[Bigjob-users] bigjob on teragrid/xsede

Wed Jan 4 15:42:13 CST 2012

Andre M, your thoughts?

This was working late nov for me. What happened?

Regards
Yaakoub El Khamra

On Wed, Jan 4, 2012 at 3:38 PM, Andre Luckow <aluckow at cct.lsu.edu> wrote:

> Hi Yaakoub,
> we have SAGA and Python in CSA space that works fine with BJ:
>
>
> https://svn.cct.lsu.edu/repos/saga-projects/deployment/tg-csa/doc/README.saga-1.6.gcc-4.4.5.ranger
>
> Unfortunately, it's broken :-( - will open a ticket:
>
> tg804093 at login3 ~$ python
> Python 2.7.1 (r271:86832, Nov 25 2011, 04:51:00)
> [GCC 4.4.5] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import saga
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>  File
> "/scratch/projects/tg/SAGA/saga/1.6/gcc-4.4.5/lib/python2.7/site-packages/saga/__init__.py",
> line 28, in <module>
>    from _engine import *         # import all classes from SAGA.engine
> ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
> found (required by
>
> /scratch/projects/tg/SAGA/saga/1.6/gcc-4.4.5/lib/libsaga_package_advert.so.1.6)
>
> Best,
> Andre
>
> On Wed, Jan 4, 2012 at 10:28 PM, Yaakoub El Khamra <yelkhamra at gmail.com>
> wrote:
> >
> > python bigjob-bootstrap.py $WORK/ECSS/bigjob_install
> >
> >      Traceback (most recent call last):
> >   File "bigjob-bootstrap.py", line 23, in ?
> >     import subprocess
> > ImportError: No module named subprocess
> >
> > SAGA on ranger was compiled with python 2.3.4, the system python. Andre
> M,
> > j'accuse!
> >
> > You have to load the python module to get bigjob. This can be better
> > coordinated IMHO.
> >
> > Regards
> > Yaakoub El Khamra
> >
> >
> >
> >
> > On Wed, Jan 4, 2012 at 3:22 PM, Andre Luckow <aluckow at cct.lsu.edu>
> wrote:
> >>
> >> Hi Yaakoub,
> >> the bootstrap script in variant c) installs virtualenv automatically
> >> for the user. Option d) should work. We just migrated to Github
> >> yesterday - so there might be some issues. Not sure why your git
> >> version doesn't accept the Github certificate. But, you can also clone
> >> the repository via HTTP.
> >>
> >> git clone http://github.com/drelu/BigJob.git
> >>
> >> or the native git protocol
> >>
> >> git clone git://github.com/drelu/BigJob.git
> >>
> >> Or alternatively, the good old SVN.
> >>
> >> I think we have many options to install BJ (maybe to many for a normal
> >> user). I personally prefer the virtualenv alternative since this is a
> >> clean way to manage all your Python libraries in user space.
> >>
> >> Best,
> >> Andre
> >>
> >>
> >> On Wed, Jan 4, 2012 at 10:02 PM, Yaakoub El Khamra <yelkhamra at gmail.com
> >
> >> wrote:
> >> >
> >> > Also can I point out something I should have pointed out a while ago:
> >> > users have to install virtualenv on almost all supercomputers. At
> least
> >> > the
> >> > top 5 on XSEDE, all the ones we have allocations on.
> >> >
> >> > This means, users have to install virtualenv to install bigjob. That's
> >> > not
> >> > practical. d) is what most users will want to use since they already
> >> > have to
> >> > add to the pythonpath from the saga installation.
> >> >
> >> > Regards
> >> > Yaakoub El Khamra
> >> >
> >> >
> >> >
> >> >
> >> > On Wed, Jan 4, 2012 at 2:39 PM, Yaakoub El Khamra <
> yelkhamra at gmail.com>
> >> > wrote:
> >> >>
> >> >> Cloning into BigJob...
> >> >> error: SSL certificate problem, verify that the CA cert is OK.
> Details:
