[Rd] compiler flags for performance

2019-06-13 Thread lejeczek via R-devel 
hi guys,

I'd like to ask, and I believe this place here should be best as who can
know better, if building R with different compilers and opt flags is
something worth investing time into?

Or maybe this a subject that somebody has already investigated. If yes
what then are the conclusion?

Reason I ask is such that, on Centos 7.6 with different compilers from
stock repo but also from so called software collections, do not
render(with flags for performance) an R binaries which would perform any
better, according to R-benchmark-25 at least, then "vanilla" packages
shipped from distro.

And that makes me curious - is it because R is such a case which is
prone to any compiler performance optimizations?

Maybe there is more structured and organized way to conduct such
different-compilers-optimizations benchmarks/test?

What do devel can say and advise with regards to compile-for-performance
subject?

many thanks, L. 


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Re: [Rd] compiler flags for performance

2019-06-14 Thread lejeczek via R-devel 
On 13/06/2019 16:14, Dirk Eddelbuettel wrote:
> On 13 June 2019 at 16:05, lejeczek via R-devel wrote:
> | I'd like to ask, and I believe this place here should be best as who can
> | know better, if building R with different compilers and opt flags is
> | something worth investing time into?
> | 
> | Or maybe this a subject that somebody has already investigated. If yes
> | what then are the conclusion?
> | 
> | Reason I ask is such that, on Centos 7.6 with different compilers from
> | stock repo but also from so called software collections, do not
> | render(with flags for performance) an R binaries which would perform any
> | better, according to R-benchmark-25 at least, then "vanilla" packages
> | shipped from distro.
> | 
> | And that makes me curious - is it because R is such a case which is
> | prone to any compiler performance optimizations?
> | 
> | Maybe there is more structured and organized way to conduct such
> | different-compilers-optimizations benchmarks/test?
> | 
> | What do devel can say and advise with regards to compile-for-performance
> | subject?
>
> Of course you do that, and add those switches to ~/.R/Makeconf.  The
> resulting binaries may become non-portable.
>
> E.g. "at work" we use -march=native quite a bit but it means can't share
> libraries from a beefier dev box with skinnier deployment boxen as they don't
> have the same chipset even thought the are both x86_64 and use the same Linux
> distro.  
>
> As for which switches help in which way on different compiler: that is
> probably best seen as a black box.  Time and profile locally, I no longer try
> to generalize.   The newer 'link-time-optimizations' can help too, they
> certainly make builds longer ...
>
> Dirk
>
I've tried the "usual" tweaks and what puzzles me is the fact, that
-march=native and -lto(s) + Os/3 do not help much, make almost invisible
improvements (again, judging by results from R-benchmark-25) with gcc >=
7 as compared to distro's package which is built with -O2 -mtune=generic
and no ltos.

Would there be other(better) way to test core R?

What king of R perf increases do you guys see with compiler's opt flags,
if any?

regards, L.




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[Rd] running R with users home dirs on a shared filesystems

2019-12-13 Thread lejeczek via R-devel 
Hi guys,

I want to ask devel for who knows better - having multiple
nodes serving users home dirs off the same shared network
filesystem : are there any precautions or must-dos &
must-donts in order to assure healthy and efficient parallel
Rs running simultaneously - and I don't mean obvious stuff,
I'm rather asking about R's internals & environment.

simple example: three nodes mount a NFS share and users on
all three nodes run R simultaneously.

many thanks, L.

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[Rd] R with Squid proxy - invalid requests ??

2020-02-11 Thread lejeczek via R-devel 
dear devel,

I thought you guys would know best - I have an R which fails to get
communicate outside via a proxy, and Squid's logs show:

...

