Posts by Tom Rinehart

1) Message boards : RALPH@home bug list : Rosetta 4.12+ (Message 6708) Posted 8 Apr 2020 by Tom Rinehart Post: I went ahead and posted the OSX update on R@h. We plan to update the rest of the platforms in the next day or so. On Rosetta@home, the Mac 4.15 app is working well. I have had 3 end in a computation error at the end of processing. I've had trouble with Rosetta Mini 3.78 app they all fail immediately like the Rosetta 4.12 Mac app. It is giving errors like: <core_client_version>7.14.4</core_client_version> <![CDATA[ <message> process exited with code 255 (0xff, -1)</message> <stderr_txt> [2020- 4- 7 19:41:47:] :: BOINC:: Initializing ... ok. [2020- 4- 7 19:41:47:] :: BOINC :: boinc_init() BOINC:: Setting up shared resources ... ok. BOINC:: Setting up semaphores ... ok. BOINC:: Updating status ... ok. BOINC:: Registering timer callback... ok. BOINC:: Worker initialized successfully. command: minirosetta_3.78_x86_64-apple-darwin -abinitio::fastrelax 1 -ex2aro 1 -frag3 00001.200.3mers -in:file:native 00001.pdb -corrections::beta_nov16 -silent_gz 1 -frag9 00001.200.9mers -out:file:silent default.out -ex1 1 -abinitio::rsd_wt_loop 0.5 -relax::default_repeats 15 -abinitio::use_filters false -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.5 -abinitio::rg_reweight 0.5 -in:file:boinc_wu_zip CF_monomer_03_data.zip -out:file:silent default.out -silent_gz -mute all -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 2413101 Registering options.. Registered extra options. Initializing broker options ... Registered extra options. Initializing core... Initializing options.... ok Options::initialize() Options::adding_options() Options::initialize() Check specs. Options::initialize() End reached ERROR: Option matching -corrections:beta_nov16 not found in command line top-level context</stderr_txt> ]]> The errors I get on the Mac 4.15 app are mostly like this one: <core_client_version>7.14.4</core_client_version> <![CDATA[ <stderr_txt> command: rosetta_4.15_x86_64-apple-darwin -run:protocol jd2_scripting -parser:protocol predictor_v11_boinc--fuse--il1r_design_boinc_v1.xml @flags_il1r2 -in:file:silent 8er4nd4m_Mini_Protein_binds_IL1R_COVID-19_design5.silent -in:file:silent_struct_type binary -silent_gz -mute all -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 8er4nd4m_Mini_Protein_binds_IL1R_COVID-19_design5.zip @8er4nd4m_Mini_Protein_binds_IL1R_COVID-19_design5.flags -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 3296593 Starting watchdog... Watchdog active. ====================================================== DONE :: 283 starting structures 29066.9 cpu seconds This process generated 283 decoys from 283 attempts ====================================================== BOINC :: WS_max 8.82074e+08 BOINC :: Watchdog shutting down... 06:57:38 (55517): called boinc_finish(0) </stderr_txt> <message> finish file present too long</message> ]]> It looks like I also got a few of these on the Mac 4.09 app.
2) Message boards : RALPH@home bug list : Rosetta 4.12+ (Message 6689) Posted 6 Apr 2020 by Tom Rinehart Post: I went ahead and posted the OSX update on R@h. We plan to update the rest of the platforms in the next day or so. 4.15 works on my three Macs where 4.12 would crash immediately. Thanks! Any chance you can change the ARM64 version so it will run on a 2GB SBC? My 2GB Odroid C2 has a little over 1.7 GB of free RAM. The error says it needs 1.9GB. I'd like to be able to run one or two WUs on it.
3) Message boards : RALPH@home bug list : Rosetta 4.12+ (Message 6659) Posted 3 Apr 2020 by Tom Rinehart Post: Mac 4.12 Computation Error I started getting 4.12 work units on my Macs in Rosetta@home. They all end in computation errors: <core_client_version>7.14.3</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255)</message> <stderr_txt> command: rosetta_4.12_x86_64-apple-darwin -run:protocol jd2_scripting -parser:protocol predictor_v11_boinc--fuse--covid_spike_design_boinc_v1.xml @flags_jhr_cv -in:file:silent 3xc3uf2h_Junior_HalfRoid_vs_COVID-19_design1.silent -in:file:silent_struct_type binary -silent_gz -mute all -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 3xc3uf2h_Junior_HalfRoid_vs_COVID-19_design1.zip @3xc3uf2h_Junior_HalfRoid_vs_COVID-19_design1.flags -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 Starting watchdog... Watchdog active. error: zipfile probably corrupt (illegal instruction) </stderr_txt> ]]> One of my other Macs is getting this error: <core_client_version>7.14.3</core_client_version> <![CDATA[ <message> process got signal 4</message> <stderr_txt> </stderr_txt> ]]> I have two linux boxes running Debian Buster that are working fine, so it looks like a Mac app problem.
4) Message boards : RALPH@home bug list : Rosetta 4.12+ (Message 6657) Posted 1 Apr 2020 by Tom Rinehart Post: Linux ARM64 Memory Needs I have an odroidc2 running Armbian for aarch64. The odroid C2 has 2 GB of RAM. I get this error message and no work units are received: Rosetta for Portable Devices needs 1907.35 MB RAM but only 1770.35 MB is available for use. Unless there is some work around, the ARM64 devices will need to have 4 GB of RAM to run work units. If one work unit needs this amount of memory, it will limit the usefulness of most ARM64 devices. Most don’t have much memory - Raspberry Pi 2 v1.2, 3, and 3+ only have 1 GB of RAM - many other ARM64 devices have 1 or 2 GB of RAM.