[sage-devel] Re: libm4ri issues with non-GNU/x86 environments.

2009-10-27 Thread Martin Albrecht

Hi David,

I am working through my todo list and thus revisited this thread. Right now, I 
am not sure what I can do to help you to fix the problems you identified (due 
to lack of knowledge about  the platforms in question) On the other hand, I am 
very interested in making M4RI truly cross-platform. 

I guess what I am saying is: if there is anything I should do to fix this, let 
me know and I will take a look.

Cheers,
Martin


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[sage-devel] Re: libm4ri issues with non-GNU/x86 environments.

2009-10-27 Thread Dr David Kirkby

On Oct 27, 11:34 am, Martin Albrecht m...@informatik.uni-bremen.de
wrote:
 Hi David,

 I am working through my todo list and thus revisited this thread. Right now, I
 am not sure what I can do to help you to fix the problems you identified (due
 to lack of knowledge about  the platforms in question) On the other hand, I am
 very interested in making M4RI truly cross-platform.

 I guess what I am saying is: if there is anything I should do to fix this, let
 me know and I will take a look.

 Cheers,
 Martin

I think the test for cach size and number of CPUs should be removed
from the configure script, for several reasons.

 From what I can gather from the autoconf list

* Both macros, which you took from the auotconf macro archive, are
badly written - not just in what they do, but in a very general
sence.

* Both will never work on non-x86 platforms.

* I'm told from the autoconf developers that those macros will not
even work properly on many x86 processors. I asume this is mainly the
one for cache size, which relies on looking up the processor type in a
list of processors. As new processors are introduced, that is going to
be less and less useful.

* Whilst I accept that most people build Sage to run on their own
machines, not everyone does. Hence deterining this at compile-time is
not the best place to do it.

Instead the tests should be move to run-time. From what I gather from
one of the autoconf developers, the 4MRI library uses OpenMP. There is
code in OpenMP which can determine the number of processors at run-
time. I've not looked at this in any detail, but a quick glace on an
OpenMP tutorial

https://computing.llnl.gov/tutorials/openMP/#OMP_SET_NUM_THREADS

shows things like:
**
#include omp.h
int omp_get_num_procs(void)

Returns the number of processors that are available to the program.

**

I suspect the cache size will be more difficult to obtain, but
findining cache size is the sort of task that computer science
students do to find out the characteristics of the processors they are
running on. Ultimatey, some run-time test is probably best. I do not
know the details, but I can imagine that reading/writing randomlly to
an array would slow dramatically once the size of the array exceeds
the cache size.

Either way, I would give the user the option to override an
automatically determined value. In particular, you might want to
consider limiting the number of processors used by default to some
number such as 8. I made this point some time back, about a patch
commited to Sage, which was later changed. My point is that if a
machine has more than 8 CPUs, it is highly likely to be a shared
system, and an individual should not be putting such a heavy load on
the machine. Instead, limit the number of procesors used to 8, but
give a user an option to set it to any number they want.

If you can get some code together I can certainly try it on a number
of multi-processor machines I have access to. I can give you access to
the HP C3600 running HP-UX 11.11. But ultimatley, to make this cross
platform, any lookup of processor types is going to be a nightmare as
new CPUs are introduced.


Dave






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[sage-devel] Re: libm4ri issues with non-GNU/x86 environments.

2009-10-27 Thread Martin Albrecht

 I think the test for cach size and number of CPUs should be removed
 from the configure script, for several reasons.

  From what I can gather from the autoconf list
 
 * Both macros, which you took from the auotconf macro archive, are
 badly written - not just in what they do, but in a very general
 sence.
 
 * Both will never work on non-x86 platforms.
 
 * I'm told from the autoconf developers that those macros will not
 even work properly on many x86 processors. I asume this is mainly the
 one for cache size, which relies on looking up the processor type in a
 list of processors. As new processors are introduced, that is going to
 be less and less useful.
 
