R, AIX 64-bit builds - trying to understand root cause for message: "Error: Line starting 'Package: tools ...' is malformed!"
I would be "pleased" if you would try packages - i.e., none of "Toolbox" or Perzl rpm's. The iconv I supply might not be working as is (I will need to install a new system to check). However, this is why I have been testing with R-3.2.3 - to side-step the system library dependencies. re: xz - I have "installp" version - and any of my packages should work side-by-side with the Toolbox/.rpm files - my PATH prefix is /opt (so, /opt/bin and /opt/sbin rather than /usr/bin, /usr/local/bin (etc.). I am testing on a Power6, usually with 2 to 4G RAM active. When I get the compile to finish I will up to 8G to test some data processing that fails with the 32-bit limitations. Another question: are you also getting lots of duplicate symbol warnings? Curious me. If you are I would like to send my modifications to configure(.ac) for you to test (I put .ac in () because I am actually editting configure atm but shall put them into configure.ac when I finish) FYI: I shall be downloading the "try and buy" xlc and xlfortran - and I think you will certainly prefer my packaging then as they work without the libgc dependencies that many of the rpm packages need. And, at your option - we can take this discussion over tools - "out of forums". Or at least start a new thread. re: unsigned short - I have adopted the convention to use the *NN_t types after running into a problem with unsigned longlong (from a very old program). It goes back many years - and maybe they have finalized short to mean 16-bits - but I remember when short was meant to help when moving from 16-bit to 32-bit and the "word" size changed - i.e., int became 32-bit same as long. nd for a long (no pun intended) long was 32-bit and long long was 64-bit. Those definitions are extinct. imho - the standard for wint_t is wrong as well - based on an assumption about how "short" is defined. And, I consider it poor practice that there are som many cases of type cast switches between ushort and int. Michael
On 04-Jan-16 01:26, Simon Urbanek wrote:
Michael, I'm using xlc + xlf - the exact flags are configure CC=xlc_r CXX=xlc++_r F77=xlf_r FC=xlf95_r LIBS='-L/opt/freeware/lib /opt/freeware/lib/libiconv.a -lpthread' --prefix=/opt/freeware CPPFLAGS=-I/opt/freeware/include with export OBJECT_MODE=64 in the env (and libiconv from perzl.org RPMs - iconv is a serious pain). I have changed the TRE typedef from "wint_t" to "unsigned int" since that is what the other platforms use anyway. On my AIX7 VM I'm running out of memory in xz when lazy-loading is enabled which his odd - the VM has 4Gb which one would think should be enough. The symptom is that installing MASS fails when creating lazy-load rds or the same happens when running make check as memCompress() test for xz fails. I wish there was a way to disable xz altogether.. I'd like to get IBM compilers to work first since those are the official ones. I may try gcc later, but I'm really interested in the IBM ones because that gives us a good non-GNU test (e.g., TRE fails in JIT due some alleged GNUisms so you can't use the strict compiler mode). Cheers, Simon On Jan 3, 2016, at 10:59 AM, Michael Felt <aixtools at gmail.com> wrote:
On 2016-01-01 23:48, peter dalgaard wrote:
Nice catch you two!!! Happy New Year -pd
I am much happier with this great start! Simon - which compiler)s) did you use: xlc and xlfortran, or gcc/gfortran? I have made some changes to configure(.ac) so maybe my problems are self-inflicted. But would be good to know what environment you are using. Thanks for looking - and finding!!! Michael
On 01 Jan 2016, at 22:06 , Simon Urbanek<simon.urbanek at r-project.org> wrote: Ok, found the problem - on platforms that support it TRE uses wint_t (from wchar.h) as its type for characters (tre_cint_t) which on AIX is *signed* int. TRE uses liberally conversions between int and tre_cint_t apparently assuming that the latter is unsigned so conversions back to int are suitable for comparisons etc. On other platforms wint_t is unsigned so it works. Manually defining tre_cint_t to unsigned int fixes the issue. Cheers, Simon On Jan 1, 2016, at 12:20 PM, Simon Urbanek<simon.urbanek at r-project.org> wrote:
Michael, thanks, I'll have a look once my PDP VMs are up again (later today). This may be a signedness issue although it's unclear why other platforms wouldn't be affected. Cheers, Simon On Dec 31, 2015, at 10:14 AM, Michael Felt<aixtools at gmail.com> wrote:
On 2015-12-30 09:58, Michael Felt wrote:
On 2015-12-29 11:02, Michael Felt wrote:
