Can I do the installation by separately installing miniconda. Is it
possible?
On Wed, Aug 21, 2019 at 1:50 PM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> Following output am getting when I ran
> amber.python -c "from parmed.scripts import clapp; print(clapp)"
>
> ----------[sunitap.ycn2 amber18]$ amber.python -c "from parmed.scripts
> import clapp; print(clapp)"
> Traceback (most recent call last):
> File
> "/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/unit/__init__.py",
> line 25, in <module>
> from simtk.unit import *
> ModuleNotFoundError: No module named 'simtk'
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> File
> "/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/__init__.py",
> line 22, in <module>
> from parmed import unit, utils
> File
> "/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/unit/__init__.py",
> line 27, in <module>
> from parmed.unit.unit import Unit, is_unit
> File
> "/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/unit/unit.py",
> line 35, in <module>
> from parmed.utils.six import iterkeys
> File
> "/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/utils/__init__.py",
> line 3, in <module>
> from parmed.utils.pairlist import find_atom_pairs
> File
> "/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/utils/pairlist.py",
> line 5, in <module>
> import numpy as np
> ModuleNotFoundError: No module named 'numpy'
> -----------------
>
> On Wed, Aug 21, 2019 at 11:42 AM Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> In this case, I don't think install another MIniconda will help.
>>
>> The error message comes from the code in AmberTools/test/test_check.sh
>>
>> try:
>>
>> from parmed.scripts import clapp
>>
>> except ImportError:
>>
>> if os.path.exists(os.path.join(ambhome, 'bin/parmed')):
>>
>> sys.stderr.write('\\nError: Could not import Amber Python modules!
>> \\n'
>>
>> ' Probably your Amber Python environment was not set up
>> correctly.\\n\\n')
>>
>> error()
>>
>>
>>
>> What's the output of the below command
>> amber.python -c "from parmed.scripts import clapp; print(clapp)"
>>
>> Hai
>>
>> On Wed, Aug 21, 2019 at 1:45 AM Sunita Patel <sunita.patel.cbs.ac.in>
>> wrote:
>>
>> > I am manually downloading Miniconda and installing it.
>> > Let me see if it can solve my problem.
>> >
>> > On Wed, Aug 21, 2019 at 10:56 AM Sunita Patel <sunita.patel.cbs.ac.in>
>> > wrote:
>> >
>> > > Dear David,
>> > >
>> > > When I tried intalling Miniconda Python package. But, am getting
>> > following
>> > > problem. I need your help to solve Amber 18 installation issue.
>> > >
>> > > ./configure_python
>> > >
>> > > This script will download and install a version of Python compatible
>> > >
>> > > with every component of AmberTools and install all required and
>> optional
>> > >
>> > > prerequisites. The Python distribution is downloaded for your
>> operating
>> > >
>> > > system from Miniconda.
>> > >
>> > >
>> > > Downloading Python 2.7 Miniconda
>> > >
>> > > Detected Linux kernel. Downloading the Linux installer
>> > >
>> > > Downloading the latest Miniconda distribution
>> > >
>> > > Detected 64-bit Linux
>> > >
>> > > --2019-08-20 11:44:34--
>> > > https://repo.continuum.io/miniconda/Miniconda2-4.3.21-Linux-x86_64.sh
>> > >
>> > > Resolving repo.continuum.io... failed: Name or service not known.
>> > >
>> > > wget: unable to resolve host address `repo.continuum.io'
>> > >
>> > > On Tue, Aug 20, 2019 at 5:54 PM David A Case <david.case.rutgers.edu>
>> > > wrote:
>> > >
>> > >> On Tue, Aug 20, 2019, Sunita Patel wrote:
>> > >> >
>> > >> >System was having older python 2.6 so installed Phython3.6 locally
>> and
>> > >> set
>> > >> >path.
>> > >>
>> > >> We strongly recommend allowing the configure script to download a
>> > >> Miniconda python package; that ensures that you have all the required
>> > >> packages available. It is installed within your Amber tree, so it
>> won't
>> > >> interfere with any existing ("system") python you may have.
>> > >>
>> > >> ....dac
>> > >>
>> > >>
>> > >> _______________________________________________
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>> > >> http://lists.ambermd.org/mailman/listinfo/amber
>> > >>
>> > >
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Received on Wed Aug 21 2019 - 05:00:02 PDT
