Rosetta 4.0+

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Jim1348

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Message 88936 - Posted: 18 May 2018, 18:54:55 UTC - in response to Message 88935.  

Is there an issue system to report this and see any progress.

I think this is the system to report. As for progress, we will see.
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[DPC]Remmus

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Message 88937 - Posted: 18 May 2018, 19:39:38 UTC - in response to Message 88936.  

Not much response yet..... :-(
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Profile [AF>Libristes]Maeda
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Message 88939 - Posted: 18 May 2018, 21:08:19 UTC - in response to Message 88937.  

It may be related, but a workaround has been found on World Community Grid project, which some project have a static link to an (quite) old glibc, and devs says they will rebuilt their apps as soon as possible, as many Linux users with recent kernel will encounter the problem.

I didn't do it as it seems to enable again some vulnerabilities...
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rjs5

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Message 88941 - Posted: 18 May 2018, 22:30:03 UTC - in response to Message 88936.  
Last modified: 18 May 2018, 22:32:18 UTC

Is there an issue system to report this and see any progress.

I think this is the system to report. As for progress, we will see.


... maybe a workaround to running static linked glibc old applications on glibc 2.27 systems.

I don't have access to sources so I had to guess how Rosetta developers had screwed up.

I installed a Fedora 28 which uses glibc 2.27 on Oracle Virtualbox and reproduced the "locale" error.
"rosetta_4.07_x86_64-pc-linux-gnu: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed."

I edited the Fedora 28 file /etc/locale.conf to add the 2 extra lines below (LC_CTYPE=C and LC_MESSAGES=C).
Rebooted the virtual machine.
Instead of Rosetta 4.07 x86_64 failing immediately, a 4.07 x86_64 WU is currently 17 minutes into computation and seems to now function.


Try this ....


cat /etc/locale.conf

LANG="en_US.UTF-8"
LC_CTYPE=C
LC_MESSAGES=C
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Jim1348

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Message 88942 - Posted: 19 May 2018, 1:33:00 UTC - in response to Message 88941.  
Last modified: 19 May 2018, 1:55:28 UTC

cat: /etc/locale.conf: No such file or directory


It doesn't find that file on Ubuntu 18.04. Is there another location?

EDIT: Never mind, I just created it and rebooted. I will report how it works on the next x64.
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rjs5

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Message 88943 - Posted: 19 May 2018, 1:59:38 UTC - in response to Message 88942.  

cat: /etc/locale.conf: No such file or directory


It doesn't find that file on Ubuntu 18.04. Is there another location?

EDIT: Never mind, I just created it and rebooted. I will report how it works on the next x64.



For Ubuntu systems try:

cat /etc/default/locale

I will build a vbox version of 18.04 so i can test it, in case that does not work.
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Jim1348

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Message 88944 - Posted: 19 May 2018, 2:04:22 UTC - in response to Message 88943.  
Last modified: 19 May 2018, 2:20:41 UTC

For Ubuntu systems try:

cat /etc/default/locale

EDIT:

Placing "locale.conf" in the /etc/ directory seems to prevent a terminal window from opening. But /etc/default/local does exit by default, so I will try that once I get rid of /etc/locale.conf.
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rjs5

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Message 88945 - Posted: 19 May 2018, 2:48:30 UTC - in response to Message 88944.  
Last modified: 19 May 2018, 3:27:53 UTC

For Ubuntu systems try:

cat /etc/default/locale

EDIT:

Placing "locale.conf" in the /etc/ directory seems to prevent a terminal window from opening. But /etc/default/local does exit by default, so I will try that once I get rid of /etc/locale.conf.



making the changes to /etc/default/locale works too. BOINC Rosetta works for x86_64.
I will work on getting the terminal part figured out.
There is a a set-locale command that probably should be used.


https://www.thomas-krenn.com/en/wiki/Configure_Locales_in_Ubuntu


Install the "Konsole" command to get a "terminal" back
Konsole is like terminal
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rjs5

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Message 88946 - Posted: 19 May 2018, 5:49:18 UTC - in response to Message 88945.  

For Ubuntu systems try:

cat /etc/default/locale

EDIT:

Placing "locale.conf" in the /etc/ directory seems to prevent a terminal window from opening. But /etc/default/local does exit by default, so I will try that once I get rid of /etc/locale.conf.



making the changes to /etc/default/locale works too. BOINC Rosetta works for x86_64.
I will work on getting the terminal part figured out.
There is a a set-locale command that probably should be used.


https://www.thomas-krenn.com/en/wiki/Configure_Locales_in_Ubuntu


Install the Ubuntu "Konsole" command to get a console back
Konsole is like terminal



I played around with the LANGUAGE SETTINGS. I set the Region/Language to Canadian which sets all the locale options, rebooted.
Terminal came back but Rosetta 4.07 started failing again.
I looked at the locale file settings and the LC_time had been removed and LANGUAGE was set to something other than "C".

