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dnanexus / dxda

CLI tool to manage the download of large quantities of files from DNAnexus
Apache License 2.0
16 stars 7 forks source link

panic: database is locked error when running the tool #61

Open kurt-mueller-osumc opened 3 years ago

kurt-mueller-osumc commented 3 years ago

I've been attempting to use the docker image to downlad files using a manifest... however, I keep getting a panic: database is locked error:

docker-compose run --rm dxda download manifest.json.bz2
Creating dxda_dxda_run ... done
Obtained token using environment
Creating manifest database manifest.json.bz2.stats.db
panic: database is locked

goroutine 1 [running]:
github.com/dnanexus/dxda.check(...)
        /go/src/github.com/dnanexus/dxda/dxda.go:42
github.com/dnanexus/dxda.CreateManifestDB(0x7ffe2b5abf08, 0x1c)
        /go/src/github.com/dnanexus/dxda/dxda.go:389 +0x822
main.(*downloadCmd).Execute(0xc0000d0428, 0x878000, 0xc0000d0010, 0xc0000c63c0, 0x0, 0x0, 0x0, 0x6c3a84)
        /go/src/github.com/dnanexus/dxda/cmd/dx-download-agent/dx-download-agent.go:42 +0x32c
github.com/google/subcommands.(*Commander).Execute(0xc00014c000, 0x878000, 0xc0000d0010, 0x0, 0x0, 0x0, 0x0)
        /go/src/github.com/google/subcommands/subcommands.go:142 +0x2fa
github.com/google/subcommands.Execute(0x878000, 0xc0000d0010, 0x0, 0x0, 0x0, 0x0)
        /go/src/github.com/google/subcommands/subcommands.go:420 +0x5f
main.main()
        /go/src/github.com/dnanexus/dxda/cmd/dx-download-agent/dx-download-agent.go:127 +0x141

Here's my docker-compose.yml file:

version: '3'

services:
  dxda:
    image: dnanexus/dxda:v0.1.4
    working_dir: /workdir

    environment:
      DX_API_TOKEN: ${DX_API_TOKEN}
    volumes:
      - .:/workdir
kpjensen commented 3 years ago

Can you try a more recent release? dnanexus/dxda:sha-c5d258d should contain the latest release v0.5.7.

kurt-mueller-osumc commented 3 years ago

No joy :(

docker-compose run --rm dxda download -max_threads=24 manifest.json.bz2
Pulling dxda (dnanexus/dxda:sha-c5d258d)...
sha-c5d258d: Pulling from dnanexus/dxda
61e03ba1d414: Pull complete
4afb39f216bd: Pull complete
e489abdc9f90: Pull complete
999fff7bcc24: Pull complete
a61d29dbfa18: Pull complete
3a9b3d1a0262: Pull complete
6d2539d5d99a: Pull complete
Digest: sha256:9a7f1b94a536f3647650b862f2a1c144aa4f1b501ccdb616574ca6b578ea9be3
Status: Downloaded newer image for dnanexus/dxda:sha-c5d258d
Creating aostor-dxda_dxda_run ... done
Logging detailed output to: manifest.json.bz2.download.log
Obtained token using environment
Downloading files using 24 threads
maximal memory chunk size: 16 MiB
Creating manifest database manifest.json.bz2.stats.db
panic: database is locked

goroutine 1 [running]:
github.com/dnanexus/dxda.check(...)
    /go/src/github.com/dnanexus/dxda/util.go:149
github.com/dnanexus/dxda.(*State).CreateManifestDB(0xc000106100, 0xc002470000, 0x19d9, 0x1e00, 0x7fffae6a8f08, 0x1c)
    /go/src/github.com/dnanexus/dxda/dxda.go:362 +0x62a
main.(*downloadCmd).Execute(0xc00001a300, 0x92f640, 0xc00001a038, 0xc0000143c0, 0x0, 0x0, 0x0, 0x0)
    /go/src/github.com/dnanexus/dxda/cmd/dx-download-agent/dx-download-agent.go:85 +0x63b
github.com/google/subcommands.(*Commander).Execute(0xc000106000, 0x92f640, 0xc00001a038, 0x0, 0x0, 0x0, 0xc00008df50)
    /go/src/github.com/google/subcommands/subcommands.go:209 +0x2f9
github.com/google/subcommands.Execute(...)
    /go/src/github.com/google/subcommands/subcommands.go:492
main.main()
    /go/src/github.com/dnanexus/dxda/cmd/dx-download-agent/dx-download-agent.go:214 +0x21e
ERROR: 2

When I rerun the command, dxda will start downloading the files.... however, the log / database doesn't update.

jstnlvns commented 3 years ago

I also receive the locked database panic error. Looks like the it creates the manifest/stats DB file, but no tables are created.

Rerunning the command:

Logging detailed output to: manifest.json.bz2.download.log
Obtained token using environment
Downloading files using 20 threads
maximal memory chunk size: 16 MiB
All files have parts, assuming they are not archived or open
Ensuring files are created for existing manifest
panic: no such table: manifest_regular_stats

goroutine 1 [running]:
github.com/dnanexus/dxda.check(...)
        /go/src/github.com/dnanexus/dxda/util.go:149
github.com/dnanexus/dxda.(*State).queryDBIntegerResult(0xc0000d0100, 0x8bbf89, 0x48, 0x0)
        /go/src/github.com/dnanexus/dxda/dxda.go:220 +0x221
github.com/dnanexus/dxda.(*State).CheckDiskSpace(0xc0000d0100, 0xc00007c210, 0x1)
        /go/src/github.com/dnanexus/dxda/dxda.go:262 +0x55
main.(*downloadCmd).Execute(0xc0000862b0, 0x92f640, 0xc000086000, 0xc00009a2a0, 0x0, 0x0, 0x0, 0x0)
        /go/src/github.com/dnanexus/dxda/cmd/dx-download-agent/dx-download-agent.go:91 +0x64c
github.com/google/subcommands.(*Commander).Execute(0xc0000d0000, 0x92f640, 0xc000086000, 0x0, 0x0, 0x0, 0xc000040f50)
        /go/src/github.com/google/subcommands/subcommands.go:209 +0x2f9
github.com/google/subcommands.Execute(...)
        /go/src/github.com/google/subcommands/subcommands.go:492
main.main()
        /go/src/github.com/dnanexus/dxda/cmd/dx-download-agent/dx-download-agent.go:214 +0x21e

It appears to create the files as if they were downloaded, but the files appear to be empty.

kpjensen commented 3 years ago

@jstnlvns could you please provide the dxda version and OS information?

jstnlvns commented 3 years ago

Apologies, I had that info in there but must have removed it when I reformatted. I have this running on a server running Ubuntu 18.04.6 (64-bit) using Docker, and I am running the latest version of this repo. After reading your response to @kurt-mueller-osumc, I recloned the repo and rebuilt the Docker image using the provided Dockerfile and tried to rerun the download and received the same result.