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
>>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Jan 09 2017 - 13:30:04 PST
