Dear David
thank you very much for your answer
as you suggested I have executed update_amber
At first I found this error:
/usr/bin/env: 'python': No such file or directory
This happens due to the fact that centos8 comes without a predefined
python interpreter. python2 and python3.6 are installed, but no
"default" one is set.
I executed the following command to define it:
alternatives --set python /usr/bin/python3
and then:
./update_amber --update
Preparing to apply updates... please wait.
No new updates available for AmberTools 21
No new updates available for Amber 20
as you can see my versions of Amber and AmberTools are totally up to date.
I have also checked my $PYTHONPATH after "sourcing" amber.sh
$ echo $PYTHONPATH
/sharelab/labapps/AMBER/CentOS-8/Amber20/lib/python3.9/site-packages
it is apparently well defined.
To avoid possible conflicts I have installed python39 (I made sure that
python39-devel was installed) and then set up alternatives for both
python and python3
alternatives --config python
alternatives --config python3
I have repeated the whole process
cmake ../amber20_src
-DCMAKE_INSTALL_PREFIX=/sharelab/labapps/AMBER/CentOS-8/Amber20
-DCOMPILER=GNU -DOPENMP=TRUE -DDOWNLOAD_MINICONDA=TRUE
-DMINICONDA_USE_PY3=TRUE -DINSTALL_TESTS=TRUE
make
make install
and the same first error reapeared:
-- Fixing Miniconda script shebangs
CMake Error at
/sharelab/labapps/AMBER/SRC/Amber20/amber20_src/cmake/FixCondaShebang/FixCondaShebang.cmake:26
(file):
file failed to open for reading (No such file or directory):
/sharelab/labapps/AMBER/CentOS-8/Amber20//bin/amber.pip
I have also checked both CMakeOutput.log and CMakeError.log files, there
is no error related to python
I have a copy of the make install output and I cannot find any error in
the make install other than the previously mentioned one
So I created a new Build dir
and executed:
cmake ../amber20_src
-DCMAKE_INSTALL_PREFIX=/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20
-DCOMPILER=GNU -DOPENMP=TRUE -DDOWNLOAD_MINICONDA=TRUE
-DMINICONDA_USE_PY3=TRUE -DINSTALL_TESTS=TRUE
make
make install
this time make install completed without error
but amber.pip was not created
I find it quite strange that make install fails the first time and not
the second since I changed nothing just the install dir.
but the make test.serial fail like always
here I'm pasting the complete "cd sanderlesapi && make test"
cd sanderlesapi && make test
make[1]: Entering directory
'/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/test/sanderlesapi'
(if [ -f
"/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20///lib/libsanderles.so" ];
then \
make test_all; \
else \
make test_none; \
fi;)
make[2]: Entering directory
'/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/test/sanderlesapi'
Testing the Fortran LES API
/usr/bin/gfortran -Wall -Wno-tabs -Wno-unused-function
-ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable
-I/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/include
-L/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/lib test.F90 -o testf
-lsanderles
Running testf
Testing GB sander interface (diffcoords w/ RDT)
PASSED
==============================================================
Testing GB sander interface (samecoords w/out RDT)
PASSED
==============================================================
Testing PME sander interface
PASSED
==============================================================
Testing the C LES API
/usr/bin/gcc -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-variable -Wno-unused-but-set-variable
-I/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/include
-L/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/lib test.c -o testc
-lsanderles
Running testc
Testing GB sander interface (diffcoords w/ RDT)
PASSED
==============================================================
Testing GB sander interface (samecoords w/out RDT)
PASSED
==============================================================
Testing PME sander interface
PASSED
==============================================================
Testing the C++ LES API
/usr/bin/g++ -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-variable -Wno-unused-but-set-variable
-I/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/include
-L/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/lib test.cpp -o
testcpp -lsanderles
Running testcpp
Testing GB sander interface (diffcoords w/ RDT)
PASSED
==============================================================
Testing GB sander interface (samecoords w/out RDT)
PASSED
==============================================================
Testing PME sander interface
PASSED
==============================================================
Testing the Python LES API
/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20//miniconda/bin/python test.py
Could not import sanderles. Skipping test
Could not import the compiled Python-sander interface. Make sure you
have the Python development libraries installed and that you have
sourced amber.sh or amber.cshmake[2]: Leaving directory
'/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/test/sanderlesapi'
make[1]: Leaving directory
'/sharelab/labapps/AMBER/CentOS-8-REDO/Amber20/test/sanderlesapi'
I hope this helps
thank you very much in advance.
OCS
Oscar Conchillo Solé
Computational Biology Group
Data Center Manager, Sysadmin and Bioinformatics
Institut de Biotecnologia i Biomedicina (UAB)
mail:ocs.bioinf.uab.es
telf:0034 93586 8939; 0034 93581 4431
On 13/9/21 14:41, David A Case wrote:
> On Mon, Sep 13, 2021, Oscar Conchillo-Solé wrote:
>>
>> 1 (ls -l of amber.pip)
>> lrwxrwxrwx 1 ocs users 58 Sep 10 14:37
>> /sharelab/labapps/AMBER/CentOS-8/Amber20/bin/amber.pip ->
>> /sharelab/labapps/AMBER/CentOS-8/Amber20/miniconda/bin/pip
>> (empty link,
>> /sharelab/labapps/AMBER/CentOS-8/Amber20/miniconda/bin/pip des not
>> exists)
>
> This is fixed in update.7 for AmberTools21. Be sure to use
> update_amber to
> get up to date, (and use the --upgrade option is you are still using
> AmberTools20.)
>
>> Testing the Python LES API
>> /sharelab/labapps/AMBER/CentOS-8/Amber20//miniconda/bin/python test.py
>> Could not import sanderles. Skipping test
>> Could not import the compiled Python-sander interface. Make sure you
>> have the Python development libraries installed and that you have
>> sourced amber.sh or amber.csh
>
> First, check your PYTHONPATH variable (which is set in the amber.sh
> file).
> Second, look at your cmake.log file for errors related to python. Third,
> re-run "make install" and study the output to see if there are messages
> related to python.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Sep 13 2021 - 11:00:02 PDT
