCG_84/MCGenerators/rivet/2.5.0/x86_64-slc6-gcc48-opt/rivetenv.sh>

That worked fine for people from CMS, ATLAS and ALICE. There were a
couple of people who had
to pruge their bashrc becaus of conflicting PYTHONPATH,
LD_LIBRARY_PATH things that
typically had to do with experiment specific setups of python.

Why don't you give that a try first?

Thanks,
Holger


On 03/08/16 10:23, Andy Buckley 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://physics.rutgers.edu/%7Eraghav/>
<http://www.google.com/url?q=http%3A%2F%2Fphysics.rutgers.edu%2F~raghav%2F&sa=D&sntz=1&usg=AFQjCNENvwedEL22DMATPxyb0WMvVEm9Bw
<http://www.google.com/url?q=http%3A%2F%2Fphysics.rutgers.edu%2F%7Eraghav%2F&sa=D&sntz=1&usg=AFQjCNENvwedEL22DMATPxyb0WMvVEm9Bw>>




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