Hi all,
Just in case it got lost in the email threads, I just want to bump this to
see if anyone has any suggestions! As per Hai, I tried to recompile Amber
but got the same error messages. Thanks in advance for everyone's help, as
always!
Best,
Alen
On Wed, Oct 16, 2019 at 6:44 PM Alen Ahmetovic <alen2.mail.usf.edu> wrote:
> 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 Tue Oct 29 2019 - 17:00:04 PDT
