Mailman 3 January 2015 - pypy-dev

JIT Spikes During Timings
by Kevin Ednalino 10 Jan '15

10 Jan '15

Hi. I'm using PyPy3 in the context of a game engine and I'm getting these spikes when timing it, such as: Engine: 3.0 ms Engine: 3.9 ms Engine: 3.0 ms Engine: 7.9 ms Engine: 25.1 ms Engine: 2.2 ms Engine: 2.2 ms Engine: 3.1 ms Engine: 3.0 ms Engine: 4.2 ms When I run the engine on CPython 3, the timings are more consistent: Engine: 1.7 ms Engine: 1.8 ms Engine: 1.2 ms Engine: 1.8 ms Engine: 1.7 ms Engine: 1.3 ms Engine: 1.6 ms Engine: 1.8 ms Engine: 1.9 ms Engine: 1.5 ms I've gotten spikes when timing much simpler things. I don't believe my code is doing anything exceptional to cause the spikes. My educated guess is it's due to the GC or more likely the JIT. When I run the engine with JIT off like so, "pypy3 --jit off main.py", the spikes disappear (albeit not as fast with it on). I've also been playing around with the minimark settings but no luck so far; possibly tweaking the JIT settings might help. Any suggestions are welcomed :). Specifications: pypy3 --version: Python 3.2.5 (b2091e973da69152b3f928bfaabd5d2347e6df46, Nov 18 2014, 20:15:54) [PyPy 2.4.0 with GCC 4.9.2] uname -a: Linux archlinux 3.17.6-1-ARCH #1 SMP PREEMPT Sun Dec 7 23:43:32 UTC 2014 x86_64 GNU/Linux Sincerely, Kevin Ednalino

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Segmentation Fault
by Stuart Axon 07 Jan '15

07 Jan '15

Hi, I'm running pypy 2.4.0 on Ubuntu Utopic. Running the pypy works OK (though it outputs 'trusty' weirdly): $ pypyPython 2.7.8 (2.4.0+dfsg-1~ppa2+trusty, Sep 25 2014, 04:35:04)[PyPy 2.4.0 with GCC 4.8.2] on linux2Type "help", "copyright", "credits" or "license" for more information.>>>> Running my program in it gives a segfault: $ sbotSegmentation fault If I run in CPython then things are OK $ sbotusage: usage: sbot [options] inputfile.bot [args] [-h] [-o FILE] [-w] [-f] [-t TITLE] [-s] [-dv] [-p SERVERPORT] [-r REPEAT] [-g GRAMMAR] [-c] [-v VARS] script [script_args]usage: sbot [options] inputfile.bot [args]: error: too few arguments I got this out of gdb: gdb -ex r --args `which pypy` `which sbot` GNU gdb (Ubuntu 7.8-1ubuntu4) 7.8.0.20141001-cvsCopyright (C) 2014 Free Software Foundation, Inc.License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>This is free software: you are free to change and redistribute it.There is NO WARRANTY, to the extent permitted by law. Type "show copying"and "show warranty" for details.This GDB was configured as "x86_64-linux-gnu".Type "show configuration" for configuration details.For bug reporting instructions, please see:<http://www.gnu.org/software/gdb/bugs/>.Find the GDB manual and other documentation resources online at:<http://www.gnu.org/software/gdb/documentation/>.For help, type "help".Type "apropos word" to search for commands related to "word"...Reading symbols from /mnt/data/home/stu/.virtualenvs/shoebot-pgi-pypy/bin/pypy...(no debugging symbols found)...done.Starting program: /mnt/data/home/stu/.virtualenvs/shoebot-pgi-pypy/bin/pypy /mnt/data/home/stu/.virtualenvs/shoebot-pgi-pypy/bin/sbot[Thread debugging using libthread_db enabled]Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". Program received signal SIGSEGV, Segmentation fault.0x00007fffecdb686e in std::_Rb_tree<std::string, std::pair<std::string const, std::pair<void const*, int> >, std::_Select1st<std::pair<std::string const, std::pair<void const*, int> > >, std::less<std::string>, std::allocator<std::pair<std::string const, std::pair<void const*, int> > > >::_M_get_insert_unique_pos(std::string const&) () from /usr/lib/x86_64-linux-gnu/libprotobuf.so.8(gdb)

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Thank You! [Question about VirtualEnv and PyPy is solved by your help!]
by 思 07 Jan '15

