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-- 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 > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Jan 09 2017 - 13:30:03 PST