 * Whilst I accept that most people build Sage to run on their own
 machines, not everyone does. Hence deterining this at compile-time is
 not the best place to do it.
 
 Instead the tests should be move to run-time. From what I gather from
 one of the autoconf developers, the 4MRI library uses OpenMP. There is
 code in OpenMP which can determine the number of processors at run-
 time. I've not looked at this in any detail, but a quick glace on an
 OpenMP tutorial
 
 https://computing.llnl.gov/tutorials/openMP/#OMP_SET_NUM_THREADS
 
 shows things like:
 ***
 *** #include omp.h
 int omp_get_num_procs(void)
 
 Returns the number of processors that are available to the program.
 
 ***
 ***
 
 I suspect the cache size will be more difficult to obtain, but
 findining cache size is the sort of task that computer science
 students do to find out the characteristics of the processors they are
 running on. Ultimatey, some run-time test is probably best. I do not
 know the details, but I can imagine that reading/writing randomlly to
 an array would slow dramatically once the size of the array exceeds
 the cache size.
 
 Either way, I would give the user the option to override an
 automatically determined value. In particular, you might want to
 consider limiting the number of processors used by default to some
 number such as 8. I made this point some time back, about a patch
 commited to Sage, which was later changed. My point is that if a
 machine has more than 8 CPUs, it is highly likely to be a shared
 system, and an individual should not be putting such a heavy load on
 the machine. Instead, limit the number of procesors used to 8, but
 give a user an option to set it to any number they want.
 
 If you can get some code together I can certainly try it on a number
 of multi-processor machines I have access to. I can give you access to
 the HP C3600 running HP-UX 11.11. But ultimatley, to make this cross
 platform, any lookup of processor types is going to be a nightmare as
 new CPUs are introduced.

I tend to agree with your point when it comes to the number of CPUs, that 
probably should be run-time instead of compile time. Btw. I just checked, this 
information isn't even used!

This is now:

http://bitbucket.org/malb/m4ri/issue/16/remove-check-for-number-of-cpus-from-
autoconf

Wrt the cache size I am not convinced. I see the problems you point out, but 
having the values as compile time constants should be make a difference, I 
should double check this though. Also, running this check on every library 
load seems like overkill to me.

I will implement something dynamic which can be used at compile time instead 
of the hardcoded checks which we use right now.

http://bitbucket.org/malb/m4ri/issue/17/implement-dynamic-run-time-check-for-
l1-and-l2-cache

Cheers,
Martin

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[sage-devel] Re: libm4ri issues with non-GNU/x86 environments.

2009-10-27 Thread David Kirkby

2009/10/27 Martin Albrecht m...@informatik.uni-bremen.de:

 I tend to agree with your point when it comes to the number of CPUs, that
 probably should be run-time instead of compile time. Btw. I just checked, this
 information isn't even used!

 This is now:

 http://bitbucket.org/malb/m4ri/issue/16/remove-check-for-number-of-cpus-from-
 autoconf

Someone on the autoconf mailing list pointed out you did not actually
use the number!

But it looks as though getting the number of CPUs at runtime will be
easy and will actually work. The autoconf does not work on my Solaris
(SPARC processors ) or my HP-UX (PA-RISC processor).

 Wrt the cache size I am not convinced. I see the problems you point out, but
 having the values as compile time constants should be make a difference, I
 should double check this though. Also, running this check on every library
 load seems like overkill to me.

Agreed.

Perhaps it is possible to compile a library 4 times - say for 1, 2, 4
and 8 MB caches, then select the right one at run-time.

An attempt to determine processor type will always be difficult, as
new processors keep coming out.

 I will implement something dynamic which can be used at compile time instead
 of the hardcoded checks which we use right now.

 http://bitbucket.org/malb/m4ri/issue/17/implement-dynamic-run-time-check-for-
 l1-and-l2-cache

 Cheers,
 Martin

Let me know when you have something. I'll give it a try on my SPARCs
(single, dual and quad processor, and my OpenSolaris Xeon box (quad
core, 8 threads).