This seems to be a problem that goes back a long time - and I hope someone who understands what tre is suppossed to be doing will look at this. A short history of other people who have reported on this on different versions of AIX. I shall only add that I get the same results on AIX 5.3 TL7, AIX 6.1 TL9 and AIX 7.1 TL3. Basically, with settings that work for AIX and 32-bit - the only changes being -maix32 becomes -maix64 and export OBJECT_MODE=32 becomes export OBJECT_MODE=64 Then to shorten the 'make' bla bla, first run just make, then cd src/library/tools make -s sysdata http://article.gmane.org/gmane.comp.lang.r.devel/38817/match=package+tools+malformed http://article.gmane.org/gmane.comp.lang.r.devel/36886/match=package+tools+malformed http://article.gmane.org/gmane.comp.lang.r.devel/23372/match=package+tools+malformed Date: 2010-01-25 06:55:41 GMT (5 years, 48 weeks, 1 day, 20 hours and 30 minutes ago) To that, to get debug data, I have * added -DTRE_DUGUG to src/extra/tre/Makefile # ALL_CFLAGS = $(ALL_CFLAGS_LO) -DTRE_DEBUG * rm src/extra/tre/tre-match-parallel.o * find . -name \*.so -exec rm {} \; * make * cd src/library/tools * make -s sysdata Attached are the two script files of the screen output. The 32-bit one is more verbose - and contains magically lines such as: found match 3037fd14 (while "found" does not occur in the 64-bit output) root at x069:[/data/prj/cran/64/R-aix-3.2.3/src/library/tools]wc /tmp/sysdata.??.* 4730 14123 139916 /tmp/sysdata.32.text 1312 3688 40528 /tmp/sysdata.64.text 6042 17811 180444 total root at x069:[/data/prj/cran/64/R-aix-3.2.3/src/library/tools]grep -c found /tmp/sysdata.??.* /tmp/sysdata.32.text:19 /tmp/sysdata.64.text:0 Hope this brings us (or me), closer to a resolution to an old concern. And, best wishes for the new year! Michael
Still hoping for someones curiosity/willingness. The differences show up in the first comparision that is made (of the string "3.2.3" it seems) - 32-bit is on the left, 64-bit on the right. Script command is started on Tue Dec 29 08:39:16 UTC 2015. | Script command is started on Tue Dec 29 08:39:56 UTC 2015. root at x069:[/data/prj/cran/32/R-aix-3.2.3/src/library/tools]make -s sysdata | root at x069:[/data/prj/cran/64/R-aix-3.2.3/src/library/tools]make -s sysdata installing 'sysdata.rda' | installing 'sysdata.rda' tre_tnfa_run_parallel, input type 1 | tre_tnfa_run_parallel, input type 1 length: -1 | length: -1 pos:chr/code | states and tags | pos:chr/code | states and tags -------------+------------------------------------------------ | -------------+------------------------------------------------ init> 30380200 3038014c 30380098 | init> 110cc3040 110cc2f28 110cc2e10 match end offset = -1 | match end offset = -1 tre_tnfa_run_parallel, input type 1 | tre_tnfa_run_parallel, input type 1 length: -1 | length: -1 pos:chr/code | states and tags | pos:chr/code | states and tags -------------+------------------------------------------------ | -------------+------------------------------------------------ init> 3037fb88 | init> 110cc3310 0: 3/00051 | 3037fb88/0:0 | 0: 3/00051 | 110cc3310/0:0 1: ./00046 | 3037fb88/0:0 | 1: ./00046 | 110cc3310/0:0 init> 3037fb88 | init> 110cc3310 1: ./00046 | 3037fb88/0:1 | 1: ./00046 | 110cc3310/0:1 2: 2/00050 | 3037fb88/0:1 | 2: 2/00050 | 110cc3310/0:1 assertion failed | assertion failed init> 3037fb88 | init> 110cc3310 2: 2/00050 | 3037fc18/0:1 3037fb88/0:2 | 2: 2/00050 | 110cc33f0/0:1 110cc3310/0:2 3: ./00046 | 3037fc18/0:1 3037fb88/0:2 | 3: ./00046 | 110cc33f0/0:1 110cc3310/0:2 assertion failed *** DIFFERENCE *** | init> 110cc3310 init> 3037fb88 | 3: ./00046 | 110cc3310/0:3 3: ./00046 | 3037fc18/0:1 3037fb88/0:3 | 4: 3/00051 | 110cc3310/0:3 4: 3/00051 | 3037fc18/0:1 3037fb88/0:3 | assertion failed assertion failed | init> 110cc3310 init> 3037fb88 | 4: 3/00051 | 110cc33f0/0:3 110cc3310/0:4 4: 3/00051 | 3037fc18/0:3 3037fb88/0:4 | 5: /00000 | 110cc33f0/0:3 110cc3310/0:4 5: /00000 | 3037fc18/0:3 3037fb88/0:4 | init> 110cc3310 found match 3037fd14 *** DIFFERENCE *** | match end offset = -1 match end offset = 5 *** DIFFERENCE *** | tre_tnfa_run_parallel, input type 1 tre_tnfa_run_parallel, input type 1 | length: -1 length: -1 | pos:chr/code | states and tags pos:chr/code | states and tags | -------------+------------------------------------------------ -------------+------------------------------------------------ | init> 110cc4780 110cc4668 110cc4550 init> 303811c0 3038110c 30381058 | match end offset = -1 match end offset = -1 | tre_tnfa_run_parallel, input type 1 tre_tnfa_run_parallel, input type 1 | length: -1 length: -1 | pos:chr/code | states and tags pos:chr/code | states and tags | -------------+------------------------------------------------ -------------+------------------------------------------------ | init> 110cc5700 110cc55e8 110cc54d0
One day further - looks like tre_compile (or just before, after all).
