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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 kill worked, no kill -9 necessary).

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:

• I was using Sage on Linux
• This function uses MixedIntegerLinearProgram. I used the default GLPK (didn't change settings)
• I used alarm() to set a time limit on each computation.
• I always believed GLPK not to be interruptible, so I am not even sure which interruption (either manual or alarm) work on Sage with this function. This may be relevant.
• The memory usage of the process stayed low. It did not stall because the memory got filled and the machine started swapping.

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 kill worked, no kill -9 necessary).

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:

• I was using Sage on Linux
• This function uses MixedIntegerLinearProgram. I used the default GLPK (didn't change settings)
• I used alarm() to set a time limit on each computation.
• I always believed GLPK not to be interruptible, so I am not even sure which interruption (either manual or alarm) work on Sage with this function. This may be relevant.
• The memory usage of the process stayed low. It did not stall because the memory got filled and the machine started swapping.

import datetime
i=1
while True:
    alarm(60)
    try:    
        dg=digraphs.RandomDirectedGNM(300,750);
        fes = dg.feedback_edge_set()
        print(len(fes))
    except AlarmInterrupt:
        print("timeout")
    cancel_alarm()
    print(i)
    print(str(datetime.datetime.now()))
    print("\n")
    i = i+1

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 kill worked, no kill -9 necessary).

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:

• I was using Sage on Linux
• This function uses MixedIntegerLinearProgram. I used the default GLPK (didn't change settings)
• I used alarm() to set a time limit on each computation.
• I always believed GLPK not to be interruptible, so I am not even sure which interruption (either manual or alarm) work on Sage with this function. This may be relevant.
• The memory usage of the process stayed low. It did not stall because the memory got filled and the machine started swapping.

Minimal example:

Put this in a source file:

import datetime
i=1
while True:
    alarm(60)
    try:    
        dg=digraphs.RandomDirectedGNM(300,750);
        fes = dg.feedback_edge_set()
        print(len(fes))
    except AlarmInterrupt:
        print("timeout")
    cancel_alarm()
    print(i)
    print(str(datetime.datetime.now()))
    print("\n")
    i = i+1

Run it as sage sourcefile.sage.

In my last test test, it took 291 iterations and ~4-5 hours before it stalled.

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 kill worked, no kill -9 necessary).

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:

• I was using Sage on Linux
• This function uses MixedIntegerLinearProgram. I used the default GLPK (didn't change settings)
• I used alarm() to set a time limit on each computation.
• I always believed GLPK not to be interruptible, so I am not even sure which interruption (either manual or alarm) work on Sage with this function. This may be relevant.
• The memory usage of the process stayed low. It did not stall because the memory got filled and the machine started swapping.

Minimal example:

Put this in a source file:

import datetime
i=1
while True:
    alarm(60)
    try:    
        dg=digraphs.RandomDirectedGNM(300,750);
        fes = dg.feedback_edge_set()
        print(len(fes))
    except AlarmInterrupt:
        print("timeout")
    cancel_alarm()
    print(i)
    print(str(datetime.datetime.now()))
    print("\n")
    i = i+1

Run it as sage sourcefile.sage.

In my last test, it took 291 iterations and ~4-5 hours before it stalled.

It appears to stall only when GLPK is used as the MIP solver (i.e. feedback_edge_set(solver='GLPK'), which is also the default). If I use solver='Coin' (which needs to be installed first using sage -i cbc) then it does not stall. However, the calculation is several times slower with Coin than with GLPK.