Commits · f8d1e985972b6d788fc8d5b7da7b95fa993d5c1f · HCL / ALTree

13 Dec, 2013 2 commits
- New release · f8d1e985
  Vincent Danjean authored Dec 13, 2013
```
* update MANIFEST
* fix make-release
```
  f8d1e985
- Do not compute more permutation than requested, even with lots of processors · 45ac2cf9
  Vincent Danjean authored Dec 13, 2013
```
If there are more processors than requested permutations, some processor
must do nothing. Before, all processors did something, sometimes corrupting
memory...
```
  45ac2cf9
30 Jun, 2013 1 commit
- Avoid too precise tests with float datatypes · 087f05b7
  Vincent Danjean authored Jul 01, 2013
```
See http://bugs.debian.org/578550 for errors fixed by this commit
```
  087f05b7
23 Apr, 2013 1 commit
- No RCS version anymore, using 1.00 version by default · 56ad04e8
  Claire Bardel authored Apr 23, 2013
  
  56ad04e8
03 Nov, 2012 6 commits
- Bump version, new release · 877ab635
  Vincent Danjean authored Nov 03, 2012
  
  877ab635
- Fix linkage for CUtils · 299a312b
  Vincent Danjean authored Nov 03, 2012
  
  299a312b
- Fix typo in function name · 4e459d61
  Vincent Danjean authored Nov 03, 2012
  
  4e459d61
- Update make-release for git · 2089b2aa
  Vincent Danjean authored Nov 03, 2012
  
  2089b2aa
- Cleanup version handling · 82a65841
  Vincent Danjean authored Nov 03, 2012
  
  82a65841
- Remove dependencies on PDL and PDL::GSL::CDF · d8938831
  Vincent Danjean authored Nov 03, 2012
```
These modules are not used anymore.
The corresponding calls after the rewrite are done directly in C
```
  d8938831
02 Nov, 2012 8 commits
- Optimize rhyper.c for our use case · e16d9f7b
  Vincent Danjean authored Nov 02, 2012
```
We do not need to get several values with the same parameters
So, we avoid to check and store the previous state
```
  e16d9f7b
- Increase compiler warning level · af98d52c
  Vincent Danjean authored Nov 02, 2012
  
  af98d52c
- If ALTREE_PARALLEL is set to -1, all available CPU are used · 92bc2b42
  Vincent Danjean authored Nov 02, 2012
```
This function need to be tested on another plateform than linux,
mainly MacOS X.
```
  92bc2b42
- Use the hypergeometric distribution · 9d86d6ce
  Vincent Danjean authored Nov 02, 2012
```
This will give us a factor about 2.5

The r-code is improved :
- use exact values for afc until 1754 (max that can be
  computed with "long double")
- use per-thread static variables to allow parallel run
  in different threads
```
  9d86d6ce
- Use internal mt19937ar_t per thread structure · 6d87827f
  Vincent Danjean authored Nov 02, 2012
```
No need to define our own.
But we still need to initialize the random generator in each thread
```
  6d87827f
- Add missing MT-aware random functions · 550af4c4
  Vincent Danjean authored Nov 02, 2012
  
  550af4c4
- Get the R code source of the hypergeometric distribution · 32b13be8
  Vincent Danjean authored Nov 02, 2012
```
The code is deactivated with "#if 0" to allow ALTree compilation
```
  32b13be8
- Fix link so that all functions are found, even if TamuAnova is not loaded · 88e5972b
  Vincent Danjean authored Nov 02, 2012
  
  88e5972b
31 Oct, 2012 22 commits

Do not compile with debug code by default · 7158a709

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@469 cf695345-040a-0410-a956-b889e835fe2e

7158a709

Fix some compilation warnings and protect debugging code · 48d5ae46

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@468 cf695345-040a-0410-a956-b889e835fe2e

48d5ae46

Parallel execution of Chi2 resampling · 1850f46e

Vincent Danjean authored Oct 31, 2012

ResamplingChi2 accepts as last parameter the level of parallelism to use:
- 0 => do not use threaded code
- >0 => use this number of threads (ie 1 is not really usefull
   unless you want to test the threaded code without real parallelism)

Note that this parameter is *OVERWRITTEN* by the
ALTREE_PARALLEL environment variable as soon as it is defined.

The random generator has been changed: the one from the system
was a real bottleneck.

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@467 cf695345-040a-0410-a956-b889e835fe2e

1850f46e

memory managed outside inner functions · 42604187

Vincent Danjean authored Oct 31, 2012

outer functions can choose to allocate memory
with malloc or on their stack

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@466 cf695345-040a-0410-a956-b889e835fe2e

42604187

Fix "Use Chi2 resampling accelerator..." · 942edb10

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@465 cf695345-040a-0410-a956-b889e835fe2e

942edb10

cleanup Manifest · 27b18069

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@464 cf695345-040a-0410-a956-b889e835fe2e

27b18069

Run altree in tree for an example · 7a52931e

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@463 cf695345-040a-0410-a956-b889e835fe2e

7a52931e

Use Chi2 resampling accelerator... · 4422f9dd

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@462 cf695345-040a-0410-a956-b889e835fe2e

4422f9dd

Rewrite Chi2 resampling in C · 460d2354

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@461 cf695345-040a-0410-a956-b889e835fe2e

460d2354

Rewrite CalculChi2 in C · aa6ec3ca

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@460 cf695345-040a-0410-a956-b889e835fe2e

aa6ec3ca

move ALTree/Chi2.pm function into CUtils · 5c25de59

Vincent Danjean authored Oct 31, 2012

ALTree/Chi2.pm contains stub to CUtils functions

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@459 cf695345-040a-0410-a956-b889e835fe2e

5c25de59

Cleanup and comments in CUtils, add debugging facilities · 3ad0ab94

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@458 cf695345-040a-0410-a956-b889e835fe2e

3ad0ab94

Remove perl version of ClassicalChi2 · e91313cf

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@457 cf695345-040a-0410-a956-b889e835fe2e

e91313cf

ClassicalChi2 as a C function with validation checks · de3bdcea

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@456 cf695345-040a-0410-a956-b889e835fe2e

de3bdcea

Cleanup name in XS functions · 05a60d72

Vincent Danjean authored Oct 31, 2012

CamlCaseName for perl stubs
underscore_name for C functions

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@455 cf695345-040a-0410-a956-b889e835fe2e

05a60d72

Cleanup headers · 0155e448

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@454 cf695345-040a-0410-a956-b889e835fe2e

0155e448

Cleanup C headers · 8cd630ff

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@453 cf695345-040a-0410-a956-b889e835fe2e

8cd630ff

Refactor code · 819d4075

Vincent Danjean authored Oct 31, 2012

Chi2 for double_permutation are computed separately

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@452 cf695345-040a-0410-a956-b889e835fe2e

819d4075

Fix depth computation · fd83552f

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@451 cf695345-040a-0410-a956-b889e835fe2e

fd83552f

Compute tree representation for efficient stat computation · 53276ce1

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@450 cf695345-040a-0410-a956-b889e835fe2e

53276ce1

Add gitignore for build files · 7bf4e9d6

Vincent Danjean authored Oct 31, 2012

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@449 cf695345-040a-0410-a956-b889e835fe2e

7bf4e9d6

Merge CleanCaseControl, CleanChi2 and CleanQuanti into CleanStats · 1f6fc27d
Vincent Danjean authored Oct 31, 2012
```
git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@448 cf695345-040a-0410-a956-b889e835fe2e
```
1f6fc27d