Thank you very much for taking the time to reply
Our goal is just to setup a local Auspice server that will be browsable by our staff internally
The solution you provided with defining the variable HOST before running auspice view does the trick. We can access the Auspice server from computer in our LAN. (No need to install the whole conda nextstrain) Thank you for that.
However I am still having issues with grey tiled map. Even when trying to build auspice with a custom config.json as explained in your post Build with newest nextstrain/ncov has API requests to mapbox 403:Forbidden - #11 by james
Here are all the steps I’ve been doing
- Install Ubuntu 20.04 server machine from scratch (8Gb RAM + 100Gb HDD)
- Install updates
- Install Nodejs 14
- Download Anaconda
- Make conda available for user ipcuser
- Create auspice environment
- Install auspice with NPM
- Create datasets folder & place my json dataset inside
- Running auspice view --datasetDir /home/ipcuser/datasets
bash /opt/Anaconda3-2021.05-Linux-x86_64.sh
source ~/.bashrc
conda create --name auspice nodejs=14
conda update conda
conda activate auspice
npm install --global auspice
auspice --version
mkdir datasets
HOST=192.168.10.139 PORT=4000 auspice view --datasetDir /home/ipcuser/datasets
= Maps are not showing (grey tile)
If i try to create a config.json with the content you listed in your post
{
“mapTiles”: {
“api”: “https://a.tile.openstreetmap.org/{z}/{x}/{y}.png”,
“attribution”: “<a href=“https://www.openstreetmap.org/copyright”>OpenStreetMap contributors”,
“mapboxWordmark”: false
}
}
And build auspice again, I’m getting a core dump :
(auspice) ipcuser@srvlxubu:~$ auspice build --verbose --extend anaconda3/envs/auspice/config.json
[verbose] Generating webpack config. Extensions? true. devMode: false
[verbose] Webpack writing output to: /home/ipcuser/dist
Running webpack compiler
[verbose] Generating Babel Config
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/lodash/lodash.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/fa/index.esm.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/npm/node_modules/ajv/dist/regenerator.min.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/ri/index.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/ri/index.esm.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/si/index.esm.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/si/index.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/fa/index.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/di/index.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/di/index.esm.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/ai/index.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/ai/index.esm.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/gi/index.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-icons/gi/index.esm.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-dom/umd/react-dom.development.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/react-dom/cjs/react-dom.development.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/@hot-loader/react-dom/umd/react-dom.development.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/node_modules/@hot-loader/react-dom/cjs/react-dom.development.js as it exceeds the max of 500KB.
[BABEL] Note: The code generator has deoptimised the styling of /home/ipcuser/anaconda3/envs/auspice/lib/node_modules/auspice/dist/auspice.chunk.core-vendors.bundle.ea6fafa4f175e7278319.js as it exceeds the max of 500KB.
<— Last few GCs —>
[9736:0x55baaed951a0] 1293410 ms: Mark-sweep (reduce) 2038.1 (2054.5) → 2037.9 (2055.2) MB, 2224.1 / 0.0 ms (average mu = 0.145, current mu = 0.003) allocation failure scavenge might not succeed
[9736:0x55baaed951a0] 1296341 ms: Mark-sweep (reduce) 2038.9 (2052.2) → 2038.6 (2053.7) MB, 2916.4 / 0.0 ms (average mu = 0.069, current mu = 0.005) allocation failure scavenge might not succeed
<— JS stacktrace —>
FATAL ERROR: MarkCompactCollector: young object promotion failed Allocation failed - JavaScript heap out of memory
1: 0x7f56005a91b9 node::Abort() [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
2: 0x7f56005a9ed9 node::OnFatalError(char const*, char const*) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
3: 0x7f56008fe1d2 v8::Utils::ReportOOMFailure(v8::internal::Isolate*, char const*, bool) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
4: 0x7f56008fe48b v8::internal::V8::FatalProcessOutOfMemory(v8::internal::Isolate*, char const*, bool) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
5: 0x7f5600a979e6 [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
6: 0x7f5600acb7aa [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
7: 0x7f5600ad319e void v8::internal::LiveObjectVisitor::VisitBlackObjectsNoFail<v8::internal::EvacuateNewSpaceVisitor, v8::internal::MajorNonAtomicMarkingState>(v8::internal::MemoryChunk*, v8::internal::MajorNonAtomicMarkingState*, v8::internal::EvacuateNewSpaceVisitor*, v8::internal::LiveObjectVisitor::IterationMode) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
8: 0x7f5600ad8f86 v8::internal::FullEvacuator::RawEvacuatePage(v8::internal::MemoryChunk*, long*) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
9: 0x7f5600ac1f2a v8::internal::Evacuator::EvacuatePage(v8::internal::MemoryChunk*) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
10: 0x7f5600ac221d [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
11: 0x7f5600ab75a5 v8::internal::ItemParallelJob::Task::RunInternal() [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
12: 0x7f5600ab79ae v8::internal::ItemParallelJob::Run() [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
13: 0x7f5600ad4478 void v8::internal::MarkCompactCollectorBase::CreateAndExecuteEvacuationTasks<v8::internal::FullEvacuator, v8::internal::MarkCompactCollector>(v8::internal::MarkCompactCollector*, v8::internal::ItemParallelJob*, v8::internal::MigrationObserver*, long) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
14: 0x7f5600ad7a33 v8::internal::MarkCompactCollector::EvacuatePagesInParallel() [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
15: 0x7f5600ad7bda v8::internal::MarkCompactCollector::Evacuate() [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
16: 0x7f5600af0c7b v8::internal::MarkCompactCollector::CollectGarbage() [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
17: 0x7f5600aab272 v8::internal::Heap::MarkCompact() [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
18: 0x7f5600aabae1 v8::internal::Heap::PerformGarbageCollection(v8::internal::GarbageCollector, v8::GCCallbackFlags) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
19: 0x7f5600aac1c4 v8::internal::Heap::CollectGarbage(v8::internal::AllocationSpace, v8::internal::GarbageCollectionReason, v8::GCCallbackFlags) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
20: 0x7f5600aaf2ed v8::internal::Heap::AllocateRawWithLightRetrySlowPath(int, v8::internal::AllocationType, v8::internal::AllocationOrigin, v8::internal::AllocationAlignment) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
21: 0x7f5600aaf356 v8::internal::Heap::AllocateRawWithRetryOrFailSlowPath(int, v8::internal::AllocationType, v8::internal::AllocationOrigin, v8::internal::AllocationAlignment) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
22: 0x7f5600a7847c v8::internal:
:NewFillerObject(int, bool, v8::internal::AllocationType, v8::internal::AllocationOrigin) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
23: 0x7f5600da63f8 v8::internal::Runtime_AllocateInYoungGeneration(int, unsigned long*, v8::internal::Isolate*) [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
24: 0x7f560076ccf9 [/home/ipcuser/anaconda3/envs/auspice/bin/…/lib/libnode.so.83]
Aborted (core dumped)
Still unsure what could be the reason for this failure when steps you listed are really straightforward