So you just keep using that working version.
The error message is a bit misleading here.: mdout_analyzer.py requires
some packages like matplotlib, Tkinter, ...
I guess your default Python (python2.6?) does not have them.
When you load python 2.7.2 from your cluster env, you will use different
python distribution that have required packages so things just work.
thanks for report.
PS: In AmberTools16 (http://ambermd.org/AmberTools16-get.html), we handle
this issue better by
offering to install a light Python distribution (having all needed
packages)for user.
Hai
On Mon, Jan 9, 2017 at 4:29 PM, Chase Zagorec-Marks <chasezgrcmrks.gmail.com
> wrote:
> If I load python 2.7.3 (I haven’t tried it with any other python versions)
> before entering that command it works without a problem, but if I don’t do
> so I get the message:
>
> Traceback (most recent call last):
> File "/uufs/chpc.utah.edu/sys/installdir/amber/amber15/bin/
> mdout_analyzer.py", line 18, in <module>
> (amberhome, amberhome))
> ImportError: Could not import Amber Python modules. Please make sure you
> have sourced /uufs/chpc.utah.edu/sys/installdir/amber/amber15/amber.sh
> (if you are using sh/ksh/bash/zsh) or /uufs/chpc.utah.edu/sys/
> installdir/amber/amber15/amber.csh (if you are using csh/tcsh)
>
> I am unsure of what version of python is kept as the stock OS but I can
> ask if need be.
>
> Chase
>
> > On Jan 9, 2017, at 2:20 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > does below
> >
> > *python $AMBERHOME/bin/mdout_analyzer.py 4LYS.mdout *
> >
> > work for you? If doesn't, what's the error?
> >
> > Hai
> >
> > On Mon, Jan 9, 2017 at 4:13 PM, Chase Zagorec-Marks <
> chasezgrcmrks.gmail.com <mailto:chasezgrcmrks.gmail.com>
> >> wrote:
> >
> >> Hai,
> >>
> >> Here is the the thread:
> >>
> >> I have been trying to use Amber14 and Amber15 mdout_analyzer tool after
> >> loading the amber15, intel, and impi modules using the following
> commands:
> >>
> >> module load intel impi amber/15
> >> mdout_analyzer.py 4LYS.mdout
> >>
> >> When I enter the last line I get the following message:
> >>
> >> Traceback (most recent call last):
> >> File "/uufs/chpc.utah.edu/sys/installdir/amber/amber15/bin/
> >> mdout_analyzer.py", line 18, in <module>
> >> (amberhome, amberhome))
> >> ImportError: Could not import Amber Python modules. Please make sure you
> >> have sourced /uufs/chpc.utah.edu/sys/installdir/amber/amber15/amber.sh
> >> (if you are using sh/ksh/bash/zsh) or /uufs/chpc.utah.edu/sys/
> >> installdir/amber/amber15/amber.csh (if you are using csh/tcsh)
> >>
> >> I am using tcsh, so I tried to follow the source listed above by
> running:
> >> source /uufs/chpc.utah.edu/sys/installdir/amber/amber15/amber.csh
> >>
> >> When I attempted to re-run the mdout_analyzer.py command I received the
> >> same error message that I had received before sourcing. Are there steps
> >> that I am missing to utilize this script from Amber (for instance am I
> not
> >> properly sourcing)? Thank you for your help.
> >> Chase Zagorec-Marks <https://jira.chpc.utah.edu/ <
> https://jira.chpc.utah.edu/>
> >> secure/ViewProfile.jspa?name=u0916868> created issue - Jan/09/2017
> 11:57
> >> AM
> >> <https://jira.chpc.utah.edu/browse/HPC-4483# <
> https://jira.chpc.utah.edu/browse/HPC-4483#>>Permalink <
> >> https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188823&page= <https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188823&page=>
> >> com.atlassian.jira.plugin.system.issuetabpanels:comment-
> >> tabpanel#comment-188823>
> >> Martin Cuma <https://jira.chpc.utah.edu/secure/ViewProfile.jspa?name= <
> https://jira.chpc.utah.edu/secure/ViewProfile.jspa?name=>
> >> u0101881>Martin Cuma added a comment - Jan/09/2017 12:32 PM
> >> Chase,
> >>
> >> what python do you use, e.g. what "which python" returns?