It looks like Konsole works fine in either case, but the "terminal" and Rosetta 4.07 64-bit have incompatibilities and seem to want conflicting locale settings.

Maybe tomorrow evening I will try to isolate the specific combination of changes needed.

Too bad someone at Rosetta cannot fix their bug.

BTW, while 4.07 64-bit is broken, for anyone wanting the object files, you can formally request that Rosetta give you the object files. If they decline then just email ( license-violation@gnu.org ) and report the lack of Rosetta 4.07 64-bit linkable object files. and that it is failing on glbc 2.27. I saw that someone earlier had requested the object files, so Rosetta is now in violation of the FSF they agreed to by static linking glibc.
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Jim1348

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Message 88947 - Posted: 19 May 2018, 6:38:50 UTC - in response to Message 88945.  
Last modified: 19 May 2018, 7:08:48 UTC


I will work on getting the terminal part figured out.
There is a a set-locale command that probably should be used.

https://www.thomas-krenn.com/en/wiki/Configure_Locales_in_Ubuntu

Install the "Konsole" command to get a "terminal" back
Konsole is like terminal

Thanks, but after unsuccessfully trying to boot into GRUB (maybe a USB problem), I changed to a PS/2 keyboard and booted into Partition Magic. Then, I used their file tool to delete /etc/locale.conf. Now I am back to normal and will proceed accordingly. It looks like it should work. You would think that Rosetta should be able to figure it out.

Thanks.

EDIT: After making those changes to /etc/default/local, I am again not able to open a terminal. I guess that is what you were saying, but I misinterpreted it. So I will just remove those lines again and wait. Best of luck.
(I think they may be putting their development efforts into Windows. I have had better luck with that recently.)
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rjs5

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Message 88950 - Posted: 19 May 2018, 13:47:56 UTC - in response to Message 88947.  


I will work on getting the terminal part figured out.
There is a a set-locale command that probably should be used.

https://www.thomas-krenn.com/en/wiki/Configure_Locales_in_Ubuntu

Install the "Konsole" command to get a "terminal" back
Konsole is like terminal

Thanks, but after unsuccessfully trying to boot into GRUB (maybe a USB problem), I changed to a PS/2 keyboard and booted into Partition Magic. Then, I used their file tool to delete /etc/locale.conf. Now I am back to normal and will proceed accordingly. It looks like it should work. You would think that Rosetta should be able to figure it out.

Thanks.

EDIT: After making those changes to /etc/default/local, I am again not able to open a terminal. I guess that is what you were saying, but I misinterpreted it. So I will just remove those lines again and wait. Best of luck.
(I think they may be putting their development efforts into Windows. I have had better luck with that recently.)



Sorry. You fell into all the traps that I did.
There is another TERMINAL program named "Konsole". You can install it

It seems that "terminal" and Rosetta 4.07 64-bit require conflicting locale settings.
"konsole" does not seem to depend on locale since I was able to set the locale variables and konsole ran both ways.


For a long time, Rosetta built its x86 version ONLY using SSE because they wanted to keep the old, old, old old systems working.
It is rather humorous that they are now (and have been for weeks) ignoring the plight of everyone running the NEW Linux distributions on leading edge machines.

The "fix" could be as simple as disabling the 64-bit version of Rosetta 4.07 until fixed.

I understood and had no problems with any of their previous positions. The project silence now is very disappointing.
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Juha

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Message 88951 - Posted: 19 May 2018, 17:21:39 UTC - in response to Message 88941.  

/etc/locale.conf


Instead of changing language options globally I would suggest limiting changes to only what is needed, in this case BOINC client.

For those using repository BOINC package and systemd distro, you can edit boinc-client.service file or add an override to the service. The override would look something like this:

[Service]
Environment=LC_ALL=C


LC_ALL overrides all the other language settings. Put the override file in /etc/systemd/system/boinc-client.service.d/locale.override.conf and restart the client with sudo systemctl restart boinc-client. If changing the distro supplied service file then find boinc-client.service and add the Environment line in Service section. Changes to the file will be overwritten any time the package is updated.

For those not using distro package or not using systemd make similar change to whatever startup script you use for the client.
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[DPC]Remmus

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Message 88952 - Posted: 19 May 2018, 20:55:15 UTC - in response to Message 88941.  

Thanks, I will try this if the system entry by Juha dows not work!
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rjs5

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Message 88954 - Posted: 19 May 2018, 23:43:42 UTC - in response to Message 88951.  

/etc/locale.conf


Instead of changing language options globally I would suggest limiting changes to only what is needed, in this case BOINC client.