1581432434.501  0 10.5.8.17 TAG_NONE/400 4064  %C5/%B6* -
HIER_NONE/- text/html
1581432497.231  0 10.5.8.17 TAG_NONE/400 4570 NONE
error:invalid-request - HIER_NONE/- text/html
1581432497.338  0 10.5.8.17 TAG_NONE/400 4300 
%AC%9E%D0Rj%84%19%8D%23O%F9%E5%D4%E9%DBj%8D%F9x%C3:%FB-%02f%FBE%E5O%92c%9A
- HIER_NONE/- text/html
1581432497.445  0 10.5.8.17 TAG_NONE/400 4570 NONE
error:invalid-request - HIER_NONE/- text/html
1581432497.552  0 10.5.8.17 TAG_NONE/400 4570 NONE
error:invalid-request - HIER_NONE/- text/html
1581432497.659  0 10.5.8.17 TAG_NONE/400 4320 
Fi%E3@%04%D3%97o0%23%13%1B%C1%08%082%E8%A5%1B%DAh%F3%18%E1%DB%A1%1E%FET%01%DD
- HIER_NONE/- text/html
1581432497.766  0 10.5.8.17 TAG_NONE/400 4452 
%01%D4%F7%8AB%CA%AE%A5%D7.%BE%C4I%B5%D4%10c%0F%9D%9B%D9%C7%BA%15%FF%A2JO%B3%60%D0%86%B8lY%8F%97%B5%BC%15%C9
- HIER_NONE/- text/html
1581432557.005  0 10.5.8.17 TAG_NONE/400 4346 
%CC6%F3%CA%F4%90%F5%E0%9B%B47%C6%DB%83%89%E1%F4%F1=%08a%81%06KK%3C%B4%DAj%AC%B7
- HIER_NONE/- text/html
1581432557.112  0 10.5.8.17 TAG_NONE/400 4320 
%DE%D3%1B%89%1Et%94R%ECQ%ADd%04%8D=r%92%9AZ%5E%98%C4%1F%F9%9F%06%FF%AB%5E%BC%D7@
- HIER_NONE/- text/html
1581432557.219  0 10.5.8.17 TAG_NONE/400 4570 NONE
error:invalid-request - HIER_NONE/- text/html
1581432557.326  0 10.5.8.17 TAG_NONE/400 4288 
%A8O%FBmW%E4%97%9E%7C%FC%C4@T8S%BA3%19%C36%9E%9C%E5%CBt%1F%C3&.7%14%C2 -
HIER_NONE/- text/html
1581432557.433  0 10.5.8.17 TAG_NONE/400 4260 
?9a%AB%8E%ECh-w%1C%C3%5D%084x%0F*%1Efw%D7+%0ED%7D%92%94%06%DA%EC%BB; -
HIER_NONE/- text/html
1581432557.540  0 10.5.8.17 TAG_NONE/400 4298 
%C5%EA?%A6%11t.%DE%FC%%C8%82o%C0%F49%BCFX%C4%D0%EEbfb%01%A8%27Y%F8%DB%C4
- HIER_NONE/- text/html

when I do anything, something like:

> install.packages("sos")

Everything else on the box uses & works fine with that Squid. Could it
be be somehow "crooked" default R on that box which is Centos 8?

Or what else?

many thanks, L.



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Re: [Rd] R with Squid proxy - invalid requests ??

2020-02-11 Thread lejeczek via R-devel 
On 11/02/2020 14:54, lejeczek via R-devel wrote:
> dear devel,
>
> I thought you guys would know best - I have an R which fails to get
> communicate outside via a proxy, and Squid's logs show:
>
> ...
>
> 1581432434.501  0 10.5.8.17 TAG_NONE/400 4064  %C5/%B6* -
> HIER_NONE/- text/html
> 1581432497.231  0 10.5.8.17 TAG_NONE/400 4570 NONE
> error:invalid-request - HIER_NONE/- text/html
> 1581432497.338  0 10.5.8.17 TAG_NONE/400 4300 
> %AC%9E%D0Rj%84%19%8D%23O%F9%E5%D4%E9%DBj%8D%F9x%C3:%FB-%02f%FBE%E5O%92c%9A
> - HIER_NONE/- text/html
> 1581432497.445  0 10.5.8.17 TAG_NONE/400 4570 NONE
> error:invalid-request - HIER_NONE/- text/html
> 1581432497.552  0 10.5.8.17 TAG_NONE/400 4570 NONE
> error:invalid-request - HIER_NONE/- text/html
> 1581432497.659  0 10.5.8.17 TAG_NONE/400 4320 
> Fi%E3@%04%D3%97o0%23%13%1B%C1%08%082%E8%A5%1B%DAh%F3%18%E1%DB%A1%1E%FET%01%DD
> - HIER_NONE/- text/html
> 1581432497.766  0 10.5.8.17 TAG_NONE/400 4452 
> %01%D4%F7%8AB%CA%AE%A5%D7.%BE%C4I%B5%D4%10c%0F%9D%9B%D9%C7%BA%15%FF%A2JO%B3%60%D0%86%B8lY%8F%97%B5%BC%15%C9
> - HIER_NONE/- text/html
> 1581432557.005  0 10.5.8.17 TAG_NONE/400 4346 
> %CC6%F3%CA%F4%90%F5%E0%9B%B47%C6%DB%83%89%E1%F4%F1=%08a%81%06KK%3C%B4%DAj%AC%B7
> - HIER_NONE/- text/html
> 1581432557.112  0 10.5.8.17 TAG_NONE/400 4320 
> %DE%D3%1B%89%1Et%94R%ECQ%ADd%04%8D=r%92%9AZ%5E%98%C4%1F%F9%9F%06%FF%AB%5E%BC%D7@
> - HIER_NONE/- text/html
> 1581432557.219  0 10.5.8.17 TAG_NONE/400 4570 NONE
> error:invalid-request - HIER_NONE/- text/html
> 1581432557.326  0 10.5.8.17 TAG_NONE/400 4288 
> %A8O%FBmW%E4%97%9E%7C%FC%C4@T8S%BA3%19%C36%9E%9C%E5%CBt%1F%C3&.7%14%C2 -
> HIER_NONE/- text/html
> 1581432557.433  0 10.5.8.17 TAG_NONE/400 4260 
> ?9a%AB%8E%ECh-w%1C%C3%5D%084x%0F*%1Efw%D7+%0ED%7D%92%94%06%DA%EC%BB; -
> HIER_NONE/- text/html
> 1581432557.540  0 10.5.8.17 TAG_NONE/400 4298 
> %C5%EA?%A6%11t.%DE%FC%%C8%82o%C0%F49%BCFX%C4%D0%EEbfb%01%A8%27Y%F8%DB%C4
> - HIER_NONE/- text/html
>
> when I do anything, something like:
>
>> install.packages("sos")
> Everything else on the box uses & works fine with that Squid. Could it
> be be somehow "crooked" default R on that box which is Centos 8?
>
> Or what else?
>
> many thanks, L.
>
>
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel

