Error installing cyclus from source

[Daniel Wojtaszek]

I'm trying to install the latest cyclus from source but get an error when I execute python install.py --clean-build >install_log.txt.  I've attached the cmake log files, install_log.txt, and the terminal output.

Cheers.

Dan

[Jin whan Bae]

Hi, this is sort of a hacky way to do it, and I'm sure other better users will give you better answers,

but a way that I went around with that problem was to delete `prey` and `predator` in `cyclus/agents/CMakeLists.txt` (lines 8 and 9) and reinstall with --clean-build.

Also maybe you can create an issue on the Github so they can be fixed / deleted.

Let me know if that works!

Cheers,

[Daniel Wojtaszek]

Thanks!  That got me further along.  Now, I get an error that it can't find cram.c.  Looking at src/CMakeLists.txt, I see that it looks for cram.c in http://raw.githubusercontent.com/data/master/cram.c but when I paste the link into my browser it says that it's not found.

Cheers.

Dan

[Jin whan Bae]

I've never seen that before, from a cursory look, I think another hacky way around it would be to download (https://github.com/pyne/data/blob/master/cram.tar.gz), untar, and copy the file into your build directory.  Maybe you can create an issue on Github as well!

Let me know if that works,

Thanks

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[Baptiste MOUGINOT (BaM)]

Hi 

Sorry Dan I am traveling today. I'll try to take a look tonight (if I have time) or tomorrow.

Could you tell us what system you are using? (And which version) I'll try to investigate and reproduce the issue 

BaM 

from my phone

On Dec 12, 2019, at 08:48, Jin whan Bae <nucle...@gmail.com> wrote:



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[Daniel Wojtaszek]

No worries.  I'm installing on ubuntu 16.04 run by oracle virtualbox.

Cheers.

Dan

On Thursday, December 12, 2019 at 9:54:58 AM UTC-5, Baptiste MOUGINOT (BaM) wrote:

Hi 

Sorry Dan I am traveling today. I'll try to take a look tonight (if I have time) or tomorrow.

Could you tell us what system you are using? (And which version) I'll try to investigate and reproduce the issue 

BaM 

from my phone

On Dec 12, 2019, at 08:48, Jin whan Bae <nucle...@gmail.com> wrote:



I've never seen that before, from a cursory look, I think another hacky way around it would be to download (https://github.com/pyne/data/blob/master/cram.tar.gz), untar, and copy the file into your build directory.  Maybe you can create an issue on Github as well!

Let me know if that works,

Thanks

On Thu, Dec 12, 2019 at 9:38 AM Daniel Wojtaszek <daniel....@cnl.ca> wrote:

Thanks!  That got me further along.  Now, I get an error that it can't find cram.c.  Looking at src/CMakeLists.txt, I see that it looks for cram.c in http://raw.githubusercontent.com/data/master/cram.c but when I paste the link into my browser it says that it's not found.

Cheers.

Dan

On Thursday, December 12, 2019 at 9:01:17 AM UTC-5, Jin whan Bae wrote:

Hi, this is sort of a hacky way to do it, and I'm sure other better users will give you better answers,

but a way that I went around with that problem was to delete `prey` and `predator` in `cyclus/agents/CMakeLists.txt` (lines 8 and 9) and reinstall with --clean-build.

Also maybe you can create an issue on the Github so they can be fixed / deleted.

Let me know if that works!

Cheers,

On Thursday, December 12, 2019 at 8:45:33 AM UTC-5, Daniel Wojtaszek wrote:

I'm trying to install the latest cyclus from source but get an error when I execute python install.py --clean-build >install_log.txt.  I've attached the cmake log files, install_log.txt, and the terminal output.

Cheers.

Dan

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[Daniel Wojtaszek]

Thanks! That did it.  Some cylus unit tests failed due to removing the predator and prey archetypes.

I installed cycamore with no problems but the ReactorTests.ByProduct unit test failed with "Invalid table name ReactorSideProducts".  Is this a critical failure that I should fix?

Cheers. 

Dan

On Thursday, December 12, 2019 at 9:48:58 AM UTC-5, Jin whan Bae wrote:

I've never seen that before, from a cursory look, I think another hacky way around it would be to download (https://github.com/pyne/data/blob/master/cram.tar.gz), untar, and copy the file into your build directory.  Maybe you can create an issue on Github as well!

Let me know if that works,

Thanks

On Thu, Dec 12, 2019 at 9:38 AM Daniel Wojtaszek <daniel....@cnl.ca> wrote:

Thanks!  That got me further along.  Now, I get an error that it can't find cram.c.  Looking at src/CMakeLists.txt, I see that it looks for cram.c in http://raw.githubusercontent.com/data/master/cram.c but when I paste the link into my browser it says that it's not found.

Cheers.

Dan

On Thursday, December 12, 2019 at 9:01:17 AM UTC-5, Jin whan Bae wrote:

Hi, this is sort of a hacky way to do it, and I'm sure other better users will give you better answers,

but a way that I went around with that problem was to delete `prey` and `predator` in `cyclus/agents/CMakeLists.txt` (lines 8 and 9) and reinstall with --clean-build.

