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20200506 20:31:09 +0200  commented answer  SSL error using sage pip install to download a package It would have been useful to warn that 
20191022 11:29:13 +0200  commented answer  Sage stalls during computation That I cannot run this specific piece of code right now (no spare machine capacity to run for a day), but it should work. It is closely based on what I used these last few days for my actual work. 
20191022 11:28:48 +0200  commented answer  Sage stalls during computation Nonworking alarm code is in the original post. That GLPK is being used: this is based on timings, code is in the comments above. You could not reproduce it. I could reproduce it on two different computers. I would suggest: (1) try on a different instance (2) verify how many CPU cores are in use when you benchmark (GLPK: always one; Coin: possibly multiple) 
20191021 15:53:24 +0200  commented answer  Sage stalls during computation @tmonteil Thanks for all the help! I do keep checking back here and I am still interested in understanding what is happening. 
20191021 13:37:50 +0200  answered a question  Sage stalls during computation This looks like a bug in Sage or Sage's GLPK interface. The practical solution that worked for me was to run the calculation in a separate process using Sage's parallelization features. It can be done by wrapping the feedback arc set calculation with a few function that has the I can confirm that even after a severalday running time, the calculation has not stalled. 
20191018 10:31:07 +0200  commented question  Sage GUI on Mac when building from source @dsejas No, I am referring to the Sage GUI available on macOS, not specific notebook formats. 
20191017 13:38:22 +0200  commented answer  Sage stalls during computation @tmonteil I finally managed to compile Sage on a Mac, and compared Coin and GLPK again. Based on the timings, it still looks like Since you seem to be involved with Sage, can you file an issue for this (solver=None should not be GLPK) if you think it is appropriate to do so? 
20191017 12:42:39 +0200  asked a question  Sage GUI on Mac when building from source I normally use the official (precompiled) app version of Sage on macOS. When I start the app, it adds a new dropdown menu to the menu bar. Now I switched to building Sage from source, as this gives access to features I could not otherwise have (e.g. install Coin MIP solver with 
20191017 11:40:21 +0200  asked a question  Printing from parallel processes I am trying to use Sage's parallelization with If I use The "Starting" and the "Finished" messages show up simultaneously, even though they are issued with a 5 second time difference. How can I print a message so that it will show up immediately? I need this when I am running a Sage script in a terminal. I am not using Sage interactively in this case and I am not using the notebook interface. 
20191017 11:04:21 +0200  commented answer  Sage stalls during computation @tmonteil I think I figured it out how to get this done with 
20191017 10:19:31 +0200  commented answer  Sage stalls during computation @tmonteil Are you aware of any feasible workarounds to this stalling? I am trying to understand how parallelization works in Sage. It appears that it will spawn subprocesses which can be killed after a time limit. I am trying to find out if I can run each computation in a new process this way, and kill the process after the time limit (instead of using 
20191016 09:05:55 +0200  commented answer  Sage stalls during computation @tomteil 2692 iterations, well over a day, and still going. We can safely say that with Coin it does not stall. However, using Coin would be a significant stepdown because its worse performance. I am still puzzled about why there is no performance difference on your computer. 
20191014 21:36:23 +0200  commented answer  Sage stalls during computation @tmonteil Wow, that's weird! Do you have any idea what could explain this difference? I verified that only a single CPU core is in use with both. I am using Sage 8.9, built from source without changing any options. The solutions that both GLPK and Coin return seem to be the same ones that you quote. I also tried the calculation with GLPK on a Mac laptop (where I have not yet managed to install CBC), and it took 20 seconds, which is consistent with the 27 s timing I got on the Linux machine. Why would it be taking a full minute on your computer? P.S. It does not look like it's going to stall with Coin, but let me keep it running for 24 hrs to be sure. 
20191014 17:53:59 +0200  commented answer  Sage stalls during computation @tomteil It's running, I'll let you know. In the meantime, could you please try if 
20191014 13:05:00 +0200  commented answer  Sage stalls during computation @tmonteil You are right that the code of 
20191014 12:56:52 +0200  commented answer  Sage stalls during computation 
20191014 12:52:29 +0200  commented answer  Sage stalls during computation @david Yes, I am sure. If I run 
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20191013 11:59:34 +0200  commented question  Sage stalls during computation @tmonteil It's not because of a specific graph. The stalling appears to be random. I know this because I normally run this on a set of precomputed graphs, so I could easily retry on the graph where it stalled. Also, running it twice on the same data won't stall at the same step. 
20191012 20:04:00 +0200  commented answer  Sage stalls during computation @tmonteil I added a minimal example. Can you try to reproduce the problem? 
20191012 20:03:32 +0200  edited question  Sage stalls during computation I was using SageMath 8.8's feedback_edge_set function on a large dataset. The calculation would take a couple of days to finish. Unfortunately, Sage would keep stalling every few hours. The CPU usage of the process would simply drop to zero, and it would stop doing anything. I had to kill the process (a simple Has anyone else experienced this? Is it a known problem? Is there a workaround? It is very frustrating to have to keep manually killing and restarting the process. This problem also prevents me from running a calculation overnight: in the morning I might find that it stopped merely an hour after I started it (if I'm unlucky). More information:
Minimal example: Put this in a source file: Run it as In my last test, it took 291 iterations and ~45 hours before it stalled. It appears to stall only when GLPK is used as the MIP solver (i.e. 
20191011 20:18:18 +0200  commented answer  Sage stalls during computation Some comments on 
20191011 20:07:27 +0200  commented answer  Sage stalls during computation Sure—I'll get back to you when I have a small example that reliably fails. It'll take time as it usually takes hours for it to fail. 
20191011 19:57:21 +0200  commented answer  Building Sage 8.9 from source fails I asked libreadlinedev, libncurses5dev and libncursesw5dev to be installed on this computer. Now Sage 8.9 compiles successfully. libreadlinedev alone was not sufficient. I did this based on the linked Google Groups thread before Dima posted here. 
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20191011 17:57:00 +0200  commented answer  Building Sage 8.9 from source fails Checking the log file more carefully revealed this line:

20191011 17:48:57 +0200  commented answer  Building Sage 8.9 from source fails It fails with the same message. The output of

20191011 17:37:57 +0200  commented answer  Building Sage 8.9 from source fails

20191011 13:06:28 +0200  asked a question  Building Sage 8.9 from source fails I am trying to build Sage 8.9 from source on Linux (Ubuntu 16.04, gcc 6). It fails. I could build Sage 8.8 on the same machine without problems. It says that python2 and python3 failed to build, and suggests to look at the log files. The log files contain: and Has anyone experienced the same and is there a simple solution? Unfortunately, I do not have root access myself, thus I can't quickly try to install the readline dev package. 
20191011 11:00:38 +0200  commented answer  Sage stalls during computation It is not that trivial to boil down the code to a minimal example. If I put in the work to do that, would you be willing to try to reproduce the problem? Trying to reproduce would also be some trouble: It would involve leaving Sage running for up to a day (or running multiple Sage processes for several hours to increase the likelihood that one of them would stall). 