[Nek5000-users] Error while compiling exo2nek

Tue Nov 21 09:52:42 CST 2017

I fixed the permission issue by opening up the permissions menu on the
install file and clicking "Allow  running as a program"

On Tue, Nov 21, 2017 at 10:49 AM <nek5000-users at lists.mcs.anl.gov> wrote:

> Ok so how did you fix the permission issue? Is there something we need to
> change on our end?
>
> -----Original message-----
> > From:nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
> > Sent: Tuesday 21st November 2017 16:44
> > To: nek5000-users at lists.mcs.anl.gov
> > Subject: Re: [Nek5000-users] Error while compiling exo2nek
> >
> > No, I ran it without sudo as well, and cchanged to sudo when I got the
> permission error.
> >
> > On an additional issue, Im generating my meshes in the exodusII format
> by using PoinWise and then exporting the exodusII file. exo2nek fails with
> the following error message when I try to use it on these files.
> >
> > EXODUS: ERROR: Attempting to open the netcdf-4 file:
> >     pw_exo1.exo
> >     . Either the netcdf library does not support netcdf-4 or there is a
> filesystem or some other issue
> > ERROR: cannot open file pw_exo1.exo
> >
> > On checking the properties of the .exo file I found that its an HDF
> document and not a netcdf file.
> > Since Marcos file converts without problems Im sure the issue lies in
> how pointwise is exporting the exodusII files.
> >
> > Is exo2nek not a viable alternative for exodusII files then?
> >
> > On Tue, Nov 21, 2017 at 10:33 AM <nek5000-users at lists.mcs.anl.gov
> <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
> > I guess the mistake was to run ./maketools exo2nek with sudo.
> >
> > -----Original message-----
> > > From:nek5000-users at lists.mcs.anl.gov <mailto:
> From%3Anek5000-users at lists.mcs.anl.gov> <nek5000-users at lists.mcs.anl.gov
> <mailto:nek5000-users at lists.mcs.anl.gov>>
> > > Sent: Tuesday 21st November 2017 16:13
> > > To: nek5000-users at lists.mcs.anl.gov <mailto:
> nek5000-users at lists.mcs.anl.gov>
> > > Subject: Re: [Nek5000-users] Error while compiling exo2nek
> > >
> > > Changed the permission of the install file and it works fine now.
> > >
> > > Also the mesh supplied by Marco has been converted sucessfully and a
> .re2 file has been generated.
> > >
> > > Thanks all!
> > >
> > > On Tue, Nov 21, 2017 at 9:45 AM <nek5000-users at lists.mcs.anl.gov
> <mailto:nek5000-users at lists.mcs.anl.gov> <mailto:
> nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>>>
> wrote:
> > >
> > > > env: ‘./install’: Permission denied
> > >
> > > Looks like you cannot run the install. Can you check the permissions.
> > >
> > > -----Original message-----
> > > > From:nek5000-users at lists.mcs.anl.gov <mailto:
> From%3Anek5000-users at lists.mcs.anl.gov> <mailto:
> From%3Anek5000-users at lists.mcs.anl.gov <mailto:
> From%253Anek5000-users at lists.mcs.anl.gov>> <
> nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>
> <mailto:nek5000-users at lists.mcs.anl.gov <mailto:
> nek5000-users at lists.mcs.anl.gov>>>
> > > > Sent: Tuesday 21st November 2017 15:38
> > > > To: nek5000-users at lists.mcs.anl.gov <mailto:
> nek5000-users at lists.mcs.anl.gov> <mailto:nek5000-users at lists.mcs.anl.gov
> <mailto:nek5000-users at lists.mcs.anl.gov>>
> > > > Subject: Re: [Nek5000-users] Error while compiling exo2nek
> > > >
> > > > Hi Marco,
> > > >
> > > > I cant get exo2nek to compile properly at all. After downloading the
> latest version I get the following error messages when I run sudo
> ./maketools exo2nek
> > > >
> > > > Make exo2nek...
> > > > ----------------------
> > > > make[1]: Entering directory /home/adutta/Nek5000/tools/exo2nek
> > > > make[1]: Warning: File makefile has modification time 17453 s in the
> future
> > > > env: ‘./install’: Permission denied
> > > > makefile:19: recipe for target lib failed
> > > > make[1]: *** [lib] Error 126
> > > > make[1]: Leaving directory /home/adutta/Nek5000/tools/exo2nek
> > > >
> > > > ERROR: exo2nek failed to compile!
> > > > makefile:4: recipe for target all failed
> > > > make: *** [all] Error 1
> > > >
> > > >
> > > >
> > > > On Tue, Nov 21, 2017 at 9:33 AM <nek5000-users at lists.mcs.anl.gov
> <mailto:nek5000-users at lists.mcs.anl.gov> <mailto:
> nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>>
> <mailto:nek5000-users at lists.mcs.anl.gov <mailto:
> nek5000-users at lists.mcs.anl.gov> <mailto:nek5000-users at lists.mcs.anl.gov
> <mailto:nek5000-users at lists.mcs.anl.gov>>>> wrote:
> > > > Can you try the exo2nek script on the attached exo mesh file and see
> if it works. It works on my machine. It has 2496 elements and 3 sidesets.
> > > >
> > > > Marco
> > > >
> > > > _______________________________________________
> > > > Nek5000-users mailing list
> > > > Nek5000-users at lists.mcs.anl.gov <mailto:
> Nek5000-users at lists.mcs.anl.gov> <mailto:Nek5000-users at lists.mcs.anl.gov
> <mailto:Nek5000-users at lists.mcs.anl.gov>> <mailto:
> Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov>
> <mailto:Nek5000-users at lists.mcs.anl.gov <mailto:
> Nek5000-users at lists.mcs.anl.gov>>>
> > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>>>
> > > > --
> > > > Amitvikram Dutta
> > > > Graduate Research Assistant
> > > > Fluid Mechanics Research Lab
> > > > University of Waterloo
> > > > _______________________________________________
> > > > Nek5000-users mailing list
> > > > Nek5000-users at lists.mcs.anl.gov <mailto:
> Nek5000-users at lists.mcs.anl.gov> <mailto:Nek5000-users at lists.mcs.anl.gov
> <mailto:Nek5000-users at lists.mcs.anl.gov>>
> > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>>
> > > _______________________________________________
> > > Nek5000-users mailing list
> > > Nek5000-users at lists.mcs.anl.gov <mailto:
> Nek5000-users at lists.mcs.anl.gov> <mailto:Nek5000-users at lists.mcs.anl.gov
> <mailto:Nek5000-users at lists.mcs.anl.gov>>
> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>>
> > > --
> > > Amitvikram Dutta
> > > Graduate Research Assistant
> > > Fluid Mechanics Research Lab
> > > University of Waterloo
> > > _______________________________________________
> > > Nek5000-users mailing list
> > > Nek5000-users at lists.mcs.anl.gov <mailto:
> Nek5000-users at lists.mcs.anl.gov>
> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov>
> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
> > --
> > Amitvikram Dutta
> > Graduate Research Assistant
> > Fluid Mechanics Research Lab
> > University of Waterloo
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at lists.mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
-- 

*Amitvikram Dutta*

Graduate Research Assistant

Fluid Mechanics Research Lab

University of Waterloo
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20171121/787076f3/attachment-0001.html>