World loading issue: not aligned/invalid sector

[aramperes]

Could be related to #965

After generating a world with Glowstone (latest build), stopping the server, and starting it again, a lot of chunk load errors appear:

23:44:50 [INFO] Preparing spawn for world...
23:44:50 [WARNING] Region "worlds\world\region\r.-1.-1.mca" not aligned: 9283814 increasing by 1818
23:44:50 [WARNING] Region "worlds\world\region\r.-1.0.mca" not aligned: 4750926 increasing by 434
23:44:51 [INFO] Preparing spawn for world: 67%
23:44:51 [WARNING] Region "worlds\world\region\r.0.-1.mca" not aligned: 5384225 increasing by 2015
23:44:51 [WARNING] Region "worlds\world\region\r.0.0.mca" not aligned: 2241954 increasing by 2654
23:44:51 [WARNING] Region "worlds\world\region\r.0.0.mca": offsets[363] = 139268 -> 544,4 does not fit
23:44:51 [INFO] Preparing spawn for world: done
23:44:51 [INFO] Preparing spawn for world_nether...
23:44:51 [WARNING] Region "worlds\world_nether\region\r.-1.-1.mca" not aligned: 2656143 increasing by 2161
23:44:51 [WARNING] Region "worlds\world_nether\region\r.-1.-1.mca": offsets[567] = 164869 -> 644,5 does not fit
23:44:51 [SEVERE] Error while loading chunk (-9,-15)
java.io.IOException: Invalid sector: 644+5 > 648
        at net.glowstone.io.anvil.RegionFile.getChunkDataInputStream(RegionFile.java:243)
        at net.glowstone.io.anvil.AnvilChunkIoService.read(AnvilChunkIoService.java:61)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:150)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:138)
        at net.glowstone.chunk.ChunkManager.populateChunk(ChunkManager.java:219)
        at net.glowstone.chunk.ChunkManager.forcePopulation(ChunkManager.java:252)
        at net.glowstone.GlowWorld.prepareSpawn(GlowWorld.java:952)
        at net.glowstone.GlowWorld.setKeepSpawnInMemory(GlowWorld.java:924)
        at net.glowstone.GlowWorld.<init>(GlowWorld.java:439)
        at net.glowstone.GlowServer.createWorld(GlowServer.java:2296)
        at net.glowstone.GlowServer.start(GlowServer.java:811)
        at net.glowstone.GlowServer.run(GlowServer.java:633)
        at net.glowstone.GlowServer.main(GlowServer.java:497)
23:44:51 [WARNING] Region "worlds\world_nether\region\r.-1.0.mca" not aligned: 1357414 increasing by 2458
23:44:51 [WARNING] Region "worlds\world_nether\region\r.-1.0.mca": offsets[23] = 83717 -> 327,5 does not fit
23:44:51 [SEVERE] Error while loading chunk (-9,0)
java.io.IOException: Invalid sector: 327+5 > 331
        at net.glowstone.io.anvil.RegionFile.getChunkDataInputStream(RegionFile.java:243)
        at net.glowstone.io.anvil.AnvilChunkIoService.read(AnvilChunkIoService.java:61)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:150)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:138)
        at net.glowstone.chunk.ChunkManager.populateChunk(ChunkManager.java:219)
        at net.glowstone.chunk.ChunkManager.forcePopulation(ChunkManager.java:252)
        at net.glowstone.GlowWorld.prepareSpawn(GlowWorld.java:952)
        at net.glowstone.GlowWorld.setKeepSpawnInMemory(GlowWorld.java:924)
        at net.glowstone.GlowWorld.<init>(GlowWorld.java:439)
        at net.glowstone.GlowServer.createWorld(GlowServer.java:2296)
        at net.glowstone.GlowServer.start(GlowServer.java:811)
        at net.glowstone.GlowServer.run(GlowServer.java:633)
        at net.glowstone.GlowServer.main(GlowServer.java:497)
23:44:52 [WARNING] Region "worlds\world_nether\region\r.0.-1.mca" not aligned: 4073080 increasing by 2440
23:44:52 [WARNING] Region "worlds\world_nether\region\r.0.-1.mca": offsets[1005] = 253445 -> 990,5 does not fit
23:44:52 [WARNING] Region "worlds\world_nether\region\r.0.0.mca" not aligned: 2292081 increasing by 1679
23:44:52 [INFO] Preparing spawn for world_nether: 85%
23:44:52 [SEVERE] Error while loading chunk (13,-1)
java.io.IOException: Invalid sector: 990+5 > 994
        at net.glowstone.io.anvil.RegionFile.getChunkDataInputStream(RegionFile.java:243)
        at net.glowstone.io.anvil.AnvilChunkIoService.read(AnvilChunkIoService.java:61)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:150)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:138)
        at net.glowstone.chunk.ChunkManager.populateChunk(ChunkManager.java:219)
        at net.glowstone.chunk.ChunkManager.forcePopulation(ChunkManager.java:252)
        at net.glowstone.GlowWorld.prepareSpawn(GlowWorld.java:952)
        at net.glowstone.GlowWorld.setKeepSpawnInMemory(GlowWorld.java:924)
        at net.glowstone.GlowWorld.<init>(GlowWorld.java:439)
        at net.glowstone.GlowServer.createWorld(GlowServer.java:2296)
        at net.glowstone.GlowServer.start(GlowServer.java:811)
        at net.glowstone.GlowServer.run(GlowServer.java:633)
        at net.glowstone.GlowServer.main(GlowServer.java:497)
