Re: [galaxy-dev] Using pbs-python with glibc version 2.12

2016-11-18 Thread Nate Coraor 
Hi David,

It looks like this is an issue with pbs_python and Torque 4.x. There's a
workaround available:

https://oss.trac.surfsara.nl/pbs_python/ticket/40

--nate

On Fri, Nov 18, 2016 at 6:06 AM, David Lee  wrote:

> Hi Nate,
>
> Thanks for your help. I now get the following error message:
>
>
> (.venv)[galaxy@newblue3 ~]$ python
> Python 2.7.5 (default, Oct 16 2013, 10:52:17)
> [GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import pbs
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/
> python2.7/site-packages/pbs/pbs.py", line 26, in 
> _pbs = swig_import_helper()
>   File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/
> python2.7/site-packages/pbs/pbs.py", line 22, in swig_import_helper
> _mod = imp.load_module('_pbs', fp, pathname, description)
> ImportError: /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/
> python2.7/site-packages/pbs/_pbs.so: undefined symbol: _Z13log_availablei
> >>>
>
>
> David
>
> On 17 November 2016 at 17:13, Nate Coraor  wrote:
>
>> Hi David,
>>
>> It sounds like you may have installed the version of pbs-python currently
>> in PyPI, which includes a copy of the Torque C library that is not
>> "manylinux"-safe (it is not backwards compatible to older systems). The
>> solution here is to install pbs-python from its source distribution:
>>
>> 1. Activate Galaxy's virtualenv: `. /panfs/panasas01/dedicated-
>> galaxy/galaxy/galaxy/.venv/bin/activate`
>> 2. `pip uninstall pbs-python`
>> 3. Download/unpack the source tarball from ftp://ftp.surfsara.nl/pub
>> /outgoing/pbs_python.tar.gz
>> 4. In the pbs_python source: `./configure --prefix=/panfs/panasas01/dedi
>> cated-galaxy/galaxy/galaxy/.venv`
>> 5. `make install`
>>
>> --nate
>>
>> On Thu, Nov 17, 2016 at 11:08 AM, David Lee 
>> wrote:
>>
>>> Hi,
>>>
>>>
>>> I'm trying to install Galaxy version 16.07 on a cluster with the PBS job
>>> scheduler that is using glibc version 2.12. The following error message
>>> suggests that pbs-python needs at least glibc version 2.14 -
>>>
>>>
>>>
>>> assert pbs is not None, PBS_IMPORT_MESSAGE
>>>
>>> AssertionError: The Python pbs-python package is required to use this
>>> feature, please install it or correct the following error:
>>>
>>> ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required
>>> by /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/py
>>> thon2.7/site-packages/pbs/_pbs.so)
>>>
>>>
>>>
>>> I'm told by an administrator of the cluster that updating to glibc
>>> version 2.14 or higher would require a major overhaul of all the software
>>> on the cluster. Does anybody have a workaround for this problem? Could a
>>> newer version of glibc be used next to version 2.12 just for installation
>>> purposes?
>>>
>>>
>>> Thanks for your help, David
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
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>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
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Re: [galaxy-dev] Using pbs-python with glibc version 2.12

2016-11-18 Thread David Lee 
Hi Nate,

Thanks for your help. I now get the following error message:


(.venv)[galaxy@newblue3 ~]$ python
Python 2.7.5 (default, Oct 16 2013, 10:52:17)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pbs
Traceback (most recent call last):
  File "", line 1, in 
  File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/
lib/python2.7/site-packages/pbs/pbs.py", line 26, in 
_pbs = swig_import_helper()
  File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/
lib/python2.7/site-packages/pbs/pbs.py", line 22, in swig_import_helper
_mod = imp.load_module('_pbs', fp, pathname, description)
ImportError: /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/
lib/python2.7/site-packages/pbs/_pbs.so: undefined symbol:
_Z13log_availablei
>>>


David

On 17 November 2016 at 17:13, Nate Coraor  wrote:

> Hi David,
>
> It sounds like you may have installed the version of pbs-python currently
> in PyPI, which includes a copy of the Torque C library that is not
> "manylinux"-safe (it is not backwards compatible to older systems). The
> solution here is to install pbs-python from its source distribution:
>
> 1. Activate Galaxy's virtualenv: `. /panfs/panasas01/dedicated-
> galaxy/galaxy/galaxy/.venv/bin/activate`
> 2. `pip uninstall pbs-python`
> 3. Download/unpack the source tarball from ftp://ftp.surfsara.nl/
> pub/outgoing/pbs_python.tar.gz
> 4. In the pbs_python source: `./configure --prefix=/panfs/panasas01/
> dedicated-galaxy/galaxy/galaxy/.venv`
> 5. `make install`
>
> --nate
>
> On Thu, Nov 17, 2016 at 11:08 AM, David Lee 
> wrote:
>
>> Hi,
>>
>>
>> I'm trying to install Galaxy version 16.07 on a cluster with the PBS job
>> scheduler that is using glibc version 2.12. The following error message
>> suggests that pbs-python needs at least glibc version 2.14 -
>>
>>
>>
>> assert pbs is not None, PBS_IMPORT_MESSAGE
>>
>> AssertionError: The Python pbs-python package is required to use this
>> feature, please install it or correct the following error:
>>
>> ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
>> /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/
>> python2.7/site-packages/pbs/_pbs.so)
>>
>>
>>
>> I'm told by an administrator of the cluster that updating to glibc
>> version 2.14 or higher would require a major overhaul of all the software
>> on the cluster. Does anybody have a workaround for this problem? Could a
>> newer version of glibc be used next to version 2.12 just for installation
>> purposes?
>>
>>
>> Thanks for your help, David
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
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Re: [galaxy-dev] Using pbs-python with glibc version 2.12

2016-11-17 Thread Nate Coraor 
Hi David,

It sounds like you may have installed the version of pbs-python currently
in PyPI, which includes a copy of the Torque C library that is not
"manylinux"-safe (it is not backwards compatible to older systems). The
solution here is to install pbs-python from its source distribution:

1. Activate Galaxy's virtualenv:
`. /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/bin/activate`
2. `pip uninstall pbs-python`
3. Download/unpack the source tarball from
ftp://ftp.surfsara.nl/pub/outgoing/pbs_python.tar.gz
4. In the pbs_python source: `./configure
--prefix=/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv`
5. `make install`

--nate

On Thu, Nov 17, 2016 at 11:08 AM, David Lee  wrote:

> Hi,
>
>
> I'm trying to install Galaxy version 16.07 on a cluster with the PBS job
> scheduler that is using glibc version 2.12. The following error message
> suggests that pbs-python needs at least glibc version 2.14 -
>
>
>
> assert pbs is not None, PBS_IMPORT_MESSAGE
>
> AssertionError: The Python pbs-python package is required to use this
> feature, please install it or correct the following error:
>
> ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
> /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/
> lib/python2.7/site-packages/pbs/_pbs.so)
>
>
>
> I'm told by an administrator of the cluster that updating to glibc version
> 2.14 or higher would require a major overhaul of all the software on the
> cluster. Does anybody have a workaround for this problem? Could a newer
> version of glibc be used next to version 2.12 just for installation
> purposes?
>
>
> Thanks for your help, David
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___
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[galaxy-dev] Using pbs-python with glibc version 2.12

2016-11-17 Thread David Lee 
Hi,


I'm trying to install Galaxy version 16.07 on a cluster with the PBS job
scheduler that is using glibc version 2.12. The following error message
suggests that pbs-python needs at least glibc version 2.14 -



assert pbs is not None, PBS_IMPORT_MESSAGE

AssertionError: The Python pbs-python package is required to use this
feature, please install it or correct the following error:

ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/python2.7/site-packages/pbs/_pbs.so)



I'm told by an administrator of the cluster that updating to glibc version
2.14 or higher would require a major overhaul of all the software on the
cluster. Does anybody have a workaround for this problem? Could a newer
version of glibc be used next to version 2.12 just for installation
purposes?


Thanks for your help, David
___
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