With TRE_DEBUG switched on in tre-compile.c and tre-ast.c I see (snip)
--- /tmp/x.32 2015-12-31 15:09:44.000000000 +0000
+++ /tmp/x.64 2015-12-31 15:09:30.000000000 +0000
@@ -1,5 +1,5 @@
- Script command is started on Thu Dec 31 15:04:39 2015.
- root at x069:[/data/prj/cran/32/R-aix-3.2.3/src/library/tools]make sysdata
+ Script command is started on Thu Dec 31 15:08:43 2015.
+ root at x069:[/data/prj/cran/64/R-aix-3.2.3/src/library/tools]make sysdata
installing 'sysdata.rda'
echo "tools:::sysdata2LazyLoadDB(\"/data/prj/cran/R-3.2.3/src/library/tools/R/sysdata.rda\",\"../../../library/tools/R\")" | \
R_DEFAULT_PACKAGES=NULL LC_ALL=C ../../../bin/R --vanilla --slave
@@ -167,7 +167,7 @@
initial: 1/1,0, assert 0
initial: 0/0, assert 0
initial: 0/0, assert 0
- final state 30370718
+ final state 110cba530
tre_compile: parsing '(^|[^%])(%%)*%V'
AST:
catenation, sub 0, 0 tags
@@ -177,7 +177,7 @@
assertions: bol
union, sub -1, 0 tags
literal (, $) (0, 36), pos 0, sub -1, 0 tags
- literal (&, M-^?) (38, 65535), pos 0, sub -1, 0 tags
+ literal (&, M-^?) (38, -1), pos 0, sub -1, 0 tags
iteration {0, -1}, sub -1, 0 tags, greedy
catenation, sub 2, 0 tags
literal (%, %) (37, 37), pos 1, sub -1, 0 tags
@@ -197,7 +197,7 @@
Union
Literal 0-36
After union left
- Literal 38-65535
+ Literal 38--1
After union right
After union right
num_tags += 2
@@ -231,7 +231,7 @@
assertions: bol
union, sub -1, 0 tags
literal (, $) (0, 36), pos 0, sub -1, 0 tags
- literal (&, M-^?) (38, 65535), pos 0, sub -1, 0 tags
+ literal (&, M-^?) (38, -1), pos 0, sub -1, 0 tags
iteration {0, -1}, sub -1, 2 tags, greedy
catenation, sub 2, 1 tags
literal (%, %) (37, 37), pos 1, sub -1, 1 tags
@@ -255,7 +255,7 @@
Union
Literal 0-36
After union left
- Literal 38-65535
+ Literal 38--1
After union right
After union right
tre_add_tag_right: tag 3
@@ -342,7 +342,7 @@
catenation, sub -1, 0 tags
union, sub -1, 0 tags
literal (, $) (0, 36), pos 0, sub -1, 0 tags
- literal (&, M-^?) (38, 65535), pos 0, sub -1, 0 tags
+ literal (&, M-^?) (38, -1), pos 0, sub -1, 0 tags
tag 4
It seems in 32-bit mode -1 is unsigned (65535) but -1 == -1 in 64-bit mode.
I suspect I will "find it" - but a proposed change is appreciated.
Happy New Year,
Michael
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