> >> >> error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate
> >> >> verify
> >> >> failed while accessing https://github.com/drelu/BigJob.git/info/refs
> >> >>
> >> >> fatal: HTTP request failed
> >> >>
> >> >> Regards
> >> >> Yaakoub El Khamra
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> On Wed, Jan 4, 2012 at 2:33 PM, Andre Luckow <aluckow at cct.lsu.edu>
> >> >> wrote:
> >> >>>
> >> >>> Hi Yaakoub,
> >> >>> with what error does d) fail for you?
> >> >>>
> >> >>> Best,
> >> >>> Andre
> >> >>>
> >> >>> On Wed, Jan 4, 2012 at 9:18 PM, Yaakoub El Khamra
> >> >>> <yelkhamra at gmail.com>
> >> >>> wrote:
> >> >>> >
> >> >>> > FYI d installation method fails. Sorry I should have told you guys
> >> >>> > about
> >> >>> > this a very long time ago when I first discovered it.
> >> >>> >
> >> >>> > Regards
> >> >>> > Yaakoub El Khamra
> >> >>> >
> >> >>> >
> >> >>> >
> >> >>> >
> >> >>> > On Wed, Jan 4, 2012 at 3:03 AM, Andre Luckow <aluckow at cct.lsu.edu
> >
> >> >>> > wrote:
> >> >>> >>
> >> >>> >> Hi Melissa,
> >> >>> >> the recommended way is to install BJ in user space. The CSA BJ
> >> >>> >> version
> >> >>> >> is a bit outdated and is already known to have a couple of bugs:
> >> >>> >>
> >> >>> >> http://faust.cct.lsu.edu/trac/bigjob/wiki/install
> >> >>> >>
> >> >>> >> Installation type b or c should be the best for you.
> >> >>> >>
> >> >>> >> Once you have setup your virtualenv, you can easily update to a
> new
> >> >>> >> version of BJ with:
> >> >>> >>
> >> >>> >> easy_install -U bigjob
> >> >>> >>
> >> >>> >> Since, I expect that we will discover some bugs on the way to
> >> >>> >> XSEDE,
> >> >>> >> this will be an important feature.
> >> >>> >>
> >> >>> >> Best,
> >> >>> >> Andre
> >> >>> >>
> >> >>> >> On Wed, Jan 4, 2012 at 4:24 AM, Melissa Romanus
> >> >>> >> <melissa.romanus at rutgers.edu> wrote:
> >> >>> >> > Hi all-
> >> >>> >> >
> >> >>> >> > I need to start either compiling information or playing around
> >> >>> >> > with
> >> >>> >> > bigjob
> >> >>> >> > on xsede/teragrid, specifically kraken, ranger, and possibly
> >> >>> >> > lonestar.
> >> >>> >> > Last
> >> >>> >> > semester, I was only working on the futuregrid. What
> >> >>> >> > documentation
> >> >>> >> > currently
> >> >>> >> > exists for getting bj running on the XSEDE machines? Also, I am
> >> >>> >> > sorry I
> >> >>> >> > have
> >> >>> >> > not been super up on email traffic, but what is the general
> >> >>> >> > consensus of
> >> >>> >> > 'how to use bj now' (in other words, install into user space vs
> >> >>> >> > CSA)? I
> >> >>> >> > am
> >> >>> >> > asking because I will soon be working closely with the chemists
> >> >>> >> > and
> >> >>> >> > want
> >> >>> >> > to
> >> >>> >> > have an easy/smooth process for them to follow.
> >> >>> >> >
> >> >>> >> > Thank you,
> >> >>> >> > Melissa
> >> >>> >> >
> >> >>> >> > _______________________________________________
> >> >>> >> > Bigjob-users mailing list
> >> >>> >> > Bigjob-users at mail.cct.lsu.edu
> >> >>> >> > https://mail.cct.lsu.edu/mailman/listinfo/bigjob-users
> >> >>> >> >
> >> >>> >> _______________________________________________
> >> >>> >> Bigjob-users mailing list
> >> >>> >> Bigjob-users at mail.cct.lsu.edu
> >> >>> >> https://mail.cct.lsu.edu/mailman/listinfo/bigjob-users
> >> >>> >
> >> >>> >
> >> >>
> >> >>
> >> >
> >
> >
>
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