23:44:52 [INFO] Preparing spawn for world_nether: done
23:44:52 [INFO] Preparing spawn for world_the_end...
23:44:52 [WARNING] Region "worlds\world_the_end\region\r.-1.-1.mca" not aligned: 405873 increasing by 3727
23:44:52 [WARNING] Region "worlds\world_the_end\region\r.-1.-1.mca": offsets[732] = 25345 -> 99,1 does not fit
23:44:52 [SEVERE] Error while loading chunk (-4,-10)
java.io.IOException: Invalid sector: 99+1 > 99
        at net.glowstone.io.anvil.RegionFile.getChunkDataInputStream(RegionFile.java:243)
        at net.glowstone.io.anvil.AnvilChunkIoService.read(AnvilChunkIoService.java:61)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:150)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:138)
        at net.glowstone.chunk.ChunkManager.populateChunk(ChunkManager.java:219)
        at net.glowstone.chunk.ChunkManager.forcePopulation(ChunkManager.java:252)
        at net.glowstone.GlowWorld.prepareSpawn(GlowWorld.java:952)
        at net.glowstone.GlowWorld.setKeepSpawnInMemory(GlowWorld.java:924)
        at net.glowstone.GlowWorld.<init>(GlowWorld.java:439)
        at net.glowstone.GlowServer.createWorld(GlowServer.java:2296)
        at net.glowstone.GlowServer.start(GlowServer.java:819)
        at net.glowstone.GlowServer.run(GlowServer.java:633)
        at net.glowstone.GlowServer.main(GlowServer.java:497)
23:44:52 [WARNING] Region "worlds\world_the_end\region\r.-1.0.mca" not aligned: 434942 increasing by 3330
23:44:52 [WARNING] Region "worlds\world_the_end\region\r.-1.0.mca": offsets[28] = 26372 -> 103,4 does not fit
23:44:52 [SEVERE] Error while loading chunk (-4,0)
java.io.IOException: Invalid sector: 103+4 > 106
        at net.glowstone.io.anvil.RegionFile.getChunkDataInputStream(RegionFile.java:243)
        at net.glowstone.io.anvil.AnvilChunkIoService.read(AnvilChunkIoService.java:61)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:150)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:138)
        at net.glowstone.chunk.ChunkManager.populateChunk(ChunkManager.java:219)
        at net.glowstone.chunk.ChunkManager.forcePopulation(ChunkManager.java:252)
        at net.glowstone.GlowWorld.prepareSpawn(GlowWorld.java:952)
        at net.glowstone.GlowWorld.setKeepSpawnInMemory(GlowWorld.java:924)
        at net.glowstone.GlowWorld.<init>(GlowWorld.java:439)
        at net.glowstone.GlowServer.createWorld(GlowServer.java:2296)
        at net.glowstone.GlowServer.start(GlowServer.java:819)
        at net.glowstone.GlowServer.run(GlowServer.java:633)
        at net.glowstone.GlowServer.main(GlowServer.java:497)
23:44:52 [WARNING] Region "worlds\world_the_end\region\r.0.-1.mca" not aligned: 1134957 increasing by 3731
23:44:52 [WARNING] Region "worlds\world_the_end\region\r.0.-1.mca": offsets[1010] = 70913 -> 277,1 does not fit
23:44:52 [WARNING] Region "worlds\world_the_end\region\r.0.0.mca" not aligned: 1364329 increasing by 3735
23:44:52 [WARNING] Region "worlds\world_the_end\region\r.0.0.mca": offsets[402] = 85249 -> 333,1 does not fit
23:44:52 [SEVERE] Error while loading chunk (-1,8)
java.io.IOException: Invalid length: 7643 > 4096
        at net.glowstone.io.anvil.RegionFile.getChunkDataInputStream(RegionFile.java:250)
        at net.glowstone.io.anvil.AnvilChunkIoService.read(AnvilChunkIoService.java:61)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:150)
        at net.glowstone.chunk.ChunkManager.loadChunk(ChunkManager.java:138)
        at net.glowstone.chunk.ChunkManager.populateChunk(ChunkManager.java:219)
        at net.glowstone.chunk.ChunkManager.forcePopulation(ChunkManager.java:252)
        at net.glowstone.GlowWorld.prepareSpawn(GlowWorld.java:952)
        at net.glowstone.GlowWorld.setKeepSpawnInMemory(GlowWorld.java:924)
        at net.glowstone.GlowWorld.<init>(GlowWorld.java:439)
        at net.glowstone.GlowServer.createWorld(GlowServer.java:2296)
        at net.glowstone.GlowServer.start(GlowServer.java:819)
        at net.glowstone.GlowServer.run(GlowServer.java:633)
        at net.glowstone.GlowServer.main(GlowServer.java:497)
23:44:52 [SEVERE] Error while loading chunk (-1,9)

[ Truncated ]

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[aramperes]

Confirmed fix is to revert change from #965. Perhaps the fix was only partial? @astei

[astei]

Yeah, it's not calculating the run-length correctly. I do have a fix, though. I'll get that soon.

[astei]

Working on this still. It seems that there were multiple causes of problems, each of which I'm now working through.

[astei]

I have most of this resolved - the only thing that's not quite working is reading from the ends of region files.

[niansa]

I have the same issue. :(

[aramperes]

Possibly fixed by #997, could someone confirm?

[aramperes]

Confirmed that it still happens on the latest dev (same steps as the OP).