For those using repository BOINC package and systemd distro, you can edit boinc-client.service file or add an override to the service. The override would look something like this:

[Service]
Environment=LC_ALL=C


LC_ALL overrides all the other language settings. Put the override file in /etc/systemd/system/boinc-client.service.d/locale.override.conf and restart the client with sudo systemctl restart boinc-client. If changing the distro supplied service file then find boinc-client.service and add the Environment line in Service section. Changes to the file will be overwritten any time the package is updated.

For those not using distro package or not using systemd make similar change to whatever startup script you use for the client.



This works for me on Ubuntu 18.04 vbox. "terminal" opens and Boinc 4.07 64-bit executes for several minutes.

I added the above to the "/lib/systemd/system/boinc-client.service" file under the [Service] section.
Should I make a new "[pre][Service]" section instead?
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[DPC]Remmus

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Message 88957 - Posted: 20 May 2018, 15:35:15 UTC - in response to Message 88954.  

I needed to create the directory boinc-client.service.d
and afterwards create the file locale.override.conf with the given entry for the service.
[Service]
Environment=LC_ALL=C

I needed to refresh the systemd services.

And now it is working for 4.07 jobs!!!!
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Juha

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Message 88958 - Posted: 20 May 2018, 19:56:55 UTC - in response to Message 88954.  
Last modified: 20 May 2018, 19:57:33 UTC

I added the above to the "/lib/systemd/system/boinc-client.service" file under the [Service] section.


That's ok.

Should I make a new "[pre][Service]" section instead?


I don't really know what systemd says if you have more than one section with the same name in the same file.
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rjs5

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Message 88959 - Posted: 21 May 2018, 0:22:47 UTC - in response to Message 88958.  

I added the above to the "/lib/systemd/system/boinc-client.service" file under the [Service] section.


That's ok.

Should I make a new "[pre][Service]" section instead?


I don't really know what systemd says if you have more than one section with the same name in the same file.



I would totally defer to those who better know the Linux internals.

Now that "[DPC]Remmus" has his system working, the Rosetta crunchers can at least make the choice to repair the Rosetta 4.07 x86_64 bug ... and have a model. That was my goal.

It would have been easier for Rosetta to properly test 4.07 first before releasing OR to respond to problems reported here ... OR even simply stop sending out the 4.07 64-bit version WUs (would probably take 60 seconds).

Thanks for your help.
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Message 88978 - Posted: 23 May 2018, 8:22:14 UTC - in response to Message 88907.  

Thanks,some time it runs very good,and after a while the error disapear,so i Guess all just ignor.
God bless the good work.

Mvh.akkin4.
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Profile Danny Kim

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Message 88983 - Posted: 23 May 2018, 23:33:55 UTC

Looks like I'm not first to post a computation error that points to the "chi angle", but I think no explanation or solution has been discussed yet. Or is that not the source of the problem?

<core_client_version>7.8.6</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: rosetta_4.09_x86_64-apple-darwin @rb_05_23_242_368_ab_t000__robetta_FLAGS -in::file::fasta t000_.fasta -psipred_ss2 t000_.spider3_ss2 -kill_hairpins t000_.nobuformat.spider3_ss2 -jumps:pairing_file t000_.fasta.bbcontacts.jumps -abinitio::use_filters false -skip_convergence_check -jumps:overlap_chainbreak -seq_sep_stages 1 1 1 -ramp_chainbreaks -sep_switch_accelerate 0.8 -jumps:random_sheets 3 1 -constraints::cst_file t000_.fasta.CB.cst -constraints:cst_weight 5.0 -constraints::cst_fa_file t000_.fasta.MIN.cst -constraints:cst_fa_weight 5.0 -in:file:boinc_wu_zip rb_05_23_242_368_ab_t000__robetta.zip -frag3 rb_05_23_242_368_ab_t000__robetta.200.3mers.index.gz -fragA rb_05_23_242_368_ab_t000__robetta.200.8mers.index.gz -fragB rb_05_23_242_368_ab_t000__robetta.200.4mers.index.gz -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1806461
Starting watchdog...
Watchdog active.
std::cerr: Exception was thrown:

File: src/core/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306
chi angle must be between -180 and 180: nan


</stderr_txt>
]]>
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Profile [VENETO] boboviz

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Message 89023 - Posted: 29 May 2018, 10:18:37 UTC

1001952207

ERROR: Unable to open weights/patch file. None of (./)beta_nov16_cart.wts or (./)beta_nov16_cart.wts.wts or minirosetta_database\scoring/weights/beta_nov16_cart.wts or minirosetta_database\scoring/weights/beta_nov16_cart.wts.wts exist
ERROR:: Exit from: ..\..\..\src\core\scoring\ScoreFunction.cc line: 2884
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

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