I forgot to add, on the last run I did of install (the original email I
sent), I tried to install setuptools manually,but it didn't help. From
today:
alen.DESKTOP-9902UPO:/mnt/c/Users/Alen/Documents/Research/amber18$ sudo apt
install python-setuptools
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.
alen.DESKTOP-9902UPO:/mnt/c/Users/Alen/Documents/Research/amber18$
On Wed, Oct 16, 2019 at 6:34 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 Wed Oct 16 2019 - 16:00:03 PDT
