Issues installing CYCLUS from source

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Wittel, Madalina

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Oct 9, 2019, 4:09:46 AM10/9/19
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Dear CYCLUS experts,

I am a Postdoc from RWTH Aachen University in Germany. Our group is highly interested in carrying out some fuel cycle studies with CYCLUS.

I am writing to kindly ask for your assistance with installing CYCLUS (version 1.5.3) from source. I am using a Ubuntu 18.04 machine and have installed all the required dependencies as per your instructions. Unfortunately, I am getting errors when executing the "python install.py" command (I am using python 3.6.8) - please find the output in the textfile "output_python_install.txt". I'm also attaching the cmake logfile ("pyInstall_CMakeError.log").

After this failed, I have also tried to install CYCLUS with cmake (version 3.10.2), however, that also throws errors - output attached as textfile "output_cmake.txt".

I would be very grateful if you could please have a look and let me know what I should do such that I can compile CYCLUS properly. Many thanks for your time!

Best wishes,
Madalina


output_cmake.txt
output_python_install.txt
pyInstall_CMakeError.log

Steve Skutnik

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Oct 9, 2019, 7:10:21 AM10/9/19
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Hi Madalina,

It looks like from your output log that you’re missing libxml2; see here for the shortcut to install all of the required dependencies:

-Steve 

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Wittel, Madalina

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Oct 9, 2019, 8:31:33 AM10/9/19
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Dear Steve,


thank you very much for your reply.


I actually followed the instructions on the webpage you linked to when installing the dependencies. As far as I can see, the libxml2 library is installed (please see attached screenshot). Could it be that I need to specify its location in a certain (i.e. non-obvious) way?



Best wishes,

Madalina



Von: cyclus...@googlegroups.com <cyclus...@googlegroups.com> im Auftrag von Steve Skutnik <sku...@gmail.com>
Gesendet: Mittwoch, 9. Oktober 2019 13:10
An: cyclus...@googlegroups.com
Betreff: Re: [cyclus-users] Issues installing CYCLUS from source
 
Screenshot_libxml2.png

Baptiste MOUGINOT (BaM)

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Oct 9, 2019, 8:49:41 AM10/9/19
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Dear Madalina, 

Could you run :

python install.py —clean-build > install_log.txt

and send us the install_log.txt file that have been generated  ?

this should not fix your issue, but will generate a log file with all the output of your installation, so we can have a better idea of what going on… 


Thank you

Baptiste


Wittel, Madalina

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Oct 9, 2019, 9:43:31 AM10/9/19
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Dear Baptiste,


thanks a lot for writing. I am attaching the output of the 'python install.py —clean-build' command. 


Many thanks for your time!


Best wishes,

Madalina




Von: cyclus...@googlegroups.com <cyclus...@googlegroups.com> im Auftrag von Baptiste MOUGINOT (BaM) <mouginot...@gmail.com>
Gesendet: Mittwoch, 9. Oktober 2019 14:49
install_log.txt

Steve Skutnik

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Oct 9, 2019, 9:50:06 AM10/9/19
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Hi Madalina,

It seems like CMake is having trouble finding your LibXml2 install directory, from what I can tell. Can you try manually providing it to the installer?

See here:


i.e., you'd use the -D flag with ./install_cyclus.py, as shown here:


-Steve
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Paul Wilson

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Oct 9, 2019, 10:26:27 AM10/9/19
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Hi Madalina,

Given where your libraries reside, CMake should be able to find those.  I wonder if there are problems finding the include files??

Did you install the libxml2 package or the libxml2-dev package?  To run Cyclus only needs the former, but to build from source requires the latter.

Paul

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Wittel, Madalina

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Oct 9, 2019, 10:47:54 AM10/9/19
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Hi Paul!


Thanks a lot for your reply. A quick search for libxml2-dev revealed the output attached as a screenshot. It seems that it is there, but maybe it's been installed in a weird location?

I did my best to install *all* the dependencies by copy-pasting the following command from the CYCLUS webpage:

sudo apt-get install -y cmake make libboost-all-dev libxml2-dev libxml++2.6-dev \
libsqlite3-dev libhdf5-serial-dev libbz2-dev coinor-libcbc-dev coinor-libcoinutils-dev \
coinor-libosi-dev coinor-libclp-dev coinor-libcgl-dev libblas-dev liblapack-dev g++ \
libgoogle-perftools-dev python3-dev python3-tables python3-pandas python3-numpy python3-nose \
python3-jinja2 cython3

I had hoped this would install all the necessary packages/libraries.

I am not entirely sure what's the right way to specify the libxml2 install path to cmake, but doing:

cmake .. -DCMAKE_INSTALL_PREFIX=~/.local/ -DLIBXML2_DIR=/usr/include/libxml2

did not help.

Incidentally, I just stumbled upon this github issue posted about two years ago:
https://github.com/cyclus/cyclus/issues/1426
I was wondering if my issue has something to do with that.


Thank you all for your time and effort!


Best wishes,

Madalina




Von: 'Paul Wilson' via Cyclus Users <cyclus...@googlegroups.com>
Gesendet: Mittwoch, 9. Oktober 2019 16:26
Screenshot_libxml2-dev.png

Baptiste MOUGINOT (BaM)

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Oct 9, 2019, 12:00:35 PM10/9/19
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Hi Madalina, 

I tried to reproduced your issue with a fresh ubuntu 18.04 install, sadly I was not able to get the same issue that you have…

I get pretty much the same error message for Xml2:
-- Dependency Include Hints (DEPS_INCLUDE_HINTS): HINTS;/usr/include
-- Could NOT find LibXml2 (missing: LibXml2_DIR)
-- LibXML++ find package args: LibXml2;HINTS;/usr
-- Could NOT find LibXml2 (missing: LibXml2_DIR)

But it did not block the installation.

I was wondering where did you get you source from ? github ?
If not I would recommend you to remove you existing cyclus folder, and get the one directly from our main repo:
git clone https:github.com/cyclus/cyclus

And then try again the install.

If you already got the source from there, could you send the output of:
`git status` 

Thank you

Baptiste

To view this discussion on the web visit https://groups.google.com/d/msgid/cyclus-users/6146ddd5ef4e4e22acb1d6c6dfe194dd%40aices.rwth-aachen.de.
<Screenshot_libxml2-dev.png>

Wittel, Madalina

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Oct 9, 2019, 1:42:26 PM10/9/19
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Dear Baptiste, Dear All,


I have good news: indeed, getting the source from github worked.
I had originally downloaded the zipped source file from here and that did not work on my machine. Getting the latest version from github and simply doing 'python install.py' finally worked. I was also able to successfully test the installation with cyclus_unit_test.

I'll now proceed with installing Cycamore.

Thank you very much to all of you for your time and for your help!


Best wishes,

Madalina


Von: cyclus...@googlegroups.com <cyclus...@googlegroups.com> im Auftrag von Baptiste MOUGINOT (BaM) <mouginot...@gmail.com>
Gesendet: Mittwoch, 9. Oktober 2019 18:00
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