[Rd] R, AIX 64-bit builds - trying to understand root cause for message: "Error: Line starting 'Package: tools ...' is malformed!"
Simon Urbanek
simon.urbanek at r-project.org
Mon Jan 4 01:26:57 CET 2016
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
>>>>>
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>> ______________________________________________
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