07 Jan '15

Dear Directors or Dear Friends: I'm so glad to get your message. My honor to you, sir. Your email reminds me. I really appreciate it and write this email formally‍ as the reply . Firstly, I found the newest version 12.0.5 and I install this in my OS(Windows 8). Secondly, I use the command as below <virtualenv -p path\to\pypy.exe path\to\vitualenv> Thirdly, I use the cmd to go into the virtual environment of Pypy built by 2nd operation. Finally, I active the <activate.bat> in cmd and I enter into the pypy environment. The picture below proved my process‍. ‍ I'm grateful for your help and informing me in time. Although PyPy has a long way to go because the 3rd packages is still not enough, I believe PyPy is the future of Python as well as Cython. The attitude of your team shows great perseverance in the face of difficulty. I will join the donation towards the 3rd site-packages or your research to render what trifling service I can‍. Best Wishes to your team and PyPy! :-) bitpeach‍‍ ------------------ 原始邮件 ------------------ 发件人: "Armin Rigo";<arigo(a)tunes.org>; 发送时间: 2015年1月7日(星期三) 晚上6:02 收件人: "思"<958816492(a)qq.com>; 抄送: "Matti Picus"<matti.picus(a)gmail.com>; "pypy-dev"<pypy-dev(a)python.org>; 主题: Re: [pypy-dev] Thank You Matti Picus AND I may have some new questions —— bitpeach from china Hi, On 14 December 2014 at 08:52, 思 <958816492(a)qq.com> wrote: (1) I check the VirtualEnv version list and the 1.11.6 is the latest by this URL. There is no newer version than that. It means that 1.11.6 version is the newest and no versions can support pypy-2.4.0. I see that the current virtualenv version is now 12.0.5 (https://pypi.python.org/pypi/virtualenv/#downloads). I assume that this means that the fixes Matti talks about are now officially part of it. Can you try again with this version 12.0.5? A bientôt, Armin.

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Re: [pypy-dev] Ask Pypy within virtualenv of Windows 7/8 for Help ---- bitpeach from china
by Matti Picus 07 Jan '15

07 Jan '15

The latest released virtualenv is version 1.11.6 which does not support pypy 2.4.0 and earlier on windows. A fix was merged into virtualenv after this version (released 17 May 2014) so any newer release will be fixed. In the mean time you can: 1. run "virtualenv -p path\to\pypy.exe new_path" and it will fail 2. copy by hand the directories lib_pypy and lib-python from path\to to new_path 3. rerun virtualenv, it should complete cleanly after installing setuptools and pip Matti > Dear Ms./Mr. Director / Dear Pypy Team: > I'm a e-pal named bitpeach. I'm so interested in your work and > admire the Pypy. > Therefore, I try to install Pypy and pratice with Pypy during my > working and studying. But I got a problem, what is worrying me is that > there is few versions of Pypy running on the Windows. So the problem > comes as follows: > (1)I want to instal Pypy but do not confuse the the 3rd packages > or libraries with Python2.7 already in my operate system Windows 7/8 > (32bit). Then I choose to follow the tutorial settings to install > VirtualEnv just like "Installing using virtualenv". > ... bitpeach > 2014-12-13 Sat. > Email From China > > > _______________________________________________ > pypy-dev mailing list > pypy-dev(a)python.org > https://mail.python.org/mailman/listinfo/pypy-dev >

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Help with finding tutors for Python, Linux, R, Perl, Octave, MATLAB and/or Cytoscape for yeast microarray analysis, next generation sequencing and constructing gene interaction networks
by thomas hahn 03 Jan '15