Dave

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[sage-devel] Re: libm4ri issues with non-GNU/x86 environments.

2009-10-14 Thread Martin Albrecht

On Wednesday 14 October 2009, Dr. David Kirkby wrote:
 libm4ri has two issues that I am aware of as soon as one tries to use a
 non-GNU or non-86 environment.
 
 
 I believe the developers hang out here, so I'll put a bit of information
 here, on the hope they see it.
 
 1) Despite the fact Sun's C compiler can compile thousands of lines of
 Sage without any problem, libm4ri's configure script says the compiler
 can't create executables:
 
 http://sagetrac.org/sage_trac/ticket/7037
 
 This is clearly is a bug that needs fixing. Plenty of other configure
 scripts have checked the compiler and decides it works.

I am the maintainer of this package and I am interested in fixing this. 
However, since I think the configure.in is quite standard I am not sure how.

 2) On HP-UX, the configure script can't work out how many CPUs I have,
 what sort they are, but then tries to determine the cache size. This
 causes the configure script to break.
 
 The macro for determining the number of CPUs
 
 http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m
 4/ax_count_cpus.m4
 
 is clearly only designed to work on linux and Mac. So it will fail on
 other platforms, including Solaris which is supported, and HP-UX which
 is not.

It should fail gracefully, doesn't it?
 
 The macro for determining cache sizes will only work on x86 CPUs.

It should fail gracefully?

 It seems to me there are two issues here.
 
 1) The code for checking the C compiler is broken.
 
 2) Code for checking CPU-related things should only be done on platforms
 where the macros work. It would clearly be very difficult to rewrite the
 macros to work on every platform, but it should not be so hard to ensure
 the macros are only called on platforms where they will work. One way to
 do this would probably be to executed bits of code only if certain
 preprocessor items are defined. I believe there is an autoconf macro
 which will determine if for example __hpux__ is defined, in which case
 execute code for HP-UX.
 
 
 I don't mind having a go at refining the macro for computing the number
 of CPUs, so it at least work on Solaris, AIX and HP-UX.

Great, that would be very much appreciated!

 Cache sizes is not something I want to get into. I think it would be
 sensible to just report 1 MB or something like that.

We fix  default values but only later in the code. We could report default 
values in configure as well.

Cheers,
Martin

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[sage-devel] Re: libm4ri issues with non-GNU/x86 environments.

2009-10-14 Thread Dr. David Kirkby

Martin Albrecht wrote:
 On Wednesday 14 October 2009, Dr. David Kirkby wrote:
 libm4ri has two issues that I am aware of as soon as one tries to use a
 non-GNU or non-86 environment.


 I believe the developers hang out here, so I'll put a bit of information
 here, on the hope they see it.

 1) Despite the fact Sun's C compiler can compile thousands of lines of
 Sage without any problem, libm4ri's configure script says the compiler
 can't create executables:

 http://sagetrac.org/sage_trac/ticket/7037

 This is clearly is a bug that needs fixing. Plenty of other configure
 scripts have checked the compiler and decides it works.
 
 I am the maintainer of this package and I am interested in fixing this. 
 However, since I think the configure.in is quite standard I am not sure how.


I'll take a look. libm4ri is to my knowledge the only program which 
thinks the Sun compiler is broken.

 2) On HP-UX, the configure script can't work out how many CPUs I have,
 what sort they are, but then tries to determine the cache size. This
 causes the configure script to break.

 The macro for determining the number of CPUs

 http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m
 4/ax_count_cpus.m4

 is clearly only designed to work on linux and Mac. So it will fail on
 other platforms, including Solaris which is supported, and HP-UX which
 is not.
 
 It should fail gracefully, doesn't it?