I think R+CURL is "crooked".

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[Rd] different compilers and mzR build fails

2016-12-21 Thread lejeczek via R-devel 
I'm not sure if I should bother you team with this, 
apologies in case it's a bother.


I'm trying gcc 6.2.1 (from devtoolset-6) with R, everything 
seems to work just fine, except for mzR.

Here is failed build:

g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o mzR.so 
cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o 
rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o 
RcppIdentModule.o ./boost/system/src/error_code.o 
./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o 
./boost/regex/src/regex_raw_buffer.o 
./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o 
./boost/regex/src/instances.o ./boost/regex/src/icu.o 
./boost/regex/src/usinstances.o ./boost/regex/src/regex.o 
./boost/regex/src/wide_posix_api.o 
./boost/regex/src/regex_traits_defaults.o 
./boost/regex/src/winstances.o 
./boost/regex/src/wc_regex_traits.o 
./boost/regex/src/c_regex_traits.o 
./boost/regex/src/cpp_regex_traits.o 
./boost/regex/src/static_mutex.o 
./boost/regex/src/w32_regex_traits.o 
./boost/iostreams/src/zlib.o 
./boost/iostreams/src/file_descriptor.o 
./boost/thread/pthread/once.o 
./boost/thread/pthread/thread.o 
./boost/filesystem/src/operations.o 
./boost/filesystem/src/path.o 
./boost/filesystem/src/utf8_codecvt_facet.o 
./boost/chrono/src/chrono.o 
./boost/chrono/src/process_cpu_clocks.o 
./boost/chrono/src/thread_clock.o 
./pwiz/data/msdata/Version.o 
./pwiz/data/common/MemoryIndex.o 
./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o 
./pwiz/data/common/ParamTypes.o 
./pwiz/data/common/BinaryIndexStream.o 
./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o 
./pwiz/data/msdata/SpectrumList_MGF.o 
./pwiz/data/msdata/DefaultReaderList.o 
./pwiz/data/msdata/ChromatogramList_mzML.o 
./pwiz/data/msdata/examples.o 
./pwiz/data/msdata/Serializer_mzML.o 
./pwiz/data/msdata/Serializer_MSn.o 
./pwiz/data/msdata/Reader.o 
./pwiz/data/msdata/Serializer_MGF.o 
./pwiz/data/msdata/Serializer_mzXML.o 
./pwiz/data/msdata/SpectrumList_mzML.o 
./pwiz/data/msdata/SpectrumList_MSn.o 
./pwiz/data/msdata/BinaryDataEncoder.o 
./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o 
./pwiz/data/msdata/References.o 
./pwiz/data/msdata/SpectrumList_mzXML.o 
./pwiz/data/msdata/IO.o 
./pwiz/data/msdata/SpectrumList_BTDX.o 
./pwiz/data/msdata/SpectrumInfo.o 
./pwiz/data/msdata/RAMPAdapter.o 
./pwiz/data/msdata/LegacyAdapter.o 
./pwiz/data/msdata/SpectrumIterator.o 
./pwiz/data/msdata/MSDataFile.o 
./pwiz/data/msdata/MSNumpress.o 
./pwiz/data/msdata/SpectrumListCache.o 
./pwiz/data/msdata/Index_mzML.o 
./pwiz/data/msdata/SpectrumWorkerThreads.o 
./pwiz/data/identdata/IdentDataFile.o 
./pwiz/data/identdata/IdentData.o 
./pwiz/data/identdata/DefaultReaderList.o 
./pwiz/data/identdata/Reader.o 
./pwiz/data/identdata/Serializer_protXML.o 
./pwiz/data/identdata/Serializer_pepXML.o 
./pwiz/data/identdata/Serializer_mzid.o 
./pwiz/data/identdata/IO.o 
./pwiz/data/identdata/References.o 
./pwiz/data/identdata/MascotReader.o 
./pwiz/data/proteome/Modification.o 
./pwiz/data/proteome/Digestion.o 
./pwiz/data/proteome/Peptide.o 
./pwiz/data/proteome/AminoAcid.o 
./pwiz/utility/minimxml/XMLWriter.o 
./pwiz/utility/minimxml/SAXParser.o 
./pwiz/utility/chemistry/Chemistry.o 
./pwiz/utility/chemistry/ChemistryData.o 
./pwiz/utility/chemistry/MZTolerance.o 
./pwiz/utility/misc/IntegerSet.o 
./pwiz/utility/misc/Base64.o 
./pwiz/utility/misc/IterationListener.o 
./pwiz/utility/misc/MSIHandler.o 
./pwiz/utility/misc/Filesystem.o 
./pwiz/utility/misc/TabReader.o 
./pwiz/utility/misc/random_access_compressed_ifstream.o 
./pwiz/utility/misc/SHA1.o 
./pwiz/utility/misc/SHA1Calculator.o 
./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o 
./RcppExports.o rampR.o R_init_mzR.o -lpthread -lnetcdf 
-L/usr/lib64/R/lib -lR

