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
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.lee@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
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import pbs Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/
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. lib/python2.7/site-packages/pbs/pbs.py", line 26, in <module> _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 <nate@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.lee@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/
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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 <david.lee@bristol.ac.uk> wrote:
Hi Nate,
Thanks for your help. I now get the following error message:
import pbs Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/
(.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. python2.7/site-packages/pbs/pbs.py", line 26, in <module> _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 <nate@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/dedi cated-galaxy/galaxy/galaxy/.venv` 5. `make install`
--nate
On Thu, Nov 17, 2016 at 11:08 AM, David Lee <david.lee@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/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" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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participants (2)
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David Lee -
Nate Coraor