> >>
> >> Thanks,
> >> MC
> >>
> >> --
> >> Martin Cuma
> >> Center for High Performance Computing
> >> Department of Geology and Geophysics
> >> University of Utah
> >>
> >> <https://jira.chpc.utah.edu/browse/HPC-4483# <
> https://jira.chpc.utah.edu/browse/HPC-4483#>>Permalink <
> >> https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188825&page= <https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188825&page=>
> >> com.atlassian.jira.plugin.system.issuetabpanels:comment-
> >> tabpanel#comment-188825>
> >> Wim Rm Cardoen <https://jira.chpc.utah.edu/
> secure/ViewProfile.jspa?name= <https://jira.chpc.utah.edu/
> secure/ViewProfile.jspa?name=>
> >> u0253283>Wim Rm Cardoen added a comment - Jan/09/2017 12:36 PM
> >> You need to use #!/usr/bin/python2.6 (that's what has used to install
> >> amber)
> >> So, if there is any version of python != 2.6 in your environment
> >> you will run into trouble
> >>
> >> Wim
> >> <https://jira.chpc.utah.edu/browse/HPC-4483# <
> https://jira.chpc.utah.edu/browse/HPC-4483#>>Permalink <
> >> https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188826&page= <https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188826&page=>
> >> com.atlassian.jira.plugin.system.issuetabpanels:comment-
> >> tabpanel#comment-188826>
> >> Martin Cuma <https://jira.chpc.utah.edu/secure/ViewProfile.jspa?name= <
> https://jira.chpc.utah.edu/secure/ViewProfile.jspa?name=>
> >> u0101881>Martin Cuma added a comment - Jan/09/2017 12:39 PM
> >> OK, looks like you're using the stock OS python that does not have some
> >> modules needed.
> >>
> >> On kingspeak (or other CentOS6 machines), "module load python/2.7.3" and
> >> then run mdout_analyzer.py as
> >> python /uufs/chpc.utah.edu/sys/installdir/amber/amber15/bin/ <
> http://chpc.utah.edu/sys/installdir/amber/amber15/bin/>
> >> mdout_analyzer.py
> >>
> >> Thanks,
> >> MC
> >>
> >> --
> >> Martin Cuma
> >> Center for High Performance Computing
> >> Department of Geology and Geophysics
> >> University of Utah
> >>
> >> <https://jira.chpc.utah.edu/browse/HPC-4483# <
> https://jira.chpc.utah.edu/browse/HPC-4483#>>Permalink <
> >> https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188828&page= <https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188828&page=>
> >> com.atlassian.jira.plugin.system.issuetabpanels:comment-
> >> tabpanel#comment-188828>
> >> Wim Rm Cardoen <https://jira.chpc.utah.edu/
> secure/ViewProfile.jspa?name= <https://jira.chpc.utah.edu/
> secure/ViewProfile.jspa?name=>
> >> u0253283>Wim Rm Cardoen added a comment - Jan/09/2017 12:44 PM
> >> This is not the way to go.
> >> The following line is hard coded in the python scripts:
> >> #!/usr/bin/python2.6
> >>
> >> You can also use python/2.7.3
> >> iff:
> >> a.the first line contains /usr/bin/env python
> >> AND
> >> b.there are NO .so files present (I don't know if this is the case)
> >>
> >> So, please use your /usr/bin/python
> >>
> >> Wim
> >> <https://jira.chpc.utah.edu/browse/HPC-4483# <
> https://jira.chpc.utah.edu/browse/HPC-4483#>>Permalink <
> >> https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188829&page= <https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188829&page=>
> >> com.atlassian.jira.plugin.system.issuetabpanels:comment-
> >> tabpanel#comment-188829> Edit <https://jira.chpc.utah.edu/ <
> https://jira.chpc.utah.edu/>
> >> secure/EditComment!default.jspa?id=117564&commentId=188829> Delete <
> >> https://jira.chpc.utah.edu/secure/DeleteComment!default <
> https://jira.chpc.utah.edu/secure/DeleteComment!default>.
> >> jspa?id=117564&commentId=188829>
> >> Chase Zagorec-Marks <https://jira.chpc.utah.edu/ <
> https://jira.chpc.utah.edu/>
> >> secure/ViewProfile.jspa?name=u0916868>Chase Zagorec-Marks added a
> comment
> >> - Jan/09/2017 12:45 PM
> >> Thanks, that was the issue. It is running now.
