Posts by CallMeFoxie

1) Message boards : Number crunching : horns5 work units (Message 99756)
Posted 23 Nov 2020 by CallMeFoxie
Post:
Yup same for me, had to cancel all horns5* because the memory usage was far too much considering I run a plethora of 2GB SBCs.
2) Message boards : Number crunching : Rosetta on ARM64 with latest glibc crashes? (Message 99587)
Posted 6 Nov 2020 by CallMeFoxie
Post:
Well in an unexpected turn of events adding 32bit armhf glibc + libgcc and upgrading kernel 5.9.1 -> 5.9.5 and the process has been running for over 6 minutes, previously it crashed in 6 seconds... What? :)
3) Message boards : Number crunching : Rosetta on ARM64 with latest glibc crashes? (Message 99552)
Posted 3 Nov 2020 by CallMeFoxie
Post:
Hi

I've built a small closed linux that contains pretty much only glibc and boinc and it seems that Rosetta crashes for no reasonable reason:

<stderr_out>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_aarch64-unknown-linux-gnu -abinitio::fastrelax 1 -ex2aro 1 -frag3 00001.200.3mers.index -in:file:native 00001.pdb -silent_gz 1 -frag9 00001.200.9mers.index -out:file:silent default.out -ex1 1 -abinitio::rsd_wt_loop 0.5 -relax::default_repeats 5 -abinitio::use_filters false -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.5 -beta 1 -abinitio::rg_reweight 0.5 -in:file:boinc_wu_zip enni5406_data.zip -out:file:silent default.out -silent_gz -mute all -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 2346184
SIGSEGV: segmentation violation
Stack trace (14 frames):
[0x74249a4]
linux-vdso.so.1(__kernel_rt_sigreturn+0x0)[0xffff97dc67bc]
/lib64/libc.so.6(__libc_malloc+0x6c)[0xffff9721b72c]
/lib64/libc.so.6(+0x61a28)[0xffff97205a28]
/lib64/libc.so.6(__nss_files_fopen+0x18)[0xffff97293a88]
/lib64/libnss_files.so.2(_nss_files_getpwuid_r+0x38)[0xffff973e55fc]
[0x757f84c]
[0x757f5e8]
[0x70bb020]
[0x49f4ffc]
[0x49f7b3c]
[0x4061f4]
[0x753db74]
[0x68cd68]

Exiting...

</stderr_txt>
]]>
</stderr_out>


any ideas? This is compiled against glibc 2.32 and gcc 10.2.0.

TN-Grid crunches fine.

Thanks
Ashley
4) Message boards : Number crunching : Rosetta running on ARM platforms (Message 94240)
Posted 12 Apr 2020 by CallMeFoxie
Post:
Today after the 4.15 update I got a sudden error on all the tasks :(
.....


it seems to have happened only with those tasks, robetta is still calculatong fine.
5) Message boards : Number crunching : Rosetta running on ARM platforms (Message 94233)
Posted 12 Apr 2020 by CallMeFoxie
Post:
Today after the 4.15 update I got a sudden error on all the tasks :(

<stderr_out>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_aarch64-unknown-linux-gnu -silent_gz -mute all -s chainA_chainB_20_04_15_28_12.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol local_docking_20_04_15_28_12.xml -out:nstruct 10000 -jd2:ntrials 100 -ex1 -ex2aro -beta -use_input_sc -in:file:native chainA_chainB_20_04_15_28_12.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -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 3988117

ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF
ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 380
BOINC:: Error reading and gzipping output datafile: default.out
14:04:47 (453): called boinc_finish(1)

</stderr_txt>
]]>
</stderr_out>


I didn't have zip installed, I wonder if that was missing? Would be nice if there was some requirements page (or did I overlook it?)
6) Message boards : Number crunching : Rosetta running on ARM platforms (Message 94164)
Posted 11 Apr 2020 by CallMeFoxie
Post:
Thanks! Easier than me going through the sources :)

meanwhile the current tasks got crunched and new ones (rb_04_11_21299_20821) appeared, which require 400 - 600MB RAM. No need to patch out boinc client for those so for now I am fine :)
7) Message boards : Number crunching : Rosetta running on ARM platforms (Message 94157)
Posted 11 Apr 2020 by CallMeFoxie
Post:
Too bad it requires 1900MB -ish, as I have a cluster of 8x Pine64+ (quadcore Cortex, aarch64, 2GB RAM) but due to how the memory is laid out I have about 1850MB after booting up available :( cannot crunch even 1 - 2 tasks. And adding a small swap gets ignored unsurprisingly.

It doesn't need 1.9GB. The highest I've seen my Pi4's using has been 918MB. We have some people using the Pi4 2GB model so it shouldn't be an issue. You'll only be able to run one at a time but given you have 8 Pine64's that is 8 tasks you could be running.


yup the problem is that when it tries to download a task it checks for available memory. I might patch it out as others did.

No idea how to change GPU memory on this platform either, tried googling with no luck tbh. And on top of GPU memory there's another 165MB reserved by kernel for some peripherals and I have no idea which ones, I removed most of the drivers I didn't even need and nothing in the DTBs. :(

time to go into the source of BOINC!
8) Message boards : Number crunching : Rosetta running on ARM platforms (Message 93950)
Posted 9 Apr 2020 by CallMeFoxie
Post:
Too bad it requires 1900MB -ish, as I have a cluster of 8x Pine64+ (quadcore Cortex, aarch64, 2GB RAM) but due to how the memory is laid out I have about 1850MB after booting up available :( cannot crunch even 1 - 2 tasks. And adding a small swap gets ignored unsurprisingly.






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