Posts by Dotsch

21) Message boards : Number crunching : Dotsch/UX 1.2 Beta (Message 64753)
Posted 3 Jan 2010 by Dotsch
Post:
I am working on a new Dotsch/UX 1.2 release in the moment in the alpha test.

Mayor changes are CUDA implementaion and CUDA tools, Live CD persistent home directory mode, a Grid Perfomance mointoring tool, integrated backup over network and to local devices, and a lot of enhancements and fixes.

I would very happy, if anybody would been interested to help beta test the new release. The beta test would start at the mid/end of the comming week.
Please contact me via PM, if you are interested in Beta test the new release.
22) Questions and Answers : Unix/Linux : Anyone working on a FreeBSD port for Rosetta? (Message 61548)
Posted 2 Jun 2009 by Dotsch
Post:
Still not successfull:
30-May-2009 16:20:02 [rosetta@home] Starting lr5_D_chbond_05_run2_rlbn_1opd_SAVE_ALL_OUT_NATIVE_NOCON_12601_185_1
30-May-2009 16:20:02 [rosetta@home] Starting task lr5_D_chbond_05_run2_rlbn_1opd_SAVE_ALL_OUT_NATIVE_NOCON_12601_185_1 using minirosetta version 171
30-May-2009 16:20:06 [rosetta@home] Computation for task lr5_D_chbond_05_run2_rlbn_1opd_SAVE_ALL_OUT_NATIVE_NOCON_12601_185_1 finished
30-May-2009 16:20:06 [rosetta@home] Output file lr5_D_chbond_05_run2_rlbn_1opd_SAVE_ALL_OUT_NATIVE_NOCON_12601_185_1_0 for task lr5_D_chbond_05_run2_rlbn_1opd_SAVE_ALL_OUT_NATIVE_NOCON_12601_185_1 absent

By some reason minirosetta doesn't run or just exits on start. Although i don't see any crash messages.


I have checked your results. Rosetta Beta works fine.

But for the Minirosetta application the file minirosetta_database.zip is missing. You can manualy download it and put it to the projects/boinc.bakerlab_rosetta/ directory. After this I think it should work.
If not the app_info.xml must be adujsted. But I will test this, too.
23) Questions and Answers : Unix/Linux : Anyone working on a FreeBSD port for Rosetta? (Message 61547)
Posted 2 Jun 2009 by Dotsch
Post:
by the way, is there a minirosetta source code? It would be easier to compile it on freebsd.

No. So far I know It's closed source. If it waould be open source I had still ported Rosetta to many platforms as posible, as I have done it for SETI, SIMAP and other projects.

Btw. SIMAP and SETI has also native FreeBSD applications...
24) Questions and Answers : Unix/Linux : Anyone working on a FreeBSD port for Rosetta? (Message 61466)
Posted 30 May 2009 by Dotsch
Post:
I have checked your results...

It looks like Rosetta 5.98 works on i386 and x64.

But the minirosetta version made some problems. All tasks fail.
I guess you are using the wrong minirosetta version. In the log I see you are using 1.28. In the moment 1.71 is available. Could you please download the binary from [/url]http://boinc.bakerlab.org/rosetta/download/minirosetta_1.71_i686-pc-linux-gnu[/url] and adjust the version in the app_info.xml, like this one : [/code]
<app_info>
<app>
<name>rosetta_beta</name>
</app>
<file_info>
<name>rosetta_beta_5.98_i686-pc-linux-gnu</name>
<executable/>
</file_info>
<app_version>
<app_name>rosetta_beta</app_name>
<version_num>598</version_num>
<file_ref>
<file_name>rosetta_beta_5.98_i686-pc-linux-gnu</file_name>
<main_program/>
</file_ref>
</app_version>

<app>
<name>minirosetta</name>
</app>
<file_info>
<name>minirosetta_1.67_i686-pc-linux-gnu</name>
<executable/>
</file_info>
<app_version>
<app_name>minirosetta</app_name>
<version_num>167</version_num>
<file_ref>
<file_name>minirosetta_1.67_i686-pc-linux-gnu</file_name>
<main_program/>
</file_ref>
</app_version>

