I forget to tell you amber20_src uses miniconda look in you dir amber20
you should have a miniconda dir ?
On 21/06/2021 17:57, aishen wrote:
> |Are you sure you delete everthing well ?|
>
> |https://ambermd.org/GetAmber.php#ambertools|
>
> cd amber20_src
> ./update_amber --upgrade
> cd build
> ./clean_build
> ./run_cmake
> make install
>
> That's all it should work
>
> If you want or use conda
>
> https://anaconda.org/conda-forge/ambertools
>
> |conda install -c conda-forge ambertools
> |
>
> |I have both install with ubuntu 20.4.02 like yours
> |
>
> |But I avoid miniconda, after installing ubuntu I installed all
> python3 all dev sagemath jupyter it's about 8 Go of python3 (but you
> don't have to do it) I do it because I use lot of libs
> |
>
>
> ||
>
> On 21/06/2021 16:54, Balogh Álex Kálmán wrote:
>
>> Thank you for your help.
>>
>> Ubuntu's version is 20.04.2 LTS.
>>
>> I have reinstalled through:
>> cd /home/sturvo
>> tar xvfj AmberTools20.tar.bz2
>> tar xvfj Amber20.tar.bz2
>> cd amber20_src/build
>> ./run_cmake
>> make install
>>
>> I still get the same error only now in the new location:
>>
>> CMake Error at
>> /home/sturvo/amber20_src/cmake/FixCondaShebang/FixCondaShebang.cmake:26
>> (file):
>> file failed to open for reading (No such file or directory):
>>
>> /home/sturvo/amber20//bin/amber.pip
>>
>> I did the tests as another person suggested:
>>
>> export DO_PARALLEL="mpirun -np 2"
>> cd $AMBERHOME
>> source amber.sh
>> make test.parallel
>>
>> And I got this message (end of it):
>>
>> Summary of AmberTools parallel tests:
>>
>> 3 file comparisons passed
>> 1 file comparisons failed (0 of which can be ignored)
>> 429 tests experienced errors
>> Test log file saved as
>> /home/sturvo/amber20///logs/test_at_parallel/2021-06-21_16-51-14.log
>> No test diffs to save!
>>
>> With export DO_PARALLEL="mpirun -np 4" I got:
>>
>> Summary of AmberTools parallel tests:
>>
>> 3 file comparisons passed
>> 3 file comparisons failed (0 of which can be ignored)
>> 385 tests experienced errors
>> Test log file saved as
>> /home/sturvo/amber20///logs/test_at_parallel/2021-06-21_16-53-10.log
>> No test diffs to save!
>>
>> Am I doing something wrong?
>>
>> Best wishes,
>> Alex
>>
>>
>> ----- Eredeti üzenet -----
>> Feladó: "aishen" <aishen.free.fr>
>> Címzett: "amber" <amber.ambermd.org>
>> Elküldött üzenetek: Csütörtök, 2021. június 17. 18:11:14
>> Tárgy: Re: [AMBER] Amber20 installation, Amber.pip file broken
>>
>> which version of ubuntu ?
>>
>> What do you call a normal installation ? For me I compile it, or I use
>> conda ambertools, any way you shouldn't have this path,
>>
>> should be something like /home/sturvo/amber20/bin done by amber20_src
>>
>> your amber20_src should be /home/sturvo/amber20_src and you should
>> compile with run... script in build dir amber20 is created when you make
>> install
>>
>>
>> On 17/06/2021 10:34, Balogh Álex Kálmán wrote:
>>> Dear Developers!
>>>
>>> I'm just a novice in Ubuntu and Amber software and I have a problem
>>> during installation of Amber20.
>>>
>>> During normal installation as it is written in the user manual
>>> without changing any options I get this error:
>>>
>>> CMake Error at
>>> /home/sturvo/Amber/bin/Amber20/amber20_src/cmake/FixCondaShebang/FixCondaShebang.cmake:26
>>> (file):
>>> file failed to open for reading (No such file or directory):
>>>
>>> /home/sturvo/Amber/bin/Amber20/amber20//bin/amber.pip
>>>
>>> I have found the file and can't open it (broken). I tried creating a
>>> new file and restarting the installation, but it is rewritten thus
>>> broken again.
>>>
>>> I would like to ask for some help with this problem.
>>>
>>> Best wishes,
>>> Álex Kálmán Balogh
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Jun 21 2021 - 09:30:02 PDT