The configure script does fail gracefully on HP-UX when it tries to 
determine the number of CPUs.

checking the number of available CPUs... unable to detect (assuming 1)
checking the number of available CPUs... unable to detect (assuming 1)

It should not take too much effort to actually get a number, so it does 
not have to assume 1.

There is a question about what do you want - is it physical processors, 
cores or hardware threads? I'm not really sure the best way to do this. 
On the Sun T5240 (t2.math), there are two physical processors, 16 cores 
and 128 threads. So what number do we want - 2, 16 or 128?  I suspect 
cores is the most useful one, to have, but I'm not sure how to get that 
information.


 The macro for determining cache sizes will only work on x86 CPUs.
 
 It should fail gracefully?

I agree it should fail gracefully, but it does not on HP-UX 11.11, as it 
appears to be multiplying 'unknown' by 1024. This machine does have 1 CPU.

checking the number of available CPUs... unable to detect (assuming 1)
checking the number of available CPUs... unable to detect (assuming 1)
checking for x86 cpuid 0x0 output... unknown
checking for the processor vendor... Unknown
checking the L1 cache size... ./configure[12992]: unknown*1024: The 
specified number is not valid for this command.
Make: No arguments or description file.  Stop.
Error building libm4ri

real0m18.971s
user0m10.570s
sys 0m5.790s
sage: An error occurred while installing libm4ri-20090617

On a dual processor machine running Solaris 10, the data is not gathered 
properly, but at least it does not exit.

checking the number of available CPUs... unable to detect (assuming 1)
checking the number of available CPUs... unable to detect (assuming 1)
checking for x86 cpuid 0x0 output... unknown
checking for the processor vendor... Unknown
checking the L1 cache size... 0 Bytes
checking the L2 cache size... 0 Bytes

Why it should fail on HP-UX but not on Solaris I do not know. But the 
failure on HP-UX has highlighted the fact the code only works on x86, so 
we can address that.

 I don't mind having a go at refining the macro for computing the number
 of CPUs, so it at least work on Solaris, AIX and HP-UX.
 
 Great, that would be very much appreciated!

Leave that bit with me.

I've just asked on relevant newsgroups on how to get the data on AIX and 
HP-UX. Solaris I know anyway. Once I get that, I'll do it.

I would add there is some pretty negative comments about that macro for 
determining the number of CPUs in the autoconf macro archive. Clearly it 
is badly written. I think the way to approach it will be me re-write it, 
then get some of the experts there to go over it.

Dave

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[sage-devel] Re: libm4ri issues with non-GNU/x86 environments.

2009-10-14 Thread Martin Albrecht

  2) On HP-UX, the configure script can't work out how many CPUs I have,
  what sort they are, but then tries to determine the cache size. This
  causes the configure script to break.
 
  The macro for determining the number of CPUs
 
  http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;
 f=m 4/ax_count_cpus.m4
 
  is clearly only designed to work on linux and Mac. So it will fail on
  other platforms, including Solaris which is supported, and HP-UX which
  is not.
 
  It should fail gracefully, doesn't it?
 
 The configure script does fail gracefully on HP-UX when it tries to
 determine the number of CPUs.
 
 checking the number of available CPUs... unable to detect (assuming 1)
 checking the number of available CPUs... unable to detect (assuming 1)
 
 It should not take too much effort to actually get a number, so it does
 not have to assume 1.
 
 There is a question about what do you want - is it physical processors,
 cores or hardware threads? I'm not really sure the best way to do this.
 On the Sun T5240 (t2.math), there are two physical processors, 16 cores
 and 128 threads. So what number do we want - 2, 16 or 128?  I suspect
 cores is the most useful one, to have, but I'm not sure how to get that
 information.

I agree cores should be the most useful one for now. Basically, whatever has 
L1 cache should be returned. Its all about cache for M4RI.

 I would add there is some pretty negative comments about that macro for
 determining the number of CPUs in the autoconf macro archive. Clearly it
 is badly written. I think the way to approach it will be me re-write it,
 then get some of the experts there to go over it.