</app_info>[/code]

There is no method to automaticly update with a app_info.xml. But, the rosetta 5.98 version is still stable since several month. The minirosetta version has a lot of new releases.
25) Questions and Answers : Unix/Linux : Anyone working on a FreeBSD port for Rosetta? (Message 61433)
Posted 28 May 2009 by Dotsch
Post:

But there should be a way to obtain fresh binaries.

sorry, I don't understand excatly.
26) Questions and Answers : Unix/Linux : Anyone working on a FreeBSD port for Rosetta? (Message 61373)
Posted 26 May 2009 by Dotsch
Post:
It works!!! =)) Thank you very much, Dotsch.

Great !


Btw, where can i get linux binaries to try rosetta on freebsd for amd64?

I am not shure, if the Linux x64 binary is a native 64 bit binary, or only a 32 bit application which run with 32 bit compat libs on x64 Linux systems.

I have not tested the Linux compat on a x64 FreeBSD system in the moment. But, all I have seen in the web, it should exactly the same procedure like on FreeBSD i386. So you can run 32 bit Linux binaries on AMD64 FreeBSD systems...
27) Questions and Answers : Unix/Linux : Anyone working on a FreeBSD port for Rosetta? (Message 61364)
Posted 25 May 2009 by Dotsch
Post:
The app_info.xml normaly was offered as a link in the howto, but the link was broken. Sorry.

You need to change the version numbers between <version_num>, <file_name> and <name>.

This app_info.xml contains the current version numbers :
<app_info>
    <app>
        <name>rosetta_beta</name>
    </app>
    <file_info>
        <name>rosetta_beta_5.98_i686-pc-linux-gnu</name>
        <executable/>
    </file_info>
    <app_version>
        <app_name>rosetta_beta</app_name>
        <version_num>598</version_num>
        <file_ref>
            <file_name>rosetta_beta_5.98_i686-pc-linux-gnu</file_name>
            <main_program/>
        </file_ref>
    </app_version>

    <app>
        <name>minirosetta</name>
    </app>
    <file_info>
        <name>minirosetta_1.67_i686-pc-linux-gnu</name>
        <executable/>
    </file_info>
    <app_version>
        <app_name>minirosetta</app_name>
        <version_num>167</version_num>
        <file_ref>
            <file_name>minirosetta_1.67_i686-pc-linux-gnu</file_name>
            <main_program/>
        </file_ref>
    </app_version>

</app_info>

28) Questions and Answers : Unix/Linux : Anyone working on a FreeBSD port for Rosetta? (Message 61354)
Posted 24 May 2009 by Dotsch
Post:
Hi! Are there any updates on this topic? I'd like to run rosetta on two FreeBSD 7.X hosts (i386 and amd64).

Yes. I have tested the FreeBSD Linux Compat successfully and written a howto : http://www.dotsch.de/boinc/BSD_Linux-Compat_howto.html
The instructions are for older rosetta/minirosetta versions. So you need to update the app_info.xml...
29) Message boards : Number crunching : Problems with Minirosetta Version 1.67 (Message 61259)
Posted 19 May 2009 by Dotsch
Post:
Simliar error at WU http://boinc.bakerlab.org/rosetta/result.php?resultid=251404320

Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
SIGBUS: bus error

Crashed executable name: minirosetta_1.67_i686-apple-darwin
built using BOINC library version 6.5.0
Machine type Intel 80486 (32-bit executable)
System version: Macintosh OS 10.5.7 build 9J61
Tue May 19 08:42:26 2009

