Posts by [VENETO] sabayonino
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1) Message boards : Science : DREAM5 E. coli dataset (Message 839)
Posted 1 Feb 2017 by Profile [VENETO] sabayonino
Hi Francesco,
very interesting.

About "DREAM5" competition --> http://gnw.sourceforge.net/index.html

right ?

if you need more computation power , just ask :D
2) Message boards : Number crunching : Gene application for GNU/Linux on ARM devices (Message 629)
Posted 8 Dec 2016 by Profile [VENETO] sabayonino
run
gcc -march=native -E -v - </dev/null 2>&1 | grep cc1


to see what flags gcc=native enable or disable

These could be different from cpuinfo flags

don't run --march=native for not ARMv7-?? models

Cortex-M , Cortex-R and so on may have some different flags that could be not recognized from all
3) Message boards : Number crunching : Badges (all of them) (Message 613)
Posted 29 Nov 2016 by Profile [VENETO] sabayonino
Thank you !!
4) Message boards : News : gene@home: Holidays are approaching (Message 478)
Posted 26 Dec 2014 by Profile [VENETO] sabayonino
Happy new year guys :)

and thanks to take busy our cpu's :D
5) Message boards : News : gene@home: October update (Message 443)
Posted 1 Nov 2014 by Profile [VENETO] sabayonino
all WU's still crunching fine on my Linux Boxes :)


no errors to be reported

:) ^^
6) Message boards : News : gene@home: October update (Message 440)
Posted 14 Oct 2014 by Profile [VENETO] sabayonino
I'm ready to crunch for TN-G. :)
7) Message boards : Number crunching : fetching WUs : HTTP error (Message 347)
Posted 24 Mar 2014 by Profile [VENETO] sabayonino
Hi Guys and welcome back :)

I got some WUs but :
sabayon 58 TN-Grid Test Platform 24/03/2014 20.17.32 Scheduler request completed: got 1 new tasks 59 TN-Grid Test Platform 24/03/2014 20.17.34 Started download of tngrid_expansion_v5_linux64 60 TN-Grid Test Platform 24/03/2014 20.17.34 Started download of separate_At2_AT120 61 TN-Grid Test Platform 24/03/2014 20.17.40 Finished download of tngrid_expansion_v5_linux64 62 TN-Grid Test Platform 24/03/2014 20.17.40 Started download of experiments.txt 63 TN-Grid Test Platform 24/03/2014 20.17.41 Giving up on download of experiments.txt: permanent HTTP error 64 TN-Grid Test Platform 24/03/2014 20.17.41 Started download of 29_tile.txt 65 TN-Grid Test Platform 24/03/2014 20.17.48 Finished download of 29_tile.txt 66 TN-Grid Test Platform 24/03/2014 20.19.39 Sending scheduler request: To report completed tasks. 67 TN-Grid Test Platform 24/03/2014 20.19.39 Reporting 1 completed tasks 68 TN-Grid Test Platform 24/03/2014 20.19.39 Not requesting tasks: don't need 69 TN-Grid Test Platform 24/03/2014 20.19.47 Scheduler request completed


and

http://gene.disi.unitn.it/test/result.php?resultid=40505

Output su Stderr <core_client_version>7.2.33</core_client_version> <![CDATA[ <message> WU download error: couldn't get input files: <file_xfer_error> <file_name>experiments.txt</file_name> <error_code>-224</error_code> <error_message>permanent HTTP error</error_message> </file_xfer_error> </message> ]]>


and so on...
8) Message boards : Unix/Linux : glibc version problem (Message 333)
Posted 25 Jan 2014 by Profile [VENETO] sabayonino
As I wrote on the BOINC @ TN thread on BOINC.Italy the 32 bit Linux executable was compiled on Ubuntu with kernel 3.2.0-56 and glib version 2.13, while the 64 bit was compiled on Ubuntu with kernel 3.2.0-23 and glib version 2.13..

I can't figure out why the 32 bit is resolved while the 64 bit still present the known issue related to the glib version.

Hope we can find out soon and solve this problem.
Thanks again for report here all the problems you guys found!


gcc version (or other compiler...) ?


@ valter : see this http://www.win.tue.nl/~aeb/linux/misc/gcc-semibug.html
memcpy seems to be pushed by gcc option

you could try to pass -fno-builtin-memcpy option to gcc comand line


[edit] memcpy function in C (Italian)

and
GCC docs
[...]-fno-builtin-function
Don't recognize built-in functions that do not begin with ‘__builtin_’ as prefix. See Other built-in functions provided by GCC, for details of the functions affected, including those which are not built-in functions when -ansi or -std options for strict ISO C conformance are used because they do not have an ISO standard meaning.

GCC normally generates special code to handle certain built-in functions more efficiently; for instance, calls to alloca may become single instructions which adjust the stack directly, and calls to memcpy may become inline copy loops. The resulting code is often both smaller and faster, but since the function calls no longer appear as such, you cannot set a breakpoint on those calls, nor can you change the behavior of the functions by linking with a different library. In addition, when a function is recognized as a built-in function, GCC may use information about that function to warn about problems with calls to that function, or to generate more efficient code, even if the resulting code still contains calls to that function. For example, warnings are given with -Wformat for bad calls to printf when printf is built in and strlen is known not to modify global memory.

With the -fno-builtin-function option only the built-in function function is disabled. function must not begin with ‘__builtin_’. If a function is named that is not built-in in this version of GCC, this option is ignored. There is no corresponding -fbuiltin-function option; if you wish to enable built-in functions selectively when using -fno-builtin or -ffreestanding, you may define macros such as:

#define abs(n) __builtin_abs ((n))
#define strcpy(d, s) __builtin_strcpy ((d), (s))
[...]



is memcpy needed ?
9) Message boards : Unix/Linux : glibc version problem (Message 329)
Posted 24 Jan 2014 by Profile [VENETO] sabayonino
i think there's link problem to the dinamic linker in 64bit platform to run 32 bit binaries

in 64 bit platform , /lib is linked to /lib64 folder.

your excutable check all libraries in /lib and /lib64

you can try this :
cd /lib && sudo ln -s /lib64/ld-linux-x86-64.so.2

(file exists ?? )

hope fine.
10) Message boards : Unix/Linux : glibc version problem (Message 326)
Posted 22 Jan 2014 by Profile [VENETO] sabayonino
Version 4 have still this problem unsolved.
Interestingly, the 32bit version seem ok and the problem is only on the 64bit.


can you share ldd output for gene application ? (for both applications 32/64)
11) Message boards : Number crunching : Abort for Output file Expansion........... absent (Message 325)
Posted 22 Jan 2014 by Profile [VENETO] sabayonino
This problem is also present in the current debian stable 64bit as also reported in linux section of this forum.
So I don't think that a good solution is to say to partecipant: upgrade your system.
Try to get it fixed via static linking or using an older linux machine for compiling.


I know... I realize that zioriga run an old Virtualized System :D
12) Message boards : Number crunching : Abort for Output file Expansion........... absent (Message 320)
Posted 22 Jan 2014 by Profile [VENETO] sabayonino
@zioriga : Dotschux is too old and no longer manteined

your glibc and boinc_client versions are too old

consider to update your (virtual) system (like last Ubuntu release or other)


as you can see : http://gene.disi.unitn.it/test/result.php?resultid=40238

<core_client_version>6.10.17</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> ../../projects/gene.disi.unitn.it_test/tngrid_expansion_v4_linux64: /lib/libc.so.6: version `GLIBC_2.14' not found (required by ../../projects/gene.disi.unitn.it_test/tngrid_expansion_v4_linux64) </stderr_txt> ]]>




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