blosc @ 1.14.4: build fails due to undefined symbols on OS X Leopard PPC

[SerpentChris (Chris Calderon)]

Build seems to go fine until it gets here:

:info:build /usr/bin/gcc-4.2 -pipe -Os -DNDEBUG -I/opt/local/include -arch ppc -mmacosx-version-min=10.5 -Wl,-search_paths_first -Wl,-headerpad_max_install_names -L/opt/local/lib -Wl,-headerpad_max_install_names CMakeFiles/bench.dir/bench.c.o  -o bench -Wl,-rpath,/opt/local/lib ../blosc/libblosc.1.14.4.dylib /opt/local/lib/liblz4.dylib /opt/local/lib/libz.dylib /opt/local/lib/libzstd.dylib 
:info:build Undefined symbols:
:info:build   "_posix_memalign", referenced from:
:info:build       _do_bench in bench.c.o
:info:build       _do_bench in bench.c.o
:info:build       _do_bench in bench.c.o
:info:build ld: symbol(s) not found
:info:build collect2: ld returned 1 exit status
:info:build make[2]: *** [bench/bench] Error 1

[kencu (Ken)]

yep, there is no posix_memalign on 10.5. I've been thinking of adding it to the macports-legacy port, and in fact I have written up the replacement already, but it didn't always seem to work as I wanted it to, so I'm still sitting on it for now.

Is this a port you really want on 10.5 PPC? You can use valloc instead, to get a block of memory aligned on a page boundary.

It would take a minor patch to the source to make it use valloc instead of posix_memalign, but it's a fairly trivial fix.

[kencu (Ken)]

I put together a little patch for this. You can check this out here if you want <​https://github.com/kencu/LeopardPorts/tree/master/archivers/blosc>. If it works for you as well, we can put together a PR for it.

[SerpentChris (Chris Calderon)]

Your patch doesn't check the alignment argument the way it is supposed to. Shouldn't a posix_memalign look more like this?

#include <stdlib.h>
#include <errno.h>

const size_t _SIZE_OF_VOID_PTR = sizeof(void *);

bool
check_power_of_two(int val)
{
  while(val&1 == 0){
    val >>= 1;
  }
  return (val == 1);
}

int
posix_memalign(void **memptr, size_t alignment, size_t size)
{
  // First check alignment
  div_t result = divmod(alignment, _SIZE_OF_VOID_PTR);
  if(!(result.rem == 0 && check_power_of_two(result.quot))){
    *memptr = NULL;
    return EINVAL;
  }
  // Do nothing if size is 0
  if(size == 0){
    *memptr = NULL;
    return 0;
  }

  errno = 0;
  *memptr = valloc(size);
  // If valloc errors, it will set errno to ENOMEM.
  // Folks online don't like posix_memalign to set errno though.
  // Also, if valloc errors it will return NULL which is OK.
  if(errno == ENOMEM){
    errno = 0;
    return ENOMEM;
  }

  return 0;
}

The problem with this (besides the fact that I haven't tested it yet ;) is that the result might not be aligned properly if the alignment is greater than the page size, but I bet that is typically not the case anyway.

[SerpentChris (Chris Calderon)]

Oh, and the reason I want blosc on Leopard is to install py37-pandas. I'm trying to get a fully modern scipy config running so I can help family members with college homework.

[kencu (Ken)]

you're right, I skipped an alignment check.

I like your extra bits. I think we can massage a bit more and find a way to find something acceptible. If alignment is <= 16 we can just use malloc, as macos guarantees 16 byte alignment at all times. That will likely save a few K of memory.

There is a very complete replacement available called dlmalloc <​ftp://g.oswego.edu/pub/misc/malloc.c> with a very liberal license. I wasn't clear how to make it only cough up posix_memalign without all the other memory functions trampling us. I was looking at that one if we could use it.

For blosc, it turns out the author has previously supported macs < 10.6 in the code; he's just recently added a new benchmark.c that doesn't . You can skip the build of benchmark.c by turning off tests. Then you have what we had before. My PR does that. So you can use that right now if you want...

btw blosc with or without the posix_memalign patch will pass nearly all tests -- high 90s -- and i suspect it always did not get 100% on 10.5 PPC as the tested part of the code has not changed.

If you have interest, please consider helping add to the macports_legacy project to help keep your PPC mac alive!

[kencu (Ken)]

In 591337f116ff9ae2ae20fab954605b943fcf7c30/macports-ports (master):

blosc: disable tests and benchmarks

not installed anyway
don't easily work
newer benchmarks use posix_memalign which fails on
some older systems

closes: #57630