atos cannot load symbols for the file minirosetta_1.67_i686-apple-darwin.
0 0x006c0345 SIGPIPE: write on a pipe with no reader
1 0x004a3d8e SIGPIPE: write on a pipe with no reader
2 0x91e5e2bb SIGPIPE: write on a pipe with no reader
3 0xffffffff SIGPIPE: write on a pipe with no reader
4 0x0002a4a7 SIGPIPE: write on a pipe with no reader
5 0x000910d0 SIGPIPE: write on a pipe with no reader
6 0x00518bdc SIGPIPE: write on a pipe with no reader
7 0x00b59c20 SIGPIPE: write on a pipe with no reader
8 0x0013b068 SIGPIPE: write on a pipe with no reader
9 0x00005db8 SIGPIPE: write on a pipe with no reader
10 0x0000292e SIGPIPE: write on a pipe with no reader
11 0x00002855
Thread 0 crashed with X86 Thread State (32-bit):
eax: 0xffffffe1 ebx: 0x91e268c2 ecx: 0xbfffc25c edx: 0x91df2286
edi: 0x00000000 esi: 0x00000000 ebp: 0xbfffc298 esp: 0xbfffc25c
ss: 0x0000001f efl: 0x00000206 eip: 0x91df2286 cs: 0x00000007
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
30) Message boards : Number crunching : Problems with Minirosetta Version 1.67 (Message 61216)
Posted 16 May 2009 by Dotsch
Post:
Got a SIGBUS from http://boinc.bakerlab.org/rosetta/result.php?resultid=250688320 :

Starting watchdog...
Watchdog active.
Continuing computation from checkpoint: chk_S_1AOGA_10_0001_FastRelax__chk1_fa ... success!
Continuing computation from checkpoint: chk_S_1S3QA_2_0001_FastRelax__chk1_fa ... success!
SIGBUS: bus error

Crashed executable name: minirosetta_1.67_i686-apple-darwin
built using BOINC library version 6.5.0
Machine type Intel 80486 (32-bit executable)
System version: Macintosh OS 10.5.6 build 9G55
Sat May 16 04:47:32 2009

atos cannot load symbols for the file minirosetta_1.67_i686-apple-darwin.
0 0x006c0345 SIGPIPE: write on a pipe with no reader
1 0x004a3d8e SIGPIPE: write on a pipe with no reader
...
31) Questions and Answers : Wish list : IRIX support, please? (Message 61215)
Posted 16 May 2009 by Dotsch
Post:
If you are interested in other BOINC project, SETI and SIMAP (bio medical project) has also binaries for IRIX available.

The SETI application and a BOINC client for IRIX is available on my homepage http://www.dotsch.de.
The SIMAP IRIX application is available on the SIMAP download page http://boinc.bio.wzw.tum.de/boincsimap/appdownloads.php
32) Message boards : Number crunching : No Work for PPC? (Message 60271)
Posted 22 Mar 2009 by Dotsch
Post:
Since there might be occasional work available, I will leave my PPC Mac attached to Rosetta.

While I am waiting I will keep my PPC Mac busy with World Community Grid and Superlink

I think SIMAP, POEM and Lattice are also very interesting projects wich has MacOS PPC support.
33) Message boards : Number crunching : Dotsch/UX - A USB/Diskless/Harddisk BOINC Linux Distribution (Message 59975)
Posted 4 Mar 2009 by Dotsch
Post:
Today I have released Dotsch/UX 1.1. Mayor changes are the availability of a 32 bit (i386) and 64 bit (x64) distribution, mixed i386 and x64 diskless client on one single diskless server, build in BOINC client 6.4.5 and bug fixes
 for the USB, hard disk, diskless server and diskless client Installation tools.

The distribution is available at http://www.dotsch.de/Dotsch_UX
34) Message boards : Number crunching : Dotsch/UX - A USB/Diskless/Harddisk BOINC Linux Distribution (Message 59690)
Posted 20 Feb 2009 by Dotsch
Post:
I am alpha testing the next Dotsch/UX relase for x86 (32 bit) and x64 (64 bit) in the moment. If anybody is interested in alpha testing the new release, please contact me via PM or email.

New features are the x64 support, mixed x64/x86 diskless clients on the same diskless server, DHCP server for a non diskless server, build in CUDA support and several bug fixes for the USB stick and diskless/server installation.
35) Message boards : Number crunching : SETI infected by Rosetta? (Message 59022)
Posted 25 Jan 2009 by Dotsch
Post:
Sorry, duplicate posting.
36) Message boards : Number crunching : SETI infected by Rosetta? (Message 59021)
Posted 25 Jan 2009 by Dotsch
Post:
I thought it was going to use the harddrive all by itself, but how could it if it didn't make it a Linux drive?

