I have plenty of thoughts though many of them are probably not very accurate or particularly useful.
If you run ./run_cmake and then make install, I am assuming the installation/compilation finishes. Are you able to install/compile ambertools21 and have you added amber home to your path?
Assuming a successful install, does this issue show up again if you re-run run_cmake?
I don’t know what the default behaviour is. If conda finds and installs the packages it needs and the compilation works I would assume that rerunning the run_cmake script should find previously installed packages. This is just my assumption though.
So if run_cmake and make install finishes without errors and re-running run_cmake still notes the missing packages, I would assume that either $AMBERHOME is not correctly added to your PATH or maybe the install is in some location requiring elevated privileges, preventing the “checks” to successfully identify previously installed packages.
Though these are just best guesses
Best regards
// Gustaf
> On 24 May 2021, at 11:39, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> Hi Olsson,
>
> Yes miniconda is fetching the required packages yet ./run_cmake throws
> error about the packages not found.
>
> While I managed to resolve the issue, run_cmake complained about not
> finding Plumed packages and library. I don't want to install Plumed.
>
> I also tried installing using the old ./configure -noX11 -mpi gcc on Linux
> cluster, this didn't work either. It was looking for pnetcdf! I don't want
> pnetcdf installation.
>
> I couldn't find anything in make files related to the above plumed or
> pnetcdf issue.
>
> Any thoughts on these?
>
> Best regards,
> Neha
>
>
>
>
> On Mon, 24 May 2021, 4:34 pm Gustaf Olsson, <gustaf.olsson.lnu.se> wrote:
>
>> I assume this is still during the ./run_cmake configuration?
>>
>> When installing, “make install”, is there any indication that miniconda is
>> fetching and installing the mentioned packages?
>>
>> Best regards
>> // Gustaf
>>
>>> On 22 May 2021, at 08:40, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>>>
>>> Hi AMBER List,
>>>
>>> I am trying to install AmberTools21 using cmake method. ./run_cmake is
>>> downloading miniconda however, the configuration fails with below missing
>>> packages. I was assuming that miniconda is downloading and installing
>>> numpy, scipy and matplotlib. I tried pip3 install numpy scipy matplotlib
>>> but it still fails.
>>> What is the work around to this solution?
>>>
>>> -- Checking for Python package numpy -- not found
>>> -- Checking for Python package scipy -- not found
>>> -- Checking for Python package matplotlib -- not found
>>>
>>> --
>>> Regards,
>>> Dr. Neha S. Gandhi,
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>>
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Received on Mon May 24 2021 - 03:30:02 PDT