I agree it is not a nice script, I just lack the proper autotools skills to 
make it really nice. Maybe those experts will help :)

Cheers,
Martin

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[sage-devel] Re: libm4ri thinks the Sun C compiler is broken

2009-09-27 Thread Dr. David Kirkby

Dr. David Kirkby wrote:
 Using
 
  * Solaris 10 update 7 on SPARC
  * sage-4.1.2.alpha2
  * Sun Studio 12.1
  * An updated configure script to allow the Sun compiler to be used 
 http://sagetrac.org/sage_trac/ticket/7021
 
 CC was set to the Sun C compiler. Despite thousands of lines of C code 
 being built, libm4ri decides the Sun C compiler is broken:
 
 checking for style of include used by make... GNU
 checking for gcc... /opt/xxxsunstudio12.1/bin/cc
 checking for C compiler default output file name...
 configure: error: in 
 `/export/home/drkirkby/sage/gcc32/sage-4.1.2.alpha2/spkg/build/libm4ri-20090617/src':
 configure: error: C compiler cannot create executables
 See `config.log' for more details.
 Error configuring libm4ri

I forgot to add, this is

http://sagetrac.org/sage_trac/ticket/7037



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[sage-devel] Re: libm4ri

2008-12-02 Thread Martin Albrecht

 I plan to upgrade png in 3.2.2 and will also attempt to do the upgrade
 to fplll 3.0.x. I guess if malb is ok with the rename we could also
 change the name next time he releases an updated version.

I named it libm4ri because this naming scheme is consistent with what Debian 
does (usually these naming conventions are somewhat consistent across Linux 
distributions). I do agree that the inconsistency should be fixed, e.g. we 
have ntl...spkg but libm4ri...spkg. 

I would vote for renaming every C/C++ library to libNAME...spkg though.

However, I don't really care deeply.

Cheers,
Martin



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[sage-devel] Re: libm4ri

2008-12-01 Thread mabshoff



On Dec 1, 8:40 pm, Robert Bradshaw [EMAIL PROTECTED]
wrote:
 I just noticed for m4ri the package is called libm4ri-*.spkg. Any  
 reason this isn't m4ri-*.spkg?

That is the name malb gave it initially and it just stuck. The same
applies for libfplll.spkg, too.

 - Robert

Cheers,

Michael
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[sage-devel] Re: libm4ri

2008-12-01 Thread Robert Bradshaw

On Dec 1, 2008, at 8:42 PM, mabshoff wrote:

 On Dec 1, 8:40 pm, Robert Bradshaw [EMAIL PROTECTED]
 wrote:
 I just noticed for m4ri the package is called libm4ri-*.spkg. Any
 reason this isn't m4ri-*.spkg?

 That is the name malb gave it initially and it just stuck. The same
 applies for libfplll.spkg, too.

Well, could I propose we change it?

- Robert



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[sage-devel] Re: libm4ri

2008-12-01 Thread mabshoff



On Dec 1, 8:51 pm, Robert Bradshaw [EMAIL PROTECTED]
wrote:
 On Dec 1, 2008, at 8:42 PM, mabshoff wrote:

  On Dec 1, 8:40 pm, Robert Bradshaw [EMAIL PROTECTED]
  wrote:
  I just noticed for m4ri the package is called libm4ri-*.spkg. Any
  reason this isn't m4ri-*.spkg?

  That is the name malb gave it initially and it just stuck. The same
  applies for libfplll.spkg, too.

 Well, could I propose we change it?

Fine by me, it could be done with a little magic to deps. But why
would you want to do so? For m1ri I would guess?

