[GRASS-user] compiling grass-7.8.5 on conda environment

[Vaclav Petras]

On Fri, Aug 6, 2021 at 1:33 AM Laura Poggio <laura.poggio at gmail.com> wrote:

> Hi Vaclav,
> thanks a lot. Your patch worked perfectly. The remaining problems were
> solved by loading the conda environment path into LD_LIBRARY.
>

That's what I do there.


>
> I will look into your repository if there is a better solution.
>

Not a one I know of, but I wouldn't mind using something else. I think the
reason for this being needed during compilation is that the things in GRASS
GIS are actually running during compilation (modules help to generate parts
of documentation).

However, feel free to check my scripts there. It is a fully reproducible
build workflow on our HPC, but maybe just a little adaptation is needed.


> But at least the environment works and grass can be updated to 7.8 and
> python3.
>

The scripts can install multiple versions which is good just for updating
to latest release as need while keeping the old versions around for
reproducibility. We are using it to be able to use also the development
versions and update them often without disturbing people who are using them.

Let me know if anything there needs more explanation.

Vaclav


>
> Thanks a lot again
> Laura
>
> On Tue, 3 Aug 2021 at 17:21, Laura Poggio <laura.poggio at gmail.com> wrote:
>
>> Hi Vaclav,
>> thanks a lot!
>> with the patch for the makefile in the repository I managed to solve the
>> previous error. Now I am getting a different error apparently linked to
>> some library conflict (same combination of libraries works in a different
>> environment):
>>
>> /home/user/conda3/envs/sg_py3_geo//lib//libspatialite.so.7: undefined
>> reference to `GEOSFrechetDistance'
>> /home/user/conda3/envs/sg_py3_geo//lib//libspatialite.so.7: undefined
>> reference to `GEOSFrechetDistance_r'
>> /home/user/conda3/envs/sg_py3_geo//lib//libspatialite.so.7: undefined
>> reference to `GEOSFrechetDistanceDensify'
>> /home/user/conda3/envs/sg_py3_geo//lib//libgdal.so.27: undefined
>> reference to `GEOSMakeValid_r'
>> /home/user/conda3/envs/sg_py3_geo//lib//libspatialite.so.7: undefined
>> reference to `GEOSFrechetDistanceDensify_r'
>>
>> Tomorrow I will try again with a clean conda environment implementing all
>> of your scripts.
>> Thanks a lot!
>>
>> Laura
>>
>>
>>
>> On Tue, 3 Aug 2021 at 15:32, Vaclav Petras <wenzeslaus at gmail.com> wrote:
>>
>>> Hi Laura,
>>>
>>> See whether the following is helpful to you. It uses everything from
>>> conda and has some local fixes for iconv. I didn't test 7.8.5 specifically,
>>> only the 7.8 release branch.
>>>
>>> GRASS GIS on HPC Henry2
>>> https://github.com/ncsu-geoforall-lab/grass-gis-on-hpc-henry2/
>>>
>>> Some more comments:
>>>
>>> On Tue, Aug 3, 2021 at 9:12 AM Laura Poggio <laura.poggio at gmail.com>
>>> wrote:
>>>
>>>>
>>>> I am trying to compile grass 7.8.5 in a conda environment (on centos7,
>>>> managed HPC) adapting this instructions here
>>>> <https://github.com/GRASS-GIS/grass-gis-experimental-ci/blob/conda-compile/configure.sh>
>>>> .
>>>>
>>>
>>> Nobody touched that repo for a while, but development happened
>>> elsewhere. We have a CentOS 7 build partially using conda in the main
>>> repo's CI. However, my experience was that the CentOS 7 Docker container in
>>> CI was very different from the CentOS 7 environment on HPC which has many
>>> customizations.
>>>
>>> https://github.com/OSGeo/grass/blob/master/.github/workflows/centos.yml
>>>
>>> There is also a conda-based build for macOS, but that would need to be
>>> adapted
>>>
>>>
>>>> conda create -y -n $conda_env python=3.8.5
>>>> conda activate $conda_env
>>>> conda install -c conda-forge geos gdal==3.3.1 -y
>>>> conda install -c conda-forge pdal fftw -y
>>>> conda install -c biobuilds libxml2
>>>> conda install -c conda-forge libiconv
>>>>
>>>
>>> The GRASS GIS on Henry 2 repo has an environment file you can use.
>>>
>>>
>>>>
>>>> compile works well. make gives a lot of errors. When I run make again
>>>> in one of the folder, I get this errors:
>>>> /home/user/grasspy3/grass-7.8.5/dist.x86_64-pc-linux-gnu/lib/
>>>> libgrass_gis.7.8.so: undefined reference to `libiconv'
>>>> /home/user/grasspy3/grass-7.8.5/dist.x86_64-pc-linux-gnu/lib/
>>>> libgrass_gis.7.8.so: undefined reference to `libiconv_open'
>>>> /home/user/grasspy3/grass-7.8.5/dist.x86_64-pc-linux-gnu/lib/
>>>> libgrass_gis.7.8.so: undefined reference to `libiconv_close'
>>>>
>>>
>>> I was not able to create a proper fix for GRASS GIS configuration, but
>>> the repo has a somewhat hacky patch applied locally which injects libiconv
>>> into more places.
>>>
>>> Let me know how this goes. With the scripts in GRASS GIS on Henry 2, I
>>> can install new versions easily, but I would like to see it more
>>> streamlined with less local customizations.
>>>
>>> Best,
>>> Vaclav
>>>
>>>
>>>>
>>>> I found this answer
>>>> <http://osgeo-org.1560.x6.nabble.com/Adding-path-iconv-library-to-configure-td5431037.html>,
>>>> but I am not sure how to continue from there.
>>>> Thanks a lot
>>>> Laura
>>>>
>>>> _______________________________________________
>>>> grass-user mailing list
>>>> grass-user at lists.osgeo.org
>>>> https://lists.osgeo.org/mailman/listinfo/grass-user
>>>>
>>>
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