Distributions of Linux

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Message 88807 - Posted: 3 May 2018, 14:43:00 UTC

Are there different distributions of Linux that perform better than others for this project or in general? Is there a difference in performance of Debian based OS's vs. Arch based? Are there certain settings/parameters you can change in the operating system that can improve performance/efficiency of crunching?

Are there also settings/parameters for windows that can be improved to speed things up?
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Message 88839 - Posted: 9 May 2018, 9:48:53 UTC - in response to Message 88807.  

Are you seeing the 3-day rb tasks with the "Computation error" status under Ubuntu 18.04? I've had a whole string of them, so I decided to visit the website and see if anyone else was reporting something along those lines... The normal deadline rb tasks seem to be okay, as are the various other tasks.

As regards performance variations among the various distros, I doubt there is much difference there. While I haven't tested between distros, the various distros are mostly using similar kernels. I do have one multi-boot machine that runs on Linux some of the time, and the performance on that machine seems pretty similar under completely different OSes. I have noticed some memory problems under Ubuntu on one machine, but I think that's a BOINC Manager problem, not a Linux thing.
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Message 88849 - Posted: 10 May 2018, 15:16:03 UTC - in response to Message 88839.  
Last modified: 10 May 2018, 15:27:36 UTC

I doubt their is any difference in Linux distributions. Rosetta is a statically linked CPU intensive app and they all should run about the same. My Fedora load is working fine.

Looks to me like a Rosetta problem that you should be able to work around.

All your jobs seem to be failing with the message "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."

The error message seems related to LC_TIME.

I Googled "loadlocale.c:129: _nl_intern_locale_data: Assertion" and there were several similar matches found. There are a couple that seem to be related to static linking and the default settings of the "locale" variables. Mine on my Fedora machine are below. Maybe that will help.


process exited with code 193 (0xc1, -63)</message>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.07_x86_64-pc-linux-gnu -frag9 00001.200.9mers -abinitio::detect_disulfide_before_relax 1 -abinitio::use_filters false -relax::default_repeats 5 -relax::minimize_bond_angles 1 -beta 1 -relax::dualspace 1 -abinitio::rsd_wt_helix 0.5 -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -relax::minimize_bond_lengths 1 -abinitio::fastrelax 1 -optimization::default_max_cycles 200 -abinitio::rsd_wt_loop 0.5 -ex2aro 1 -beta_cart 1 -frag3 00001.200.3mers -ex1 1 -in:file:native 00001.pdb -out:file:silent_struct_type binary -ignore_unrecognized_res 1 -in:file:boinc_wu_zip DRH_curve_X_h18_l4_h30_l4_02870_1_loop_57_0001_one_fragments_data.zip -out:file:silent default.out -silent_gz 1 -mute all -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 2390139
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.
SIGABRT: abort called
Stack trace (17 frames):
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Message boards : Number crunching : Distributions of Linux

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