[galaxy-dev] Using pbs-python with glibc version 2.12
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/
Re: [galaxy-dev] Using pbs-python with glibc version 2.12
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 <n...@bx.psu.edu> 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 <david@bristol.ac.uk>
> 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] Conda problem
Hi Peter,
Thanks for your reply which nudged me in the right direction and the problem
seems to be solved. Although I uninstalled samtools and samba from Galaxy there
were remnants of the packages remaining in
galaxy/database/dependencies/_conda/envs and
galaxy/database/dependencies/_conda/pkgs/. After I deleted these directories
the error messages disappeared and tools are running again.
Cheers, David
From: Peter Cock <p.j.a.c...@googlemail.com>
Sent: 24 May 2018 14:22:40
To: David Lee
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Conda problem
On Thu, May 24, 2018 at 2:14 PM, David Lee <david@bristol.ac.uk> wrote:
> Hi,
>
>
> I hope somebody can help me with this. I've been maintaining a Galaxy
> installation for the past few months that has suddenly developed a problem
> that I can't undo.
Which version of Galaxy? Can you tell what version of conda it is using?
> I think it occurred after installing samtools and sambamba packages
> which I have subsequently uninstalled but which has made no
> difference. Every tool I try to run fails with this error:
>
> "Conda dependency failed to build job environment. This is most likely
> a limitation in conda. You can try to shorten the path to the
> job_working_directory."
>
There are some very long path names used in Conda, perhaps
something has pushed you over an OS limit (like the longest
allowed command line)?
>
> Also, in the paster.log file I'm seeing this error that I've never seen
> before:
>
>
> "CondaError: RuntimeError('EnforceUnusedAdapter called with url
> https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2018.4.16-0.tar.bz2\nThis
> command is using a remote connection in offline mode.\n',)"
>
>
> Any suggestions?
This could be a different issue with similar symptoms, but there
is a known issue in conda 4.3.17, fixed in conda 4.4.0, which looks
related: https://github.com/conda/conda/issues/5443
Peter
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[galaxy-dev] Conda problem
Hi,
I hope somebody can help me with this. I've been maintaining a Galaxy
installation for the past few months that has suddenly developed a problem that
I can't undo. I think it occurred after installing samtools and sambamba
packages which I have subsequently uninstalled but which has made no
difference. Every tool I try to run fails with this error:
"Conda dependency failed to build job environment. This is most likely a
limitation in conda. You can try to shorten the path to the
job_working_directory."
Also, in the paster.log file I'm seeing this error that I've never seen before:
"CondaError: RuntimeError('EnforceUnusedAdapter called with url
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2018.4.16-0.tar.bz2\nThis
command is using a remote connection in offline mode.\n',)"
Any suggestions?
Regards, David
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