Hi,
Your Miniconda is not successfully installed, so please try a fresh install
of AmberTools again.
You can also try to install Miniconda by yourself (
https://docs.conda.io/en/latest/miniconda.html) and
use --with-python option to specify path to miniconda python
./configure --with-python /path/to/your/python gnu
source amber.sh
make install
Hope this help and I am sorry for the long delay.
Hai
On Wed, Oct 16, 2019 at 6:35 PM Alen Ahmetovic <alen2.mail.usf.edu> wrote:
> Hai,
>
> I think the amber site is down because the link you gave plus trying to go
> onto the site from google gave a server error... Anyways, I deleted all
> amber folders I had (including old install of amber 12 (not sure if this is
> relevant or not)) and tried to install again.
>
> Here is the full log in the attached file, minus the tar command for
> ambertools19.tar and the following output, as to make this more bearable to
> read (it tarred fine from what I can tell):
> Below are the important segments that I had to "intervene" in:
>
> after configure failed the first time:
>
> ------ I use these commands to solve the exception: dst exists
>
> alen.DESKTOP-9902UPO:/mnt/c/Users/Alen/Documents/Research/amber18$ sudo
> apt
> install attr
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> attr is already the newest version (1:2.4.47-2).
> 0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
> alen.DESKTOP-9902UPO:/mnt/c/Users/Alen/Documents/Research/amber18$
> setfattr
> -n system.wsl_case_sensitive -v 1
> /mnt/c/Users/Alen/Documents/Research/amber18/
>
> ---The install part starts from after my command to "make install", the
> beginning part was cut off because my terminal window doesn't let me look
> that far back:
>
> It failed in the same place it did previously with the same error. To
> piggyback off it this, that is why I had miniconda3 installed. I was trying
> to get the proper program installed following directions on github, it told
> me to install conda as this was the preferred method to get the program.
> Please refer to this link:
> https://amber-md.github.io/pytraj/latest/installation
>
> Just as a side note, I didn't tar the actual amber18.tar file, I read
> somewhere it will do it automatically in install or test if everything goes
> right, butr I can't find it now to reference it, so I may be wrong.. Can
> you confirm this? Could this be a possible source of error as to why
> install won't get passed the pytraj part?
>
> Thanks so much,
>
> Alen
>
>
> On Mon, Oct 14, 2019 at 11:28 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > hi Alen,
> >
> > What's exact commands did you specify?
> > You have "amber18//lib/python2.7/" folder but you say you also have
> > "AMBERHOME/amber18/miniconda3", which is a python3 distribution. So
> there
> > are some conflicts here.
> >
> > If possible, please try again with the latest AmberTools 19 that can work
> > with your amber18.
> > I suggest to
> > - download the tarfile from amber website:
> > http://ambermd.org/AmberTools.php
> > - open a new terminal and untar it and follow the instructions in amber
> > manual to compile the suite.
> >
> > PS: During the installation process, I suggest to say "Yes" (again) so
> > Python will be installed via Miniconda.
> > Please record your commands + the output logs to make it easier to debug.
> >
> > cheers
> > Hai
> >
> > On Mon, Oct 14, 2019 at 10:28 PM Alen Ahmetovic <alen2.mail.usf.edu>
> > wrote:
> >
> > > Hi all,
> > >
> > > I am trying to install Amber and Tools18 on my PC. I am running through
> > > Ubuntu. When doing the installation, I keep getting stuck with the
> > > following error:
> > >
> > > make[5]: Leaving directory
> > >
> '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj/src'
> > > make[4]: Leaving directory
> > > '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj'
> > > make[3]: Leaving directory
> > > '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src'
> > > (cd pytraj && AMBERHOME=/mnt/c/Users/Alen/Documents/Research/amber18/
> > > AMBER_PREFIX=/mnt/c/Users/Alen/Documents/Research/amber18/
> > >
> > >
> >
> PYTHONPATH=/mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages
> > > /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python setup.py
> > > install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/
> > > --disable-openmp > build.log )
> > > Traceback (most recent call last):
> > > File "setup.py", line 18, in <module>
> > > from setuptools import setup, Extension
> > > ImportError: No module named setuptools
> > > Makefile:505: recipe for target 'pytraj' failed
> > > make[2]: *** [pytraj] Error 1
> > > make[2]: Leaving directory
> > > '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src'
> > > Makefile:26: recipe for target 'serial' failed
> > > make[1]: *** [serial] Error 2
> > > make[1]: Leaving directory
> > > '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src'
> > > Makefile:7: recipe for target 'install' failed
> > > make: *** [install] Error 2
> > >
> > > alen.DESKTOP-9902UPO:/mnt/c/Users/Alen/Documents/Research/amber18$
> sudo
> > > apt-get install python-setuptools
> > > [sudo] password for alen:
> > > Reading package lists... Done
> > > Building dependency tree
> > > Reading state information... Done
> > > python-setuptools is already the newest version (20.7.0-1).
> > > 0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
> > >
> > > then I try:
> > >
> > > alen.DESKTOP-9902UPO:/mnt/c/Users/Alen/Documents/Research/amber18$
> > python
> > > ./setup.py install
> > > python: can't open file './setup.py': [Errno 2] No such file or
> directory
> > >
> > > I have tried to do a clean install and still get the same error. I have
> > > made all of the possible patch updates and relevant program downloads
> > based
> > > off the errors given throughout the process, and I still end up in the
> > same
> > > place. I don't have any coding experience other than what I've learned
> > > using Amber and copy/pasting commands I find online to fix these
> > problems,
> > > otherwise I am totally lost. I added the last two commands to show
> that I
> > > have the setuptools its telling me I don't have, and the fact that
> asking
> > > it to specifically download setup.py does not work. What am I missing?
> > >
> > > Does setuptools need to be in the proper directory for python within
> > amber
> > > to use it correctly? Currently it's in AMBERHOME/amber18/miniconda3.
> > >
> > > Thanks in advance for your help.
> > >
> > > Alen
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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Received on Tue Oct 29 2019 - 19:30:02 PDT
