Hi Jason,
I managed to install Amber12Tools on my Ubuntu 11.1 machine
Here's what I did:
1. logged in as a superuser
2. Used a version of Python stored on a local folder instead of the root directory
I'm not sure if 1 or 2 did the trick, but I'm not complaining :-)
Anyway, thanks for your help.
Adam
ps. It could be that the previous Python versions had problems relating to 32/64 bit architecture or single/double precision compatibility with Openmm/fftw. But this is highly speculative.
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Adam Jion <adamjion.yahoo.com>
Cc: AMBER Mailing List <amber.ambermd.org>
Sent: Friday, June 8, 2012 10:16 AM
Subject: Re: [AMBER] Problems installing AmberTools12 on Ubuntu
These are strange errors that I have not seen before... What version of Ubuntu are you using exactly? Perhaps someone can see if they see this issue, too.
On Thu, Jun 7, 2012 at 9:41 PM, Adam Jion <adamjion.yahoo.com> wrote:
Ok, attached is the build.log
>And here's what I see on my terminal:
>
>
>Thanks,
>Adam
>
>
>ps. Here's what I see on my terminal:
>adam.adam-MS-7750:~/amber12$ make install 2>&1 > build.log
>vardata.c: In function ‘pr_bvals’:
>vardata.c:491: warning: format not a string literal and no format arguments
>vardata.c:501: warning: format not a string literal and no format arguments
>vardata.c: In function ‘pr_svals’:
>vardata.c:539: warning: format not a string literal and no format arguments
>vardata.c:549: warning: format not a string literal and no format arguments
>vardata.c: In function ‘pr_ivals’:
>vardata.c:589: warning:
format not a string literal and no format arguments
>vardata.c:599: warning: format not a string literal and no format arguments
>vardata.c: In function ‘pr_fvals’:
>vardata.c:637: warning: format not a string literal and no format arguments
>vardata.c:647: warning: format not a string literal and no format arguments
>vardata.c: In function ‘pr_dvals’:
>vardata.c:685: warning: format not a string literal and no format arguments
>vardata.c:695: warning: format not a string literal and no format arguments
>This is not dpkg install-info anymore, but GNU install-info
>See the man page for ginstall-info for command line arguments
>rm: cannot remove `.libs/libDiagnostics.a': Permission denied
>rm: cannot remove `.libs/libDiagnostics.la': Permission denied
>rm: cannot remove `.libs/libDiagnostics.lai': Permission denied
>ar: could not create temporary file whilst writing archive: No more archived files
>make[5]: ***
[libDiagnostics.la] Error 1
>make[4]: *** [all-recursive] Error 1
>make[3]: *** [all-recursive] Error 1
>make[2]: *** [all] Error 2
>make[1]: *** [install_mtkpp] Error 2
>
>make: *** [install] Error 2
>adam.adam-MS-7750:~/amber12$
>
>
>
>
>
>________________________________
> From: Jason Swails <jason.swails.gmail.com>
>To: Adam Jion <adamjion.yahoo.com>
>Cc: AMBER Mailing List <amber.ambermd.org>
>Sent: Friday, June 8, 2012 9:31 AM
>
>Subject: Re: [AMBER] Problems installing AmberTools12 on Ubuntu
>
>
>
>It would help to see the entire build log, since I can't tell what happened beforehand. Try running it like this:
>
>
>cd $AMBERHOME
>make clean uninstall
>./configure gnu
>make install 2>&1 > build.log
>
>
>Then, attach the build.log.
>
>
>Thanks!
>Jason
>
>
>
>On Thu, Jun 7, 2012 at 9:22 PM, Adam Jion <adamjion.yahoo.com> wrote:
>
>Hi Jason,
>>
>>
>>Yes, I have Python in the directories:
>>/usr/local/bin/python2.7
>>and
>>/usr/bin/python
>>
>>
>>I configured without problem using:
>>./configure --with-python /usr/bin/python gnu
>>
>>
>>But when I ran:
>>make install
>>I got the following error message:
>>./py_setup.sh /home/adam/amber12/bin /usr/bin/python
>>
>>Error importing cpinutil.py python modules! cpinutil will not work.
>>make[2]: *** [python] Error 1
>>make[2]: Leaving directory `/home/adam/amber12/AmberTools/src/etc'
>>make[1]: *** [serial] Error 2
>>make[1]: Leaving directory `/home/adam/amber12/AmberTools/src'
>>make: *** [install] Error
2
>>
>>
>>Regards,
>>Adam
>>
>>
>>
>>________________________________
>> From: Jason Swails <jason.swails.gmail.com>
>>To: Adam Jion <adamjion.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
>>Sent: Thursday, June 7, 2012 10:40 PM
>>Subject: Re: [AMBER] Problems installing AmberTools12 on Ubuntu
>>
>>
>>Is there a /usr/local/bin/python2.7?
>>
>>Is there a /usr/bin/python?
>>
>>If so, then use the configure command:
>>
>>./configure --with-python /usr/bin/python gnu
>>
>>HTH,
>>Jason
>>
>>On Thu, Jun 7, 2012 at 4:47 AM, Adam Jion <adamjion.yahoo.com> wrote:
>>
>>> Hi,
>>>
>>> I'm having problems installing AmberTools12 on my Ubuntu machine.
>>> Most likely is due to an incorrect path to Python.
>>> Can anyone tell me which version of Python I should use, and into which
>>> the directory I should install Python for AmberTools12 to work out of the
>>> box?
>>>
>>> Regards,
>>> Adam
>>>
>>> ps. The error log is given below:
>>> ./py_setup.sh /home/adam/amber12/bin /usr/local/bin/python2.7
>>> Error importing cpinutil.py python modules! cpinutil will not work.
>>> make[2]: *** [python] Error 1
>>> make[2]: Leaving directory `/home/adam/amber12/AmberTools/src/etc'
>>> make[1]: *** [serial] Error 2
>>> make[1]: Leaving directory `/home/adam/amber12/AmberTools/src'
>>> make: *** [install] Error 2
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>>--
>>Jason M. Swails
>>Quantum Theory Project,
>>University of Florida
>>Ph.D. Candidate
>>352-392-4032
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>
>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
>
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 07 2012 - 20:00:05 PDT