03 Jan '15

*Help with finding tutors for Python, Linux, R, Perl, Octave, MATLAB and/or Cytoscape for yeast microarray analysis, next generation sequencing and constructing gene interaction networks* Hi I am a visually impaired bioinformatics graduate student using microarray data for my master’s thesis aimed at deciphering the mechanism by which the yeast wild type can suppress the rise of free reactive oxygen species (ROS) induced by caloric restriction (CR) but the Atg15 and Erg6 knockout mutant cannot. Since my remaining vision is very limited I need very high magnification. But that makes my visual field very small. Therefore I need somebody to teach me how to use these programming environments, especially for microarray analysis, next generation sequencing and constructing gene and pathway interaction networks. This is very difficult for me to figure out without assistance because Zoomtext, my magnification and text to speech software, on which I am depending because I am almost blind, has problems reading out aloud many programming related websites to me. And even those websites it can read, it can only read sequentially from left to right and then from top to bottom. Unfortunately, this way of acquiring, finding, selecting and processing new information and answering questions is too tiresome, exhausting, ineffective and especially way too time consuming for graduating with a PhD in bioinformatics before my funding runs out despite being severely limited by my visual disability. I would also need help with writing a good literature review and applying the described techniques to my own yeast Affimetrix microarray dataset because I cannot see well enough to find all relevant publications on my own. Some examples for specific tasks I urgently need help with are: 1. Analyzing and comparing the three publically available microarray datasets that can be accessed at: A. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41860 B. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38635 C. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9217 2. Learning how to use the Affymetrics microarray analysis software for the Yeast 2 chip, which can be found at http://www.affymetrix.com/support/technical/libraryfilesmain.affx 3. For Cytoscape I need somebody, who can teach me how to execute the tutorials at the following links because due to my very limited vision field I cannot see tutorial and program interface simultaneously. A. http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytosc… B. http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Filtering_and_Editing_… C. http://cytoscape.org/manual/Cytoscape2_8Manual.html#Import%20Fixed-Format%2… D. http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats 4. Learning how to use the TopGo R package to perform statistical analysis on GO enrichments. Since I am legally blind the rehab agency is giving me money to pay tutors for this purpose. Could you please help me getting in touch regarding this with anybody, who could potentially be interested in teaching me one on one thus saving me time for acquiring new information and skills, which I need to finish my thesis on time, so that I can remain eligible for funding to continue in my bioinformatics PhD program despite being almost blind? The tutoring can be done remotely via TeamViewer 5 and Skype. Hence, it does not matter where my tutors are physically located. Currently I have tutors in Croatia and UK. But since they both work full time jobs while working on their PhD dissertation they only have very limited time to teach me online. Could you therefore please forward this request for help to anybody, who could potentially be interested or, who could connect me to somebody, who might be, because my graduation and career depend on it? Who else would you recommend me to contact regarding this? Where else could I post this because I am in urgent need for help? Could you please contact me directly via email at Thomas.F.Hahn2(a)gmail.com and/or Skype at tfh002 because my text to speech software has problems to read out this website aloud to me? I thank you very much in advance for your thoughts, ideas, suggestions, recommendations, time, help, efforts and support. With very warm regards, *Thomas Hahn* 1) *Graduate student in the Joint Bioinformatics Program at the University of Arkansas at Little Rock (UALR) and the University of Arkansas Medical Sciences (UAMS) &* 2) *Research & Industry Advocate, Founder and Board Member of RADISH MEDICAL SOLUTIONS, INC. (**http://www.radishmedical.com/thomas-hahn/* <http://www.radishmedical.com/thomas-hahn/>*) * *Primary email: **Thomas.F.Hahn2(a)gmail.com* <Thomas.F.Hahn2(a)gmail.com> *Cell phone: 318 243 3940* *Office phone: 501 682 1440* *Office location: EIT 535* *Skype ID: tfh002* *Virtual Google Voice phone to reach me while logged into my email (i.e. * *Thomas.F.Hahn2(a)gmail.com* <Thomas.F.Hahn2(a)gmail.com>*), even when having no cell phone reception, e.g. in big massive buildings: *(501) 301-4890 <%28501%29%20301-4890> *Web links: * 1) https://ualr.academia.edu/ThomasHahn 2) https://www.linkedin.com/pub/thomas-hahn/42/b29/42 3) http://facebook.com/Thomas.F.Hahn <https://www.facebook.com/Thomas.F.Hahn> 4) https://twitter.com/Thomas_F_Hahn

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minor question about configure.Works()
by Matti Picus 03 Jan '15

03 Jan '15

if Works() fails, it currently prints the compiler error to stderr. This is confusing since the error has no context to determine if the "fatal error" reported during translation is actually important or not. I started a "quieter-translation" branch where I silenced the error entirely, does anyone have opinions one way or another? Matti

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Fwd: [Python-Dev] More compact dictionaries with faster iteration
by Armin Rigo 03 Jan '15

03 Jan '15

Hi all, About ordered dictionaries: ---------- Forwarded message ---------- From: Armin Rigo <arigo(a)tunes.org> Date: 3 January 2015 at 17:39 Subject: Re: [Python-Dev] More compact dictionaries with faster iteration To: Maciej Fijalkowski <fijall(a)gmail.com> Cc: Serhiy Storchaka <storchaka(a)gmail.com>, "<python-dev(a)python.org>" <python-dev(a)python.org> Hi all, On 1 January 2015 at 14:52, Maciej Fijalkowski <fijall(a)gmail.com> wrote: > PS. I wonder who came up with the idea first, PHP or rhettinger and > who implemented it first (I'm pretty sure it was used in hippy before > it was used in Zend PHP) We'd need to look more in detail to that question, but a quick look made me find this Java code from 2012: https://code.google.com/r/wassermanlouis-guava/source/browse/guava/src/com/… which implements almost exactly the original idea of Raymond. (It has a twist because Java doesn't support arrays of (int, int, Object, Object), and instead encodes it as one array of long and one array of Objects. It also uses a chain of buckets instead of open addressing.) A bientôt, Armin.

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stdlib-2.7.9!
by Alex Gaynor 02 Jan '15

02 Jan '15

Hey all, Earlier today I created the 2.7.9 branch, with the copy of the 2.7.9 stdlib. http://buildbot.pypy.org/summary?branch=stdlib-2.7.9 is the branch summary. It's no surprise, the biggest work to be done is for the ssl module, 2.7.9 contains a complete backport of 3.4's ssl module. We have up through 3.2s version of the ssl module implemented on the py3k branch. I'd like some feedback from folks on how you think we should best handle finishing the 2.7.9 work. Should I copy the work from py3k, finish anything missing, and then when we get to python 3.4 on the py3k branch the work is just "already done"? Something else? Feedback please! Alex

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