Too many heap sections: Increase MAXHINCR or MAX_HEAP_SECTS macaulay

[kutschan]

I'm having the "Too many heap sections: Increase MAXHINCR or MAX_HEAP_SECTS macaulay"-problem, when calculating a Gröbner basis with Macaulay2.

The program fills up all 8GB of RAM and then only a little fraction of my swap space before prompting this error and exiting. I tried setting "export MAX_HEAP_SECTS=1000000000000" just before running ./M2 which didn't help.

I have the 64 bit version from github compiled on a 64 bit Ubuntu.

How exactly can I increase MAX_HEAP_SECTS?

[mikestillman]

The problem is that if you are using the Boehm garbage collector that comes with your packaging system (the default for many systems), it often is compiled for small memory use.

Here is one relevant environment variable for controlling the garbage collector:

GC_INITIAL_HEAP_SIZE=<bytes> -  Initial heap size in bytes.  May speed up
                                process start-up.  Optionally, may be
                                specified with a multiplier ('k', 'M' or 'G')
                                suffix.

For example, try running (in bash, or in emacs, by using meta-f12 to reset the M2 command line):

GC_INITIAL_HEAP_SIZE=8G M2

or, as you suggest:

export GC_INITIAL_HEAP_SIZE=8G
M2

I had a similar problem where I hit the same issue (even compiled with large memory use), which I think gives the error message you obtained at about 130 GB, so I set this environment variable to 300G, and M2 then ran to completion (the machine had 512 GB of RAM, and ended up using most of it)

— mike

[DanGrayson]

You may also see some settings this way:

i30 : GCstats()

o30 = HashTable{don't expand => false           }
                finalize on demand => false
                full freq => 19
                GC_ALL_INTERIOR_POINTERS => 
                GC_all_interior_pointers => 1
                GC_BACKTRACES => 
                GC_DISABLE_INCREMENTAL => 
                GC_DONT_GC => 
                GC_DUMP_REGULARLY => 
                GC_ENABLE_INCREMENTAL => 
                GC_FIND_LEAK => 
                GC_FORCE_UNMAP_ON_GCOLLECT => 
                GC_FREE_SPACE_DIVISOR => 
                GC_free_space_divisor => 12
                GC_FULL_FREQUENCY => 
                GC_IGNORE_GCJ_INFO => 
                GC_INITIAL_HEAP_SIZE => 
                GC_LARGE_ALLOC_WARN_INTERVAL => 
                GC_LOG_FILE => 
                GC_LOOP_ON_ABORT => 
                GC_MARKERS => 
                GC_MAXIMUM_HEAP_SIZE => 
                GC_NO_BLACKLIST_WARNING => 
                GC_NPROCS => 
                GC_PAUSE_TIME_TARGET => 
                GC_PRINT_ADDRESS_MAP => 
                GC_PRINT_BACK_HEIGHT => 
                GC_PRINT_STATS => 
                GC_PRINT_VERBOSE_STATS => 
                GC_RETRY_SIGNALS, => 
                GC_TRACE => 
                GC_UNMAP_THRESHOLD => 
                GC_USE_GETWRITEWATCH => 
                heap size => 449941504
                java finalization => true
                max retries => 0
                number of collections => 31
                parallel => true
                time limit => 999999

o30 : HashTable

[kutschan]

This solution works.

With
export GC_INITIAL_HEAP_SIZE=50G
M2

it now writes to my swap space which is about 50G after having filled up all RAM.

Thank you!

[imanbj]

Dear All,

the code "export GC_INITIAL_HEAP_SIZE=50G" works for me too. But it just works in terminal, not in Aquamacs. Any suggestion?

Best wishes,
Iman.

[mikestillman]

Here is one way that should solve this problem: In emacs, if you hit: control-u, followed by f12, you get to change the command line for M2. Change the line to look something like this: GC_INITIAL_HEAP_SIZE=50G M2 (Followed by the commands line options for M2 that it is using). Best regards, Mike

…

On Jan 17, 2018, at 10:43 AM, Iman Bahmani ***@***.***> wrote: Dear All, the code "export GC_INITIAL_HEAP_SIZE=50G" works for me too. But it just works in terminal, not in Aquamacs. Any suggestion? Best wishes, Iman. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#500 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAGPR9OlphDltTjBWSEezQ2TtV6MiuFuks5tLhUkgaJpZM4JQv0Y>.