Hello Will,
The second command returns the container.hpp inside the directory of the torque source
which i used to install it:
find / -name container.hpp
/home/user/torque-5.1.1.2-1_18e4a5f1/src/include/container.hpp
I noticed there is also a log.h file there.
the first command doesn't return anything (I've search manually too, nothing
inside /usr/local/include/).
How do I fix this? Shall I change the export command of PBS_PYTHON_INCLUDEDIR?
Thank you,
Makis
Date: Thu, 24 Sep 2015 08:31:07 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: wholtz(a)lygos.com
To: makis4ever(a)hotmail.com
CC: galaxy-dev(a)lists.galaxyproject.org
And does find /usr/local/include -name container.hppor find / -name container.hppreturn
torque/src/include/container.hpp ?
My guess is you installed binaries for Torque, but the scrambling requires the Torque
source (or at least the header files form Torque).
-Will
On Thu, Sep 24, 2015 at 1:16 AM, Makis Ladoukakis <makis4ever(a)hotmail.com> wrote:
Hello Will,
Thanks again for your reply. Yes I had already tried these but I got the same
container.hpp error.
The only thing different in my case is that the names of the directories of the
directories are a bit different:
export PBS_PYTHON_INCLUDEDIR=/usr/local/include/
export PBSCONFIG=/usr/local/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/lib/libtorque.so
python scripts/scramble.py -e pbs_python
Any ideas?
Kind regards,
Makis
Date: Wed, 23 Sep 2015 07:06:32 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: wholtz(a)lygos.com
To: makis4ever(a)hotmail.com
CC: galaxy-dev(a)lists.galaxyproject.org
Hi Makis,
The thread I posted does have the exact same container.hpp error and proposes a solution.
Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include directory,
as mentioned in that thread?
from the thread:export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/
export PBSCONFIG=/usr/local/torque/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so
-Will
On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4ever(a)hotmail.com> wrote:
Hello Will,
Thank you for your reply. I had already checked this thread before as I browsed through
the mailing list for "pbs_python" issues. It doesn't have the same errors
(can't locate log.h and when i provide it it wants the container.hpp ) and up to one
point i've already followed the "rescrambling" of the pbs_python.
Anyone else had any experience with that?
Thank you,
Makis
Date: Tue, 22 Sep 2015 09:35:11 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: wholtz(a)lygos.com
To: makis4ever(a)hotmail.com
CC: galaxy-dev(a)lists.galaxyproject.org
Here is an old thread that looks rather similar to your
problems:https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/...
-Will
On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever(a)hotmail.com> wrote:
Hello everyone,
I'm trying to set up a Galaxy instance on a multi-core server in my university so
according to the instructions here:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python
and tried to setup pbs_python via scramble:
LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
When I did that I got the error:
Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via
PBS_PYTHON_INCLUDEDIR variable)
Traceback (most recent call last):
File "scripts/scramble.py", line 50, in <module>
egg.scramble()
File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble
self.run_scramble_script()
File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in
run_scramble_script
raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % (
sys._getframe().f_code.co_name, self.name, self.version ) )
galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for
pbs_python 4.4.0
so I did some digging around and found that the file I need is in
/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
(please correct me if I am wrong)
So I tried again using:
PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
but then I got the error:
In file included from src/C++/pbs_ifl.h:90:0,
from src/C++/pbs_wrap.cxx:2978:
/usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or
directory
#include "container.hpp"
Can someone help me please?
Kind regards,
Makis
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