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 Post subject: import pyroms error
PostPosted: Fri May 18, 2018 1:59 am 
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Joined: Mon Nov 30, 2015 5:22 pm
Posts: 11
Location: NUIST
Hello,
I tried to install pyroms in Ubuntu18.04LTS, the Prerequisites of pyroms list in https://github.com/ESMG/pyroms have been installed. Such as liblpsolve55.so (tutorial1 and tutorial2) and scrip.so (tutorial) can be seen in
Code:
henry@ubuntu:~$ find -name liblpsolve55.so
./lp_solve_5.5/lpsolve55/bin/ux64/liblpsolve55.so
./anaconda3/lib/liblpsolve55.so
./anaconda3/lib/python3.6/site-packages/liblpsolve55.so
./anaconda3/pkgs/lpsolve-5.5.2.3-4/lib/liblpsolve55.so
henry@ubuntu:~$ find -name scrip.so
./anaconda3/lib/scrip.so
./anaconda3/lib/python3.6/site-packages/scrip.so
./anaconda3/lib/python3.6/site-packages/pyroms/scrip.so
./anaconda3/lib/python3.6/site-packages/pyroms/remapping/scrip.so

However, when I import pyroms, gives the error message:
Code:
>>> import pyroms
scrip.so not found. Remapping function will not be available

I have added the three packages of pyroms into mypkpath.pth which located in /home/henry/anaconda3/lib/python3.6/site-packages and can import lpsolve55 smoothly.
How can I sove this problem?
Thanks,
Henry


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 Post subject: Re: import pyroms error
PostPosted: Fri May 18, 2018 6:23 am 
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Joined: Wed Jul 02, 2003 5:29 pm
Posts: 3517
Location: IMS/UAF, USA
Does your LD_LIBRARY_PATH include any of the places with these libraries? Mine does.


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 Post subject: Re: import pyroms error
PostPosted: Fri May 18, 2018 8:22 am 
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Joined: Mon Nov 30, 2015 5:22 pm
Posts: 11
Location: NUIST
kate wrote:
Does your LD_LIBRARY_PATH include any of the places with these libraries? Mine does.

Yes, I have set LD_LIBRARY_PATH=/home/henry/anaconda3/lib that includes scrip.so, and I also change the LD_LIBRARY_PATH to other path that include scrip.so but
the error still exists.
Furthermore, I met another problem when python make_YELLOW_grd_v1.py that matplotlib.mlab.griddata: the griddata function was deprecated in version 2.2 (https://matplotlib.org/api/mlab_api.html), however I have solved this problem through reducing the version of matplotlib lower than version2.2, but dose have other ways to solve this problem?

Thanks for your reply,
Henry


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 Post subject: Re: import pyroms error
PostPosted: Fri May 18, 2018 3:44 pm 
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Joined: Wed Jul 02, 2003 5:29 pm
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Location: IMS/UAF, USA
The deprecated message should be just a warning. Do they provide a suggestion for what routine to use instead?


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 Post subject: Re: import pyroms error
PostPosted: Fri May 18, 2018 6:51 pm 
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Location: IMS/UAF, USA
I just got some of those warnings:
Quote:
/import/u/u1/uaf/kshedstrom/.conda/envs/snowdrifts/lib/python3.5/site-packages/mpl_toolkits/basemap/__init__.py:3608: MatplotlibDeprecationWarning: The ishold function was deprecated in version 2.0.
b = ax.ishold()
/import/u/u1/uaf/kshedstrom/.conda/envs/snowdrifts/lib/python3.5/site-packages/mpl_toolkits/basemap/__init__.py:3677: MatplotlibDeprecationWarning: axes.hold is deprecated.
Note that the warnings don't refer to pyroms code but to code in another package. These things should clear up in good time and can be ignored in the mean time.


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 Post subject: Re: import pyroms error
PostPosted: Sat May 19, 2018 8:21 am 
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Joined: Mon Nov 30, 2015 5:22 pm
Posts: 11
Location: NUIST
kate wrote:
The deprecated message should be just a warning. Do they provide a suggestion for what routine to use instead?

As you say, The deprecated message just a warning, matplotlib.mlab.griddata can work on version 2.2.
However, my first problem cannot be solved.
I re-installed the pyroms according https://houstonthereisaproblem.blogspot ... -1072.html.
My pyroms is installed into /home/henry/pyroms and all external packages are installed into /home/henry/pyroms/ext.
The scrip*.so is localed at
Code:
henry@ubuntu:~$ find -name scrip*.so
./Downloads/pyroms-python3/pyroms/external/scrip/source/scrip.cpython-36m-x86_64-linux-gnu.so
./pyroms/ext/lib/scrip.cpython-36m-x86_64-linux-gnu.so
./pyroms/lib/scrip.cpython-36m-x86_64-linux-gnu.so
./pyroms/lib/python3.6/site-packages/pyroms/remapping/scrip.cpython-36m-x86_64-linux-gnu.so
./pyroms/scrip.cpython-36m-x86_64-linux-gnu.so

and then set the following environment variables
Code:
export PYROMS=/home/henry/pyroms
export PYROMS_GRIDID_FILE=/home/henry/Downloads/pyroms-python3/pyroms/pyroms/gridid.txt
export PYTHONPATH=$PYROMS/lib/python3.6/site-packages:$PYTHONPATH
export PYTHONPATH=$PYROMS/ext/lib:$PYTHONPATH
export DYLD_LIBRARY_PATH=$PYROMS/lib/python3.6/site-packages/bathy_smoother:$DYLD_LIBRARY_PATH
export DYLD_LIBRARY_PATH=$PYROMS/ext/lib:$DYLD_LIBRARY_PATH
export PATH=$PYROMS/ext/lib:$PATH
export LD_LIBRARY_PATH=$PYROMS/lib:LD_LIBRARY_PATH=$PYROMS/ext/lib:$LD_LIBRARY_PATH

but still have the message that
Code:
>>> import pyroms
scrip.so not found. Remapping function will not be available


I have no idea to solve this prolbem, please give me some advises!


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