Hi - I've just finished installing a ROCKS 5.4.3 cluster and am now adding
Galaxy to it.  We are using torque instead of SGE.  I see the Wiki docs at
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster state I need to
scramble pbs_python by doing:

LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python

I have libtorque installed in /usr/lib64:

[galaxy@bic x86_64]$ ll /usr/lib64/libtorque.*
-rw-r--r-- 1 root root 536862 Dec 28 12:32 /usr/lib64/libtorque.a
-rwxr-xr-x 1 root root    810 Dec 28 12:32 /usr/lib64/libtorque.la
lrwxrwxrwx 1 root root     18 Dec 28 13:50 /usr/lib64/libtorque.so ->
libtorque.so.2.0.0
lrwxrwxrwx 1 root root     14 Dec 28 13:50 /usr/lib64/libtorque.so.0 ->
libtorque.so.2
lrwxrwxrwx 1 root root     18 Dec 28 13:50 /usr/lib64/libtorque.so.2 ->
libtorque.so.2.0.0
-rwxr-xr-x 1 root root 766431 Dec 28 12:32 /usr/lib64/libtorque.so.2.0.0

So I then run (and get the error shown at the bottom):
[galaxy@bic x86_64]$ cd
[galaxy@bic ~]$ cd galaxy-dist/
[galaxy@bic galaxy-dist]$ LIBTORQUE_DIR=/usr/lib64/libtorque.so.2.0.0
python scripts/scramble.py -e pbs_python
fetch_one(): Trying to fetch:
  http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz
fetch_one(): Fetched to:
  /home/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.1.0.tar.gz
unpack_source(): Unpacked to:

/home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python
copy_build_script(): Using build script
/home/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py
run_scramble_script(): Beginning build
run_scramble_script(): Executing in
/home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python:
  /share/apps/Python-2.6.7/bin/python scramble.py

---------------------------------------------------------------------------
This script requires setuptools version 0.6c11 to run (even to display
help).  I will attempt to download it for you (from
http://pypi.python.org/packages/2.6/s/setuptools/), but
you may need to enable firewall access for this script first.
I will start the download in 8 seconds.

(Note: if this machine does not have network access, please obtain the file


http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg

and place it in this directory before rerunning this script.)
---------------------------------------------------------------------------
Downloading
http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg
checking for pbs-config... /usr/bin/pbs-config
Found torque version: 2.5.9
checking for python... /share/apps/Python-2.6.7/bin/python
checking for python version... 2.6
checking for python platform... linux2
checking for python script directory...
${prefix}/lib/python2.6/site-packages
checking for python extension module directory...
${exec_prefix}/lib/python2.6/site-packages
configure: creating ./config.status
config.status: creating Makefile
config.status: creating setup.py
scramble(): Patching setup.py
running egg_info
creating src/pbs_python.egg-info
writing src/pbs_python.egg-info/PKG-INFO
writing top-level names to src/pbs_python.egg-info/top_level.txt
writing dependency_links to src/pbs_python.egg-info/dependency_links.txt
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
reading manifest file 'src/pbs_python.egg-info/SOURCES.txt'
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.6
copying src/pbs.py -> build/lib.linux-x86_64-2.6
copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6
running build_ext
building '_pbs' extension
creating build/temp.linux-x86_64-2.6
creating build/temp.linux-x86_64-2.6/src
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -DTORQUE_2_4
-I/share/apps/Python-2.6.7/include/python2.6 -c src/pbs_wrap.c -o
build/temp.linux-x86_64-2.6/src/pbs_wrap.o
src/pbs_wrap.c:2622: warning: function declaration isn't a prototype
src/pbs_wrap.c:2630: warning: function declaration isn't a prototype
gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o
-L/usr/lib64 -ltorque -o build/lib.linux-x86_64-2.6/_pbs.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/pbs.py -> build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/PBSQuery.py ->
build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/_pbs.so -> build/bdist.linux-x86_64/egg
byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc
byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc
creating stub loader for _pbs.so
byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/PKG-INFO ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/SOURCES.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/dependency_links.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/top_level.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/pbs_python-4.1.0-py2.6-linux-x86_64.egg' and adding
'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Traceback (most recent call last):
  File "scripts/scramble.py", line 50, in <module>
    egg.scramble()
  File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in
scramble
    raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to
fail, but no egg found to copy from expected path:\n  %s" % (
sys._getframe().f_code.co_name, self.name, new_egg ) )
galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pbs_python
did not appear to fail, but no egg found to copy from expected path:

/home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python/dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs2.egg
[galaxy@bic galaxy-dist]$ cd scripts/scramble
[galaxy@bic scramble]$ ll
total 20
drwxrwxr-x 2 galaxy galaxy 4096 Dec 29 16:21 archives
drwxrwxr-x 3 galaxy galaxy 4096 Dec 29 16:21 build
drwxrwxr-x 2 galaxy galaxy 4096 Dec 29 16:22 lib
drwxrwxr-x 7 galaxy galaxy 4096 Dec 29 13:25 patches
drwxrwxr-x 2 galaxy galaxy 4096 Dec 29 13:25 scripts
[galaxy@bic scramble]$ cd build/
[galaxy@bic build]$ ll
total 4
drwxrwxr-x 3 galaxy galaxy 4096 Dec 29 16:21 py2.6-linux-x86_64-ucs2
[galaxy@bic build]$ cd py2.6-linux-x86_64-ucs2/
[galaxy@bic py2.6-linux-x86_64-ucs2]$ ll
total 4
drwx------ 7 galaxy galaxy 4096 Dec 29 16:22 pbs_python
[galaxy@bic py2.6-linux-x86_64-ucs2]$ cd pbs_python/dist/
[galaxy@bic dist]$ ll
total 180
-rw-rw-r-- 1 galaxy galaxy 178869 Dec 29 16:22
pbs_python-4.1.0-py2.6-linux-x86_64.egg


I see the egg is created, but not with the name expected by galaxy.  How do
I fix this?
___________________________________________________________
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:

  http://lists.bx.psu.edu/

Reply via email to