The error say numpy is mising, so just install it.
Hai
On Wed, Aug 21, 2019 at 7:56 AM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> 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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> >> > >> AMBER.ambermd.org
> >> > >> http://lists.ambermd.org/mailman/listinfo/amber
> >> > >>
> >> > >
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> >>
> >
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Received on Wed Aug 21 2019 - 06:00:03 PDT
