Re: [AMBER] Amber 20 installation, problems with the testing phase

From: Beatriz Gomes Guimaraes <beatriz.guimaraes.fiocruz.br>
Date: Wed, 6 Jan 2021 16:17:11 +0000

Dear Dr Case,
Thank you for your reply.
I did what you suggested (include ../../config.h in the Makefile) and the error message changed:

(cd AmberTools/test && make test)
make[1]: Entering directory '/usr/local/amber20/AmberTools/test'
./test_at_serial.sh

Error: Could not import Amber Python modules!
   Probably your Amber Python environment was not set up correctly.

We recommend adding the line:

   test -f /usr/local/amber20///amber.sh && source /usr/local/amber20///amber.sh (sh/bash/zsh)
or
   test -f /usr/local/amber20///amber.csh && source /usr/local/amber20///amber.csh (csh/tcsh)

to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc).

make[1]: *** [Makefile:8: test] Error 1
make[1]: Leaving directory '/usr/local/amber20/AmberTools/test'
make: [Makefile:13: test.serial] Error 2 (ignored)
make[1]: Entering directory '/usr/local/amber20/test'
Makefile:4: /config.h: No such file or directory
make[1]: *** No rule to make target '/config.h'. Stop.
make[1]: Leaving directory '/usr/local/amber20/test'

Summary of AmberTools serial tests:

cat: ../logs/test_at_serial/at_summary: No such file or directory
make: *** [Makefile:14: test.serial] Error 1


A couple informations more:

echo $AMBERHOME
/usr/local/amber20

echo $PYTHONPATH
/usr/local/amber20/lib/python3.8/site-packages:/usr/local/amber20/lib/python3.8/site-packages

which python && python --version
/usr/bin/python
Python 3.8.5

which gcc && gcc --version
/usr/bin/gcc
gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0


Thanks again for your help!
Beatriz

--------------------------
Beatriz Guimar„es
Laboratory of Structural Biology and Protein Engineering
Instituto Carlos Chagas - ICC / FIOCRUZ ParanŠ
Rua Prof. Algacyr Munhoz Mader, 3775 Bloco C
CIC 81350-010
Curitiba - PR, Brasil
Tel.:+55(41)3316-3225/2104-3438
________________________________
De: David A Case <david.case.rutgers.edu>
Enviado: quarta-feira, 6 de janeiro de 2021 00:37
Para: AMBER Mailing List <amber.ambermd.org>
Assunto: Re: [AMBER] Amber 20 installation, problems with the testing phase

On Tue, Jan 05, 2021, Beatriz Gomes Guimaraes wrote:

>I think my AMBERHOME environment variable is OK. I had included a line in
>the .bashrc and if I type cd $AMBERHOME it goes to /usr/local/amber20.

It's worth typing "echo $AMBERHOME" as well.

>>
>>When I try make test.serial
>>I get the following message:
>>(cd AmberTools/test && make test)
>>make[1]: Entering directory '/usr/local/amber20/AmberTools/test'
>>Makefile:2: /config.h: No such file or directory
> ^^^^^^^^^^^

If you go to the AmberTools/test directory, and look at line 2 of the
Makefile, you should see this:

include $(AMBERHOME)/config.h

Somehow, the make variable $(AMBERHOME) is not set for you and you get a
blank string before the "/config.h" part. Not sure why.

You could try this: change line 2 (above) to this:

include ../../config.h

That should(?) be OK, since line 3 of the Makefile exports AMBERHOME to your
environment.

Let me know if this helps.

....dac


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Received on Wed Jan 06 2021 - 08:30:02 PST
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