Mailman 3 January 2015 - pypy-dev

JIT Spikes During Timings
by Kevin Ednalino Jan. 10, 2015

Jan. 10, 2015

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 … [View More]

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Segmentation Fault
by Stuart Axon Jan. 7, 2015

Jan. 7, 2015

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]… [View More] [-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) [View Less]

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Thank You! [Question about VirtualEnv and PyPy is solved by your help!]
by 思 Jan. 7, 2015

Jan. 7, 2015

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 … [View More]

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Re: [pypy-dev] Ask Pypy within virtualenv of Windows 7/8 for Help ---- bitpeach from china
by Matti Picus Jan. 7, 2015

Jan. 7, 2015

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 … [View More]

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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 Jan. 4, 2015

Jan. 4, 2015

*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 … [View More]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 [View Less]

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minor question about configure.Works()
by Matti Picus Jan. 3, 2015

Jan. 3, 2015

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 Jan. 3, 2015

Jan. 3, 2015

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 … [View More]

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stdlib-2.7.9!
by Alex Gaynor Jan. 2, 2015

Jan. 2, 2015

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 … [View More]

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