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
> 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/
> secure/ViewProfile.jspa?name=u0916868> created issue - Jan/09/2017 11:57
> AM
> <https://jira.chpc.utah.edu/browse/HPC-4483#>Permalink <
> 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=
> 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#>Permalink <
> 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=
> 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#>Permalink <
> 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=
> 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/
> 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#>Permalink <
> 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=
> 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#>Permalink <
> 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/
> secure/EditComment!default.jspa?id=117564&commentId=188829> Delete <
> https://jira.chpc.utah.edu/secure/DeleteComment!default.
> jspa?id=117564&commentId=188829>
> Chase Zagorec-Marks <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#>Permalink <
> 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=
> 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 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
> 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#>Permalink <
> 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=
> 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
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jan 09 2017 - 13:30:03 PST