 - Robert

Cheers,

Michael
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[sage-devel] Re: libm4ri

2008-12-01 Thread Robert Bradshaw

On Dec 1, 2008, at 8:54 PM, mabshoff wrote:

 On Dec 1, 8:51 pm, Robert Bradshaw [EMAIL PROTECTED]
 wrote:
 On Dec 1, 2008, at 8:42 PM, mabshoff wrote:

 On Dec 1, 8:40 pm, Robert Bradshaw [EMAIL PROTECTED]
 wrote:
 I just noticed for m4ri the package is called libm4ri-*.spkg. Any
 reason this isn't m4ri-*.spkg?

 That is the name malb gave it initially and it just stuck. The same
 applies for libfplll.spkg, too.

 Well, could I propose we change it?

 Fine by me, it could be done with a little magic to deps. But why
 would you want to do so? For m1ri I would guess?

Just for consistency. I actually had trouble finding it (first looked  
for m*, then unpacked linbox to see if it was in there...)

- Robert


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[sage-devel] Re: libm4ri

2008-12-01 Thread mabshoff



On Dec 1, 9:11 pm, Robert Bradshaw [EMAIL PROTECTED]
wrote:
 On Dec 1, 2008, at 8:54 PM, mabshoff wrote:



  On Dec 1, 8:51 pm, Robert Bradshaw [EMAIL PROTECTED]
  wrote:
  On Dec 1, 2008, at 8:42 PM, mabshoff wrote:

  On Dec 1, 8:40 pm, Robert Bradshaw [EMAIL PROTECTED]
  wrote:
  I just noticed for m4ri the package is called libm4ri-*.spkg. Any
  reason this isn't m4ri-*.spkg?

  That is the name malb gave it initially and it just stuck. The same
  applies for libfplll.spkg, too.

  Well, could I propose we change it?

  Fine by me, it could be done with a little magic to deps. But why
  would you want to do so? For m1ri I would guess?

 Just for consistency. I actually had trouble finding it (first looked  
 for m*, then unpacked linbox to see if it was in there...)

Ok, currently we have the following in the tree:

Sprocketer:~ michaelabshoff$ cd Desktop/sage-3.2.1.rc1-qf/spkg/
standard/
Sprocketer:standard michaelabshoff$ ls -al *lib*
-rw-r--r--@ 1 michaelabshoff  staff   272776 Nov 26 22:28
cddlib-094b.p3.spkg
-rw-r--r--@ 1 michaelabshoff  staff  1593104 Nov 26 22:28
eclib-20080310.p7.spkg
-rw-r--r--@ 1 michaelabshoff  staff   293382 Nov 26 22:28
libfplll-2.1.6-20071129.p5.spkg
-rw-r--r--@ 1 michaelabshoff  staff   970913 Nov 26 22:28
libgcrypt-1.4.0.p2.spkg
-rw-r--r--@ 1 michaelabshoff  staff   383786 Nov 26 22:28
libgpg_error-1.6.p0.spkg
-rw-r--r--@ 1 michaelabshoff  staff   713789 Nov 26 22:28
libm4ri-20080909.spkg
-rw-r--r--@ 1 michaelabshoff  staff   626176 Nov 26 22:28
libpng-1.2.22.p8.spkg
-rw-r--r--@ 1 michaelabshoff  staff  4832798 Nov 26 22:28
matplotlib-0.98.3.p3.spkg
-rw-r--r--@ 1 michaelabshoff  staff   436207 Nov 26 22:28
zlib-1.2.3.p4.spkg

I plan to upgrade png in 3.2.2 and will also attempt to do the upgrade
to fplll 3.0.x. I guess if malb is ok with the rename we could also
change the name next time he releases an updated version.

I think we can eliminate libgpg_error and libgcrypt since gnutls these
days contains its own copy of those two libraries and builds them on
demand when it does not detect them externally. Having the in tree
versions is certainly a good thing since less can go wrong.

So if we do this we can do some cleanup and reducing the number of
spkgs is always a good thing IMHO. :)

Does anybody else have an opinion? If we do this I can open tickets
for the various tasks that need to be done.

 - Robert

Cheers,

Michael
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