g++: error: cramp.o: No such file or directory
g++: error: ramp_base64.o: No such file or directory
g++: error: ramp.o: No such file or directory
g++: error: RcppRamp.o: No such file or directory
g++: error: RcppRampModule.o: No such file or directory
g++: error: rnetCDF.o: No such file or directory
g++: error: RcppPwiz.o: No such file or directory
g++: error: RcppPwizModule.o: No such file or directory
g++: error: RcppIdent.o: No such file or directory
g++: error: RcppIdentModule.o: No such file or directory
/usr/share/R/make/shlib.mk:6: recipe for target 'mzR.so' failed
make: *** [mzR.so] Error 1

It did compile with 5.2.x (from devtoolset-4) and worked fine.
I'm hoping you guys could confirm it is purely compiler 
problem? Or point me(not a real programmer) a way to 
troubleshoot it properly?

many thanks,
L.

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Re: [Rd] different compilers and mzR build fails

2016-12-21 Thread lejeczek via R-devel 


I do this on a vanilla-clean R installation, simply:
> biocLite("mzR")
it pulls some deps in which compile fine, only mzR fails.
... meanwhile...
I grabbed devtools and comiled github master - still fails.
Should I attach build log? One should not send attachments 
to the list.. I don't suppose?


On 21/12/16 17:06, Martin Morgan wrote:
mzR is a Bioconductor package, so better to ask on the 
Bioconductor support forum


  https://support.bioconductor.org

Oh, I see you did, and then the advice is to avoid 
cross-posting!


The missing .o files would have been produced in an 
earlier compilation step; they likely failed in some way, 
so you need to provide the complete compilation output.


Did you do this on a version of the package that did not 
have any previous build artifacts (e.g., via biocLite() or 
from a fresh svn checkout)?


Martin

On 12/21/2016 12:00 PM, lejeczek via R-devel wrote:
I'm not sure if I should bother you team with this, 
apologies in case

it's a bother.

