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 Wed Oct 16 2019 - 16:00:02 PDT
