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linminhtoo / gist:d897a2f4bda7c4315c202c19ad7e2e49
Created January 22, 2024 18:56
java stack with jtrace
minhtoo@minhtoo:~/.nextflow/capsule/deps$ jstack 63923
2024-01-23 02:54:51
Full thread dump OpenJDK 64-Bit Server VM (17.0.6+10-LTS mixed mode, sharing):
Threads class SMR info:
_java_thread_list=0x00007f46f0001890, length=38, elements={
0x00007f4748028010, 0x00007f4748167420, 0x00007f4748168800, 0x00007f4748177b10,
0x00007f4748178ec0, 0x00007f474817a2d0, 0x00007f474817bd00, 0x00007f474817d230,
0x00007f474817e6a0, 0x00007f47481b30f0, 0x00007f47481b5050, 0x00007f4748fc0990,
0x00007f474892a1c0, 0x00007f4748de2880, 0x00007f4749203220, 0x00007f47494b6d80,
@linminhtoo
linminhtoo / gist:acdbd650351a64a7a6b98d20a4811d05
Created January 22, 2024 18:46
.nextflow.log
Jan-23 02:39:35.355 [main] DEBUG nextflow.cli.Launcher - $> nextflow run genepi/nf-gwas -r v1.0.4 -profile test,docker
Jan-23 02:39:35.404 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1
Jan-23 02:39:35.422 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/minhtoo/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3.3,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.1
Jan-23 02:39:35.429 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jan-23 02:39:35.430 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jan-23 02:39:35.432 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jan-23 02:39:35.440 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jan-23 02:39:35.452 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/minhtoo/.nextflow/scm
Jan-23 02:
@linminhtoo
linminhtoo / fold_error.txt
Created August 22, 2023 09:53
error when running colabfold_batch
2023-08-22 18:58:05,566 Running colabfold 1.3.0 (26de12d3afb5f85d49d0c7db1b9371f034388395)
2023-08-22 18:58:28,127 Unable to initialize backend 'tpu_driver': NOT_FOUND: Unable to find driver in registry given worker:
2023-08-22 18:58:28,382 Unable to initialize backend 'tpu': INVALID_ARGUMENT: TpuPlatform is not available.
2023-08-22 18:58:35,545 generated new fontManager
Traceback (most recent call last):
File "/g/data/if89/apps/colabfold_batch/1.4.0/python3/3.9.2/bin/colabfold_batch", line 8, in <module>
sys.exit(main())
File "/g/data/if89/apps/colabfold_batch/1.4.0/python3/3.9.2/lib/python3.9/site-packages/colabfold/batch.py", line 1728, in main
run(
File "/g/data/if89/apps/colabfold_batch/1.4.0/python3/3.9.2/lib/python3.9/site-packages/colabfold/batch.py", line 1210, in run
@linminhtoo
linminhtoo / log.txt
Last active May 9, 2022 02:38
dMaSIF + GNN for PLB, memory leak
2022-05-09 06:05:52.196 | INFO | __main__:<module>:251 - conv time: 0.3250s
2022-05-09 06:05:52.196 | INFO | __main__:<module>:252 - backprop time: 2.8490s
2022-05-09 06:05:52.196 | INFO | __main__:<module>:253 - prediction time: 0.6112s
2022-05-09 06:05:52.197 | INFO | __main__:<module>:254 - iteration time: 3.4713s
2022-05-09 06:05:52.197 | INFO | __main__:<module>:255 - preprocess time: 0.0104s
2022-05-09 06:05:52.197 | INFO | __main__:<module>:256 - memory usage: 1962986564.9562
0%| | 0/66 [00:00<?, ?it/s]2022-05-09 06:05:52.967 | INFO | data_iteration:iterate:195 - clearing CUDA memory
loss_plb_batch: 0.01481, loss_aux_batch: 0.00142, loss_plb_batch (unscaled): 1.81466: 9%|▉ | 6/66 [00:04<00:37, 1.60it/s]2022-05-09 06:05:56.900 | INFO | data_iteration:iterate:195 - clearing CUDA memory
loss_plb_batch: 0.01408, loss_aux_batch: 0.00130, loss_plb_batch (unscaled): 1.72521: 18%|█▊ | 12/66 [00:07<00:32, 1.68it/s]2022-05-09 06:06:00.618 | INFO
@linminhtoo
linminhtoo / SAVE_SLOT_2.dfq
Created January 6, 2018 16:28
relevant files and save 6
<data>
<engine version="2.1.6" name="defq1"/>
<game name="DQ1"/>
<version number="0.0.0"/>
<demo_mode value="false"/>
<party>
<class_entry value="mcguffin">
<character hero="true" sex="null" handle="mcguffin" name="Lin">
<info xp="69854" level="60"/>
<skills points="0">
@linminhtoo
linminhtoo / _error.txt 6
Created January 6, 2018 16:26
SystemData
{
OS : Windows 10 (Pre-release)
RAM: 12469292 KB (11.89 GB)
CPU: Intel(R) Core(TM) i7-4720HQ CPU @ 2.60GHz
GPU: NVIDIA GeForce GTX 950MIntel(R) HD Graphics 4600, driver v. 22.21.13.847620.19.15.4549
}
--------------------------------------
game id: DQ1
filename: DefendersQuest
@linminhtoo
linminhtoo / SAVE_SLOT_2.dfq
Created January 4, 2018 18:03
Null Object Reference Error on latest hotfix
<data>
<engine version="2.1.6" name="defq1"/>
<game name="DQ1"/>
<version number="0.0.0"/>
<demo_mode value="false"/>
<party>
<class_entry value="mcguffin">
<character hero="true" sex="null" handle="mcguffin" name="Lin">
<info xp="69854" level="60"/>
<skills points="0">
@linminhtoo
linminhtoo / _error.txt 5
Created January 4, 2018 18:02
Null Object Reference Error
SystemData
{
OS : Windows 10 (Pre-release)
RAM: 12469292 KB (11.89 GB)
CPU: Intel(R) Core(TM) i7-4720HQ CPU @ 2.60GHz
GPU: NVIDIA GeForce GTX 950MIntel(R) HD Graphics 4600, driver v. 22.21.13.847620.19.15.4549
}
--------------------------------------
game id: DQ1
filename: DefendersQuest
@linminhtoo
linminhtoo / SAVE_SLOT_2.dfq
Created January 3, 2018 08:27
Save 4
<data>
<engine version="2.1.6" name="defq1"/>
<game name="DQ1"/>
<version number="0.0.0"/>
<demo_mode value="false"/>
<party>
<class_entry value="mcguffin">
<character hero="true" sex="null" handle="mcguffin" name="Lin">
<info xp="69854" level="60"/>
<skills points="0">
@linminhtoo
linminhtoo / _error.txt 4
Created January 3, 2018 08:26
Null Object Reference Error 4
SystemData
{
OS : Windows 10 (Pre-release)
RAM: 12469292 KB (11.89 GB)
CPU: Intel(R) Core(TM) i7-4720HQ CPU @ 2.60GHz
GPU: NVIDIA GeForce GTX 950MIntel(R) HD Graphics 4600, driver v. 22.21.13.847620.19.15.4549
}
--------------------------------------
game id: DQ1
filename: DefendersQuest