No. The CD boot is in the moment thought for booting the OS and do the installation on the desired media.


I will look forward to the next release and try that with a USB stick. Will a 1gb stick be enough?

I think, you did not need to wait, because the hard disk and USB stick installation is already implemented. With the actual release, it is posible to boot Dotsch/UX from the CD, and make a hard disk or an USB stick installation and boot from them.
The USB installation is described on part 2.1 ([url]http://www.dotsch.de/boinc/DotschUX-USB_Installation.html[url]), and the hard disk install at part 2.2 (http://www.dotsch.de/boinc/DotschUX-HDD_Installation.html) of the manual.

I am not shure, if a 1 GB USB stick is enought for Rosetta, because Rosetta has a lot of HDD space requirements. On the Rosetta system requirments are 400 MB available diskspace listed. - The USB stick OS has about 500 MB, plus 128 MB for storing OS data and changes and the rest will be used for the BOINC home directory for storing the BOINC Client and projects data. - With a 1 GB stick, are this about 400 MB. - You can try, if rosetta would work with a 1 GB stick, eventualy you can change the disk preferences, that BOINC uses the whole space. If this would not work, you have to use a 2 GB stick.
37) Message boards : Number crunching : SETI infected by Rosetta? (Message 59016)
Posted 24 Jan 2009 by Dotsch
Post:
P.S. As for the project list being empty, its sounds like Dotsch forgot to include an all_projects.xml file. That's the file that stores the names and URLs of the projects in the project list. BOINC client updates all_projects.xml about once a week so eventually you would get one.

The all_projects.xml would normaly automaticly downloaded from the BOINC servers. If it would not been downloaded, eventualy the network was not configured. Per default the installation uses DHCP till you configure it manualy.
38) Message boards : Number crunching : SETI infected by Rosetta? (Message 59014)
Posted 24 Jan 2009 by Dotsch
Post:
Thank you very much Mikey for testing my distribution and your report.

If I understood your report right, you have used the BOINC client directly from the CDROM without installing directly to a USB or HDD ? - In the moment this is not really the good way, because your data would not be written to any media and saved for recovering from any power failures and you have got to save the data manualy. I recommend you to create a USB stick or install the OS to a hard disk to get persistant data of your BOINC data.
Eric Meyers had some very good ideas for a improvment which makes a "live cd" mode posible, which should handle this. I think this is very good idea and I will develop and impment this in the next releases. The idea is that the users can boot from CD, insert a USB stick or connect a network share, and the BOINC client data would be written permanent or periodcaly to the USB stick.

Edit: Your're both right Dotsch/UX is based on Ubuntu and from users sight it's usable like Ubuntu, and has the tools to setup a BOINC diskless/USB/hard disk system as easy as posible.
39) Message boards : Number crunching : Performance settings help 4 Noob (Message 58910)
Posted 18 Jan 2009 by Dotsch
Post:
BitSpit at XPC has a diskless linux cluster, but it's a lot more demanding to set up than CF, and it's also quite picky about the LAN chipset/BIOS I believe. Very elegant solution though...


Definitely not a "simple fix", most semi-modern network adapters and BIOS support the options, however configuration can be a bit difficult at times.

wanted to add one more link that has a lot of useful info, and links to other detailed how-to's.

http://www.kegel.com/linux/pxe.html

I have released Dotsch/UX 1.0. - Dotsch/UX is a Linux distribution for BOINC which easily installs and boot from a USB stick, hard disk and from diskless clients and also has some interfaces to setup the diskless server and the clients automatically.

For more informations have a look at http://www.dotsch.de/Dotsch_UX
40) Message boards : Number crunching : Dotsch/UX - A USB/Diskless/Harddisk BOINC Linux Distribution (Message 58842)
Posted 15 Jan 2009 by Dotsch
Post:
Today I have released Dotsch/UX 1.0. - Dotsch/UX is a Linux distribution for BOINC which easily installs and boot from a USB stick, hard disk and from diskless clients and also has some interfaces to setup the diskless server and the clients automatically.

For more informations have a look at http://www.dotsch.de/Dotsch_UX


Previous 20 · Next 20



©2024 University of Washington
https://www.bakerlab.org