VOS keeps restarting - Githubissues

marieBvr commented 1 year ago

Hi, I am very interested in your VOS. I have tried to launch it, but it seems to fail. Docker-compose keeps restarting and I can never get access to the endpoint. I have this message:

/virtuoso-entrypoint.sh: line 219:   146 Killed     "$VIRTUOSO" -f +checkpoint-only
** SQL SCRIPT FAILED **

I have increased memory usage by default, but that doesn't change anything.

Do you have any tips to manage this issue?

Thanks, Marie

mkarikom commented 1 year ago

Hi Marie, Sorry to hear of this issue. Can you please try the following:

please add your user to the docker group, which should exist automatically (some docker-compose issues can be solved this way) sudo usermod -aG docker $USER
please do the following to log any errors:
1. remove any previously created VOS container
2. remove the previously-cloned PathwayCommons-VOS repo
3. run the following command to log the full output of compose (this will create everything.txt):
```
~$ git clone git@github.com:mkarikom/PathwayCommons-VOS.git
~$ cd PathwayCommons-VOS
PathwayCommons-VOS$ docker-compose up > everything.txt 2>&1
```

Please note that when docker-compose succeeds it will pre-load PathwayCommons and NextProt which will take a long time (hours on a 16-core machine).

When the command completes, the output of everything.txt will look like:

Creating Virtuoso-7.2.8_PathwayCommons-12 ...
Creating Virtuoso-7.2.8_PathwayCommons-12 ... done
Attaching to Virtuoso-7.2.8_PathwayCommons-12
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Checking Plugins section
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Applying settings to virtuoso.ini
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Generating password
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Creating initial database
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m                 Wed May 31 2023
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08 { Loading plugin 1: Type `plain', file `geos' in `../hosting'
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   plain version 1.2.3235 from OpenLink Software
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   GEOS plugin based on Geometry Engine Open Source library from Open Source Geospatial Foundation
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   SUCCESS plugin 1: loaded from ../hosting/geos.so }
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08 { Loading plugin 2: Type `plain', file `graphql' in `../hosting'
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   GraphQL/SPARQL Bridge version 0.9.1 (64e6ecd39) from OpenLink Software
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   Support functions for GraphQL/SPARQL Bridge
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   SUCCESS plugin 2: loaded from ../hosting/graphql.so }
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08 { Loading plugin 3: Type `plain', file `proj4' in `../hosting'
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   plain version 1.1.3235 from OpenLink Software
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   Cartographic Projections support based on Frank Warmerdam's proj4 library
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   SUCCESS plugin 3: loaded from ../hosting/proj4.so }
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08 { Loading plugin 4: Type `plain', file `shapefileio' in `../hosting'
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   ShapefileIO version 0.1virt71 from OpenLink Software
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   Shapefile support based on Frank Warmerdam's Shapelib
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08   SUCCESS plugin 4: loaded from ../hosting/shapefileio.so }
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08 OpenLink Virtuoso Universal Server
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08 Version 07.20.3235-pthreads for Linux as of Oct 19 2022
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08 uses OpenSSL 1.1.1  11 Sep 2018
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:08 uses parts of PCRE, Html Tidy
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:18 SQL Optimizer enabled (max 1000 layouts)
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:18 Compiler unit is timed at 0.000344 msec
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:21 Checkpoint started
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:22 Checkpoint finished.
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:22 Roll forward started
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:22 Roll forward complete
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:22 PL LOG: Installing Virtuoso Conductor version 1.00.8846 (DAV)
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:22 PL LOG: Installing with dependencies Virtuoso Conductor version 1.00.8846/2022-10-19 14:10 (DAV)
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:22 Checkpoint started
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:23 Checkpoint finished, log reused
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:25 Checkpoint started
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:25 Checkpoint finished, log reused
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:25 PL LOG: Installation with dependencies complete
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:25 PL LOG: Initializing DB.DBA.SYS_PROJ4_SRIDS
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:25 PL LOG: ... checking for data files in "/usr/share/proj"
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:25 PL LOG: ... using built-in data
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:25 PL LOG: Initializing DB.DBA.SYS_PROJ4_SRIDS using built-in data
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:25 PL LOG: DB.DBA.SYS_PROJ4_SRIDS initialized with 8650 spatial reference systems
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:26 Checkpoint started
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:26 Checkpoint finished, log reused
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m 23:14:26 Server exiting
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Running initialization scripts
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m * Running SHELL script: [01-get-vad.sh]
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m --2023-05-31 23:14:27--  http://download3.openlinksw.com/uda/vad-vos-packages/7.2/rdf_mappers_dav.vad
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Resolving download3.openlinksw.com (download3.openlinksw.com)... 18.212.21.227
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Connecting to download3.openlinksw.com (download3.openlinksw.com)|18.212.21.227|:80... connected.
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m HTTP request sent, awaiting response... 301 Moved Permanently
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Location: https://download3.openlinksw.com/uda/vad-vos-packages/7.2/rdf_mappers_dav.vad [following]
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m --2023-05-31 23:14:27--  https://download3.openlinksw.com/uda/vad-vos-packages/7.2/rdf_mappers_dav.vad
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Connecting to download3.openlinksw.com (download3.openlinksw.com)|18.212.21.227|:443... connected.
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m HTTP request sent, awaiting response... 200 OK
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Length: 4970157 (4.7M) [application/octet-stream]
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m Saving to: 'rdf_mappers_dav.vad'
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m      0K .......... .......... .......... .......... ..........  1%  710K 7s
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m     50K .......... .......... .......... .......... ..........  2%  715K 7s
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m    100K .......... .......... .......... .......... ..........  3%  727K 7s
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m    150K .......... .......... .......... .......... ..........  4% 48.7M 5s
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m    200K .......... .......... .......... .......... ..........  5%  744K 5s
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m    250K .......... .......... .......... .......... ..........  6% 44.5M 4s
ESC[36mVirtuoso-7.2.8_PathwayCommons-12 |ESC[0m    300K .......... .......... .......... .......... ..........  7% 66.8M 4s

mkarikom commented 1 year ago

Hi, @marieBvr, just wondering if everything above worked out? If so would it be okay to close this issue?

marieBvr commented 1 year ago

Hi @mkarikom, I am still having the same problem. I think it is because I haven't put in enough memory. What size of RAM would you recommend?

mkarikom commented 1 year ago

Hi @marieBvr, I'm running it on a machine with 512GB but it's actual footprint is far less than that. If you could please post the contents of everything.txt from the above command, I can check the error in detail, Thanks!

mkarikom / PathwayCommons-VOS

VOS keeps restarting #1