> >>
> >> Chase
> >> <https://jira.chpc.utah.edu/browse/HPC-4483# <
> https://jira.chpc.utah.edu/browse/HPC-4483#>>Permalink <
> >> https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188830&page= <https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188830&page=>
> >> com.atlassian.jira.plugin.system.issuetabpanels:comment-
> >> tabpanel#comment-188830>
> >> Martin Cuma <https://jira.chpc.utah.edu/secure/ViewProfile.jspa?name= <
> https://jira.chpc.utah.edu/secure/ViewProfile.jspa?name=>
> >> u0101881>Martin Cuma added a comment - Jan/09/2017 12:49 PM
> >> Wim,
> >>
> >> the problem with /usr/bin/python is that some of the modules it includes
> >> does not contain functions that the Amber python modules need. Your
> Python
> >> 2.7.3 has them.
> >>
> >> Just look into
> >> /uufs/chpc.utah.edu/sys/installdir/amber/amber15/bin/mdout_analyzer.py
> <http://chpc.utah.edu/sys/installdir/amber/amber15/bin/mdout_analyzer.py>
> and
> >> see the first 10 lines of it. In CentOS6 stock python, this fails:
> >> from mdoutanalyzer.graphproperties import GraphControlWindow
> >>
> >> While in 2.7.3 it does not.
> >>
> >> Loading the python/2.7.3 and then executing the
> >> /uufs/chpc.utah.edu/sys/installdir/amber/amber15/bin/mdout_analyzer.py
> <http://chpc.utah.edu/sys/installdir/amber/amber15/bin/mdout_analyzer.py>
> >> with it will ignore the first line in the script,
> >> #!/usr/bin/python2.6
> >>
> >> and thus executing it with 2.7.3 and making it to work.
> >>
> >> MC
> >>
> >> --
> >> Martin Cuma
> >> Center for High Performance Computing
> >> Department of Geology and Geophysics
> >> University of Utah
> >>
> >> <https://jira.chpc.utah.edu/browse/HPC-4483# <
> https://jira.chpc.utah.edu/browse/HPC-4483#>>Permalink <
> >> https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188831&page= <https://jira.chpc.utah.edu/browse/HPC-4483?
> focusedCommentId=188831&page=>
> >> com.atlassian.jira.plugin.system.issuetabpanels:comment-
> >> tabpanel#comment-188831>
> >> Wim Rm Cardoen <https://jira.chpc.utah.edu/
> secure/ViewProfile.jspa?name= <https://jira.chpc.utah.edu/
> secure/ViewProfile.jspa?name=>
> >> u0253283>Wim Rm Cardoen added a comment - Jan/09/2017 12:57 PM
> >> What will cause grief to /usr/bin/python ?
> >> A may be a good suggestion to the developers to
> >> use /usr/bin/env python instead of /usr/bin/python
> >>
> >> Thanks,
> >> Chase Zagorec-Marks
> >> C
> >>> On Jan 9, 2017, at 2:05 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >>>
> >>> yes please make more descriptive report here.
> >>>
> >>> btw, newest AmberTools requires python >= 2.7.
> >>> And I recommend to upgrade to AmberTools16 if you have not done so.
> >>>
> >>> Hai
> >>>
> >>> On Mon, Jan 9, 2017 at 3:53 PM, Chase Zagorec-Marks <
> >> chasezgrcmrks.gmail.com
> >>>> wrote:
> >>>
> >>>> Hello,
> >>>>
> >>>> I was working through the tutorial on constant pH MD, and when I went
> to
> >>>> use the mdout_analyzer.py script to graph the energies of the
> >>>> minimization’s output file I received an error line from the cluster I
> >> was
> >>>> working in at the time. While I was being helped a suggestion for the
> >>>> Amber Developers to replace the first line in the Amber python
> programs
> >>>> from whatever you probe in the system, e.g. in our case
> >>>> #!/usr/bin/python26
> >>>> to
> >>>> #!/usr/bin/env python
> >>>>
> >>>> was put forth. If more details would be helpful I can provide the full
> >>>> thread of the issue and its resolution.
> >>>>
> >>>> Thanks,
> >>>> Chase Zagorec-Marks
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
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> >> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>
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Received on Mon Jan 09 2017 - 14:00:02 PST
