Re: [AMBER] Amber20 installation, Amber.pip file broken

From: Balogh Álex Kálmán <balogh.alex.science.unideb.hu>
Date: Mon, 21 Jun 2021 16:54:30 +0200 (CEST)

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 - 08:00:03 PDT
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