[Bigjob-users] bigjob on teragrid/xsede

[Andre Luckow]

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
>> >>> >
>> >>> >
>> >>
>> >>
>> >
>
>