Also maybe you can create an issue on the Github so they can be fixed / deleted.

Let me know if that works!

Cheers,

On Thursday, December 12, 2019 at 8:45:33 AM UTC-5, Daniel Wojtaszek wrote:

I'm trying to install the latest cyclus from source but get an error when I execute python install.py --clean-build >install_log.txt.  I've attached the cmake log files, install_log.txt, and the terminal output.

Cheers.

Dan

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[Jin whan Bae]

Cool! I'm gald. That's odd that that unit test fails. Can you make an issue of it in Cycamore?

Thanks,

[Jin whan Bae]

And no, they are not critical. It's just recording something on the output database to simulate reactor generation of side products like hydrogen or water.

Let me know if you have any other questions.

Cheers,

[Paul Wilson]

Hi Dan,

It shouldn't look for that file in that location.  I don't see that in the output you provided.  How do you know it is looking there?  I do expect it to look for the tarball in the location that Jin pointed you to.

Paul

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[Baptiste MOUGINOT (BaM)]

Hi Dan,

I jsut saw that you rely on anaconda to install your dependencies….

I am wondering: 

Do you have an other use than cyclus for conda in your VM. if not I strongly suggest you drop conda and use apt-get ( and pip to get the last version of cython)

-> I was able on a fresh ubuntu 16.04 (on docker) to install cyclus smoothly…. (not install hack required.. ;) )

 

If you use anaconda for something else, it might come from the version of the package you are using… this might get trickier but I can definitely give it a try…

Otherwise I did not had an issue with the c=CRAM thing, my guess is either you VM had an issue with internet, or more likely gist was temporary down… and so you were not able to download it.

Let me know if you need me to try the anaconda install for dependencies (even if I don’t recommand it if you don’t ABSOLUTLY need conda to be installed for something else…)

Best,

Baptiste 

------------------------------------

Baptiste Mouginot, PhD

Assistant Scientist, Nuclear Engineering

University of Wisconsin-Madison

moug...@wisc.edu/mouginot...@gmail.com

+1 (608)-263-5646

To view this discussion on the web visit https://groups.google.com/d/msgid/cyclus-users/806e217f-d80b-f338-9533-3ee06b6d461f%40wisc.edu.

[Daniel Wojtaszek]

Hi Paul and Baptiste.

Here's the bit about looking for cram.c in the terminal output from the file I had attached:

CMake Error at src/CMakeLists.txt:215 (ADD_LIBRARY):
  Cannot find source file:
 

cram.c 

Anyway, Baptiste is correct that my VM is having internet issues, which is due to CNL's network blocking things so I've had to use some work-arounds to get things installed.  When I have more time I'll try removing anaconda and doing a fresh install from my home network.

Cheers.

On Thursday, December 12, 2019 at 6:16:04 PM UTC-5, paul.wilson wrote:

Hi Dan,

It shouldn't look for that file in that location.  I don't see that in the output you provided.  How do you know it is looking there?  I do expect it to look for the tarball in the location that Jin pointed you to.

Paul

On 12/12/19 08:38, Daniel Wojtaszek wrote:

Thanks!  That got me further along.  Now, I get an error that it can't find cram.c.  Looking at src/CMakeLists.txt, I see that it looks for cram.c in http://raw.githubusercontent.com/data/master/cram.c but when I paste the link into my browser it says that it's not found.

Cheers.

Dan

On Thursday, December 12, 2019 at 9:01:17 AM UTC-5, Jin whan Bae wrote:

Hi, this is sort of a hacky way to do it, and I'm sure other better users will give you better answers,

but a way that I went around with that problem was to delete `prey` and `predator` in `cyclus/agents/CMakeLists.txt` (lines 8 and 9) and reinstall with --clean-build.

Also maybe you can create an issue on the Github so they can be fixed / deleted.

Let me know if that works!

Cheers,

On Thursday, December 12, 2019 at 8:45:33 AM UTC-5, Daniel Wojtaszek wrote:

I'm trying to install the latest cyclus from source but get an error when I execute python install.py --clean-build >install_log.txt.  I've attached the cmake log files, install_log.txt, and the terminal output.

Cheers.

Dan

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[Paul Wilson]

Hi Dan,

The installation process does a few things to implement this CRAM capability.  The `cram.c` file is auto-generated by a python script as it hard codes all the symbolic math to achieve a high-performance implementation of the CRAM methodology for decay.  The `cram.c` file is quite large but, more importantly, takes a very long time to compile.  Therefore, we also distribute a `cram.s` file that is an intermediate product of the compilation process.  This file is platform dependent, and itself quite large, and distributed in a .tar.gz tarball.

If your installation can't find `cram.s`, it will try to download the tarball, and if that fails for some reason (e.g. network trouble), it will look for the `cram.c` to embark on the slow compilation process.

Thus, the error that you can't find this file could be caused by a variety of things and it require a little more engagement to get to the root cause.

I've tried to provide a modest amount of detail here, because I'm not sure how many details you want to know, but let me know if you have additional questions.

Regards,

Paul

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