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

From: Oscar Conchillo-Solé <>
Date: Tue, 14 Sep 2021 14:08:08 +0200

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.


Oscar Conchillo Solé
Computational Biology Group
Data Center Manager, Sysadmin and Bioinformatics
Institut de Biotecnologia i Biomedicina (UAB)
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"
>> $ 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
>> 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
>> 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
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