Dear Dr. Case and Amber Users,
Updating my testing problem ...
I tried to run make test.serial as root (after setting the AMBERHOME environment variable in the /root/.bashrc file) and it worked.
I did the intallation as superuser (but not root) and using "sudo make test.serial" (AMBERHOME environment variable in /etc/bash.bashrc) I was encountering the problems described in my previous messages.
I don't understand why "make test" would only work for root in my case. I do not have a large knowledge of linux or programming in general ... but maybe I do not have an installation problem after all...
Thanks a lot
Beatriz
--------------------------
Beatriz Guimarães
Laboratory of Structural Biology and Protein Engineering
Instituto Carlos Chagas - ICC / FIOCRUZ Paraná
Rua Prof. Algacyr Munhoz Mader, 3775 Bloco C
CIC 81350-010
Curitiba - PR, Brasil
Tel.:+55(41)3316-3225/2104-3438
________________________________
De: Beatriz Gomes Guimaraes <beatriz.guimaraes.fiocruz.br>
Enviado: quarta-feira, 6 de janeiro de 2021 13:17
Para: AMBER Mailing List <amber.ambermd.org>
Assunto: RE: [AMBER] Amber 20 installation, problems with the testing phase
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 Guimarães
Laboratory of Structural Biology and Protein Engineering
Instituto Carlos Chagas - ICC / FIOCRUZ Paraná
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 Thu Jan 07 2021 - 05:30:02 PST