I'm trying gcc 6.2.1 (from devtoolset-6) with R, 
everything seems to

work just fine, except for mzR.
Here is failed build:

g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o 
mzR.so cramp.o
ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o 
rnetCDF.o RcppPwiz.o

RcppPwizModule.o RcppIdent.o RcppIdentModule.o
./boost/system/src/error_code.o 
./boost/regex/src/posix_api.o
./boost/regex/src/fileiter.o 
./boost/regex/src/regex_raw_buffer.o

./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o
./boost/regex/src/instances.o ./boost/regex/src/icu.o
./boost/regex/src/usinstances.o ./boost/regex/src/regex.o
./boost/regex/src/wide_posix_api.o
./boost/regex/src/regex_traits_defaults.o 
./boost/regex/src/winstances.o
./boost/regex/src/wc_regex_traits.o 
./boost/regex/src/c_regex_traits.o
./boost/regex/src/cpp_regex_traits.o 
./boost/regex/src/static_mutex.o
./boost/regex/src/w32_regex_traits.o 
./boost/iostreams/src/zlib.o
./boost/iostreams/src/file_descriptor.o 
./boost/thread/pthread/once.o
./boost/thread/pthread/thread.o 
./boost/filesystem/src/operations.o

./boost/filesystem/src/path.o
./boost/filesystem/src/utf8_codecvt_facet.o 
./boost/chrono/src/chrono.o

./boost/chrono/src/process_cpu_clocks.o
./boost/chrono/src/thread_clock.o 
./pwiz/data/msdata/Version.o
./pwiz/data/common/MemoryIndex.o 
./pwiz/data/common/CVTranslator.o

./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o
./pwiz/data/common/BinaryIndexStream.o 
./pwiz/data/common/diff_std.o
./pwiz/data/common/Unimod.o 
./pwiz/data/msdata/SpectrumList_MGF.o

./pwiz/data/msdata/DefaultReaderList.o
./pwiz/data/msdata/ChromatogramList_mzML.o 
./pwiz/data/msdata/examples.o
./pwiz/data/msdata/Serializer_mzML.o 
./pwiz/data/msdata/Serializer_MSn.o
./pwiz/data/msdata/Reader.o 
./pwiz/data/msdata/Serializer_MGF.o

./pwiz/data/msdata/Serializer_mzXML.o
./pwiz/data/msdata/SpectrumList_mzML.o
./pwiz/data/msdata/SpectrumList_MSn.o
./pwiz/data/msdata/BinaryDataEncoder.o 
./pwiz/data/msdata/Diff.o

./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o
./pwiz/data/msdata/SpectrumList_mzXML.o 
./pwiz/data/msdata/IO.o
./pwiz/data/msdata/SpectrumList_BTDX.o 
./pwiz/data/msdata/SpectrumInfo.o
./pwiz/data/msdata/RAMPAdapter.o 
./pwiz/data/msdata/LegacyAdapter.o
./pwiz/data/msdata/SpectrumIterator.o 
./pwiz/data/msdata/MSDataFile.o
./pwiz/data/msdata/MSNumpress.o 
./pwiz/data/msdata/SpectrumListCache.o

./pwiz/data/msdata/Index_mzML.o
./pwiz/data/msdata/SpectrumWorkerThreads.o
./pwiz/data/identdata/IdentDataFile.o 
./pwiz/data/identdata/IdentData.o
./pwiz/data/identdata/DefaultReaderList.o 
./pwiz/data/identdata/Reader.o

./pwiz/data/identdata/Serializer_protXML.o
./pwiz/data/identdata/Serializer_pepXML.o
./pwiz/data/identdata/Serializer_mzid.o 
./pwiz/data/identdata/IO.o
./pwiz/data/identdata/References.o 
./pwiz/data/identdata/MascotReader.o
./pwiz/data/proteome/Modification.o 
./pwiz/data/proteome/Digestion.o
./pwiz/data/proteome/Peptide.o 
./pwiz/data/proteome/AminoAcid.o
./pwiz/utility/minimxml/XMLWriter.o 
./pwiz/utility/minimxml/SAXParser.o

./pwiz/utility/chemistry/Chemistry.o
./pwiz/utility/chemistry/ChemistryData.o
./pwiz/utility/chemistry/MZTolerance.o 
./pwiz/utility/misc/IntegerSet.o
./pwiz/utility/misc/Base64.o 
./pwiz/utility/misc/IterationListener.o
./pwiz/utility/misc/MSIHandler.o 
./pwiz/utility/misc/Filesystem.o

./pwiz/utility/misc/TabReader.o
./pwiz/utility/misc/random_access_compressed_ifstream.o
./pwiz/utility/misc/SHA1.o 
./pwiz/utility/misc/SHA1Calculator.o
./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o 
./RcppExports.o
rampR.o R_init_mzR.o -lpthread -lnetcdf 
-L/usr/lib64/R/lib -lR

g++: error: cramp.o: No such file or directory
g++: error: ramp_base64.o: No such file or directory
g++: error: ramp.o: No such file or directory
g++: error: RcppRamp.o: No such file or directory
g++: error: RcppRampModule.o: No such file or directory
g++: error: rnetCDF.o: No such file or directory
g++: error: RcppPwiz.o: No