Dear David
again thank you very much.
as requested:
amber20_src]$ ./update_amber --show-applied-patches
AmberTools 21 Applied Patches:
------------------------------
update.1 (modifies sander)
update.2 (modifies pytraj, pdb4amber)
update.3 (modifies N/A)
update.4 (modifies packmol-memgen)
update.5 (modifies pdb4amber)
update.6 (modifies none)
update.7 (modifies cmake, installation)
update.8 (modifies pmemd, pmemd.cuda, updated, mcmd, test, cases)
Amber 20 Applied Patches:
-------------------------
update.1, update.2, update.3, update.4, update.5, update.6, update.7,
update.8, update.9, update.10,
update.11, update.12
I commented both lines
-cd sanderapi && $(MAKE) test
-cd sanderlesapi && $(MAKE) test
and tests finished apparently without error.
While doing it I realized that both tests (sanderapi and snaderlesapi
were failing in the python API)
I don't think we are going to need them so I will consider that my
installation is ok
thank you very much for all your help.
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 21:32, David A Case wrote:
> On Mon, Sep 13, 2021, Oscar Conchillo-Solé wrote:
>
>> ./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.
>
> As a sanity check, please try "update_amber --show-applied-patches".
> If you
> have update.7, then that update must not be catching all of the problems.
>
>>
>> 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
>
> Just a reminder: you can totally ignore this error. It is the very last
> step of the installation, and there is no need to even create an
> "amber.pip"
> executable any way, as far as I can see.
>
>> 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
>
> This sounds good: amber.pip is not needed, and it's not supposed to
> report
> any errors.
>
>> I find it quite strange that make install fails the first time and
>> not the second since I changed nothing just the install dir.
>
> I have nothing to add.
>
>>
>> but the make test.serial fail like always
>> here I'm pasting the complete "cd sanderlesapi && make test"
>>
>
> If you don't need the python API to sander.LES (and few people do), you
> can just comment out those lines in the test (labeled "#API tests") in
> the $AMBERHOME/test/Makefile. I'm not sure how to easily debug this
> problem.
>
> ....dac
>
>
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Received on Tue Sep 14 2021 